The decoding and understanding of the intricacies of the microbiome has allowed for the development of additives that aim to support and maintain the gut integrity of production animals. But, according to gastrointestinal analytics service company, Alimetrics Diagnostics, it is a study that some in the animal nutrition industry might not be approaching correctly.
As the company’s Business Development Lead, Tommi Timoharju explained to Feedinfo in a recent chat, research in the industry has focused heavily on the structures of bacterial communities in the microbiome and that a switch to understanding the individual bacterial functions in the gut might be a better tactic. By taking this route, the company has developed a multidimensional approach to the analysis of gut health in production animals which, it believes, can give its customers a fuller, more helpful picture of the impact that their products have on the microbiome, and the gut integrity and performance of livestock.
In this Industry Perspectives, we take a dive into the steps that make up Alimetrics Diagnostics’s gastrointestinal analysis approach, including how the combination of its BioFreeze™ sample preservation solution and quantitative real-time PCR ensures the accuracy and validity of results. We also look at the five diagnostics panels the company has developed that target a specific intestinal segment and how these can be employed in the optimisation of production animal diets.
[Feedinfo] For those who are not familiar with Alimetrics Diagnostics, what are its core activities?
[Tommi Timoharju] Alimetrics Diagnostics is a laboratory services provider operating in Finland. We specialise in intestinal microbiology and gut health of production animals and humans.
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Through first-class microbiome and immunological analyses, we support our customers in evaluating the mode-of-action and benefits their products have on animal performance and health and well-being. With animal health such a big focus for the industry today, companies are increasingly looking to accurately measure gut health. Alimetrics consists of two business units: Alimetrics Research and Alimetrics Diagnostics. Alimetrics Research began the whole journey, with Alimetrics Diagnostics established in 2016 to meet the customer need for high-throughput laboratory analysis services. |
Tommi Timoharju
[Feedinfo] What do you think some in the industry are getting wrong in their approach to the study of the intestinal microbiology of production animals?
[Tommi Timoharju] Gut health-related research in the animal production industry has focused heavily on studying the intestinal bacterial community structures, rather than trying to understand what functions bacteria are carrying out in different parts of intestinal tract. This is, in most part, due to the popularity of fashionable next-generation sequencing techniques, which have become more available and common during the past 10 years.
However, we must acknowledge that gut microbiota is an organised community comparable to any other tissue in warm-blooded animals. It not only affects nutrition and energy capture, but also regulates many important physiological functions of the host.
That’s why we have chosen to adopt a multidimensional approach to studying intestinal microbiology, which comprises monitoring of gut health-associated microbial functions, microbial metabolic end-products and immunological markers along with the microbial community analysis.
[Feedinfo] How is this approach better for developing diets for these animals?
[Tommi Timoharju] This has brought totally new criteria for diet and additive development. Today, animal health is a big issue. With the industry shifting away from the use of antibiotics as growth promoters, companies are interested in measuring the specific impact products can have on microbial functions, immune functions and so on. Of course, performance parameters continue to be very important, but end users want to see more. How do I screen product candidates and rank them if criteria are related to reduction of pathogens, inflammation, butyrate production, etc.? We are answering this demand in an easy and affordable way.
[Feedinfo] So, let’s look a little bit closer at your gastrointestinal analysis process. How does it work? What are the main steps?
[Tommi Timoharju] The shared view of feed additive companies and their clients is that when evaluating animal performance, traditional feeding and weighing of animals is no longer enough. As methods to study the microbiome have developed rapidly, end users also now want to see scientific proof of how the product works in the animal. And thus, they are grappling with the question of how to accurately and effectively measure gut health.
At Alimetrics, we have 20 years’ experience in intestinal microbiology and have conducted more than a thousand research projects for international clients, all of which has enabled us to identify biomarkers relevant for gut health. To make life easier for our clients, we have constructed pre-built diagnostic panels which cover analyses of the different functions of the microbiome and the host.
Furthermore, an important part of studying the microbiome is representative and standardised sample collection and delivery logistics. For this purpose, we developed the BioFreeze™ sample preservation solution, to make sample collection easier and provide cost-efficient transportation worldwide.
[Feedinfo] So let’s look at BioFreeze™ a bit and how it contributes to the validity and accuracy of results.
[Tommi Timoharju] When studying intestinal processes and microbe-mediated gut health, the first step is to collect digesta and/or faecal specimens. Standardised sample collection and easy-to-use materials are critical when streamlining the sampling process to generate reliable scientific data. Immediate freezing of samples is regarded as the gold standard of intestinal sample storage, although freezing and thawing may lead to bacterial lysis and some loss of DNA.
When intestinal samples are collected, molecular, immunological or chemical analyses are seldom or never performed immediately at the trial site. Thus, collection of biological samples and secure transportation can be an obstacle to the ultimate success of trials. Based on customer feedback, we know that they find it tedious to determine the appropriate sampling method, the appropriate container to use and the best transportation service. One may also need additional materials, such as vessels and spoons, for representative and standardised sampling at the site.
This is why we developed our solution, BioFreeze™, that overcomes these challenges and preserves valuable samples after collection and during shipment. BioFreeze™ conserves the intestinal sample at ambient temperature and prevents bacterial lysis and endonuclease activity, as well as preserving immunological and chemical analytes. This enables a wide variety of markers to be analysed from the same sample and therefore gains maximum benefit from each trial – not to mention being a more efficient, hassle-free process for our customers.
[Feedinfo] Another key step in the Alimetrics Diagnostics process is the quantitative real-time PCR. Can you talk us through what it is and how this results in a fuller picture/better understanding of an animal’s intestinal microbiology and gut health?
[Tommi Timoharju] Quantitative real-time PCR is a practical DNA-based method for accurate and targeted quantification of specific intestinal microbial species and groups, as well as functional genes. This is essentially our DNA-based method of choice if the targets of interest (for example, certain microbial taxa or functions) are already known. Briefly, the real-time PCR reaction is performed on both the experimental samples and reference standards, to determine the concentration of a target gene present in an intestinal microbial DNA sample.
Today, certain functions of intestinal bacteria are of particular interest to the animal production industry due to their demonstrated health benefits. One example is butyrate production, which has been associated with a healthy intestinal epithelium and consequently improved animal gut health and immunity.
Through quantitative real-time PCR, the genes encoding the key enzymes catalysing the microbial butyrate production can be accurately quantified and considered an indication of the potential of the microbiota to produce butyrate. Being armed with such data is especially advantageous, given a healthy gut is a prerequisite to enhancing animal health, growth and performance.
[Feedinfo] What are the various gut health panels you offer and what do they look at? How can they help make sense of data for the optimization of animal diets?
[Tommi Timoharju] We have five different Diagnostics Panels in our product portfolio, which use a combination of three different methods – quantitative real-time PCR, gas chromatography and ELISA – to help in the optimisation of diets.
Our QuantiBiom™ panel quantifies the density metabolic activity of the overall microbiome in the different parts of the intestine of interest. With ProxiMap™ one can measure the relative abundance of the seven most relevant bacterial taxa present in the small intestine. DistaMap™ works in a similar way, but is designed for the caecum and colon. EpiHealth™ focuses on epithelial health and the potential for butyrate production and immune status, while InflaScore™ assesses the animal’s infection and inflammation status using common intestinal pathogens and immunological markers.
As we’ve already touched upon, clients developing feed additives simply want to get a more comprehensive picture of the effects their products induce. And companies are looking to develop products which target a specific intestinal segment or pathogen. Our analyses shed light on such effects, and we also customise our set of analysis so that it’s tailored to the customer’s exact needs.
[Feedinfo] How long does this entire process take, from sample collection to panel results?
[Tommi Timoharju] Once a project outline has been agreed with a customer, BioFreeze™ sampling kits are dispatched to the trial site. These can be located all over the world, but thanks to our logistics operation we can reach even the remotest destinations.
After intestinal samples are collected and introduced in the BioFreeze™ solution, they are ready to be shipped back to our Alimetrics Diagnostics laboratory, a process which usually takes one to two business days. Once the samples have been received and the customer has confirmed the order of the Diagnostic panel, the turnaround time for results is between two and four weeks.
[Feedinfo] Are there any upcoming developments at Alimetrics Diagnostics that the animal nutrition industry should be aware of? Any exciting projects you’re working on in this space?
[Tommi Timoharju] I’m excited to say that early in the new year, we will be launching a new diagnostic panel to specifically measure biomarkers connected to protein fermentation – an area where we are seeing huge interest, including from our clients.
We’ve long recognised the importance of protein fermentation in the lower intestine, such as the colon and caecum. It’s a big intestinal health issue for both production animals and humans. Many products of protein fermentation are toxic and are suspected to be behind serious health issues in humans, such as increased incidence of colon cancer, for example.
Alimetrics Research is perhaps the first research unit that started to pay attention to this issue with production animals. By measuring toxic metabolites, not only can we quantify the levels of toxic substances in the gut to see the impact on gut health status, but we are also able to use the data to study protein digestibility, to assess how efficiently the animal uses the protein feed. When dietary protein is not digested by the host, it will be fermented in the caecum or colon, producing characteristic metabolites.
As the old saying goes, ‘knowledge is power’, and for our customers being armed with such data is critical to ensuring optimal animal health and performance. Which is why we’re delighted to be expanding our product offering even further in 2023.
Published in association with Alimetrics Diagnostics
