07 June 2021- Improving our understanding of the microbiome has been transformative for animal nutrition and health. Today, a vast array of solutions exists to maintain healthy gut microflora. However, the development of further new solutions is of little use if the farms meant to deploy them don’t have an accurate picture of what’s happening at a microbiome level on their own farms. Before you can address any imbalance, you must detect it.
Having accumulated a significant amount of expertise in the various -omics technologies, BIOMIN is now on a mission to make this sort of microbiome analysis accessible to a wider swathe of the world’s livestock producers. Today, Raj Murugesan, Head of Gut Performance Management at BIOMIN, & Franz Waxenecker, Managing Director of BIOMIN, share more about the evolution of the company’s service offerings in the microbiome-analysis space and discuss why this is important for both individual producers and the wider industry.
[Feedinfo] Can you give an overview of BIOMIN’s offerings in terms of microbiome analysis? What kinds of services do you provide under this umbrella?
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[Raj Murugesan] At BIOMIN, we have applied -omics technologies to address animal/bird gut health and performance aspects on-site at commercial operations over the past several years. By bringing portable sequencing devices onto farms, we’re able to offer insights into the quantification of microbiota and identify potential health risks before they become problematic. |
Raj Murugesan |
[Feedinfo] Who are these services targeted at?
[Franz Waxenecker] Our goal is to eventually make these precision animal farming tools available to the entire animal protein industry. We started this work with broilers and have now added breeders, and we’re going to continue onto swine and ruminants in the near future.
[Feedinfo] How has this part of BIOMIN’s activities evolved over time?
[Raj Murugesan] Our research and development scientists initially began cooperation with several leading key broiler producers globally as part of collaborative field research projects in 2017. Our longstanding relationships with these producers, along with the large data sets we’re able to collect from these projects, gave us an opportunity to co-create effective analytical techniques and solutions to diagnose and address the producers’ issues. This initial success has led us to further build out this platform of rapid, on-site portable sequencing, cloud computing-based analysis and reporting.
[Feedinfo] What can you tell me about the technology underlying these services?
[Raj Murugesan] We use sophisticated portable sequencing devices based on the -omics technologies developed in just the past few years. These devices are faster and relatively cheaper than traditional tools, and have a clear advantage in that they can be used on-site at commercial operations.
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Franz Waxenecker
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[Franz Waxenecker] Microbiome sequencing analysis creates a massive data set. One round of sampling from a poultry house generates bacterial sequences equivalent to 7 - 15 times the size of the human genome. The ability to process and, most importantly, interpret the data in a way that is meaningful in terms of the current and future health status and performance of animals/birds, and to suggest effective intervention strategies, is what producers value most. |
[Feedinfo] What does the “resistome” refer to? How is BIOMIN involved in helping producers better understand the implications for their farms?
[Raj Murugesan] The resistome is a list of all the detected antibiotic resistant genes and their abundance in a microbial community. Resistome analysis refers to a way of interpreting metagenome data in terms of antibiotic resistance. A healthy gut microbiome should have a relatively low number of resistant genes, while a microbiota with many different antibiotic resistant genes against diverse classes of antibiotics is considered a risk for performance and health, along with the risk of being less responsive to treatments, and potentially transmitting those resistant genes to the human population through the food chain.
Our goal is to help producers identify the potential risks in their operations and take appropriate steps. It’s tricky to interpret the resistome because the results are not straight-forward. Instead, this data is evaluated by our team, who looks at how diverse the resistome is and how resistomes from different samples compare in order to arrive at the final interpretation.
[Franz Waxenecker] In trials with post-weaning piglets and in several collaboration projects with broiler producers, we were able to show how gut performance feed additives were able to reduce the number of antibiotic resistant genes in feces, thereby mitigating the risk associated with antimicrobial resistance.
We at BIOMIN put a lot of emphasis on this topic, as the emergence of antibiotic-resistant bacteria is a global concern not just for animal husbandry but also for the future of human medicine.
[Feedinfo] Beyond antibiotic resistance, what are some of the practical challenges BIOMIN is helping producers to meet through a better understanding of gut indicators? Can you give any examples of how these analytical tools are being deployed?
[Raj Murugesan] Because next generation sequencing is a versatile tool, we can help producers in a number of ways. We can give a general overview about the microbial species present in the microbiome, which itself is an indicator of growth and health of the flock/herd. Furthermore, we can specifically detect the presence of pathogens like Salmonella, and the presence of beneficial bacteria like those that produce short-chain fatty acids. On the gene level, we can assess the resistome as well as the virulome which is the totality of all genes related to pathogenicity, like toxicity or cell invasion.
Besides these general analyses, we can also answer questions specific to individual producers, which go beyond the usual feed conversion or growth focused ones, such as on specific pathogens relevant to their operation or comparing different feeding regimens, etc.
To give a concrete example: during a collaboration with a key broiler producer in Asia, we sequenced the bacteria from the litter and were able to show that the very same virulent strains of Salmonella that became detectable by classical boot swab methods at the end of a production cycle were already present in the rice bran used as litter material. This helped the producer to lower Salmonella prevalence in their flock and avoid meat condemnations.
[Feedinfo] Let’s talk about the practical details of gut indicator analyses. How are they carried out—stool samples, blood samples, other tissue samples, etc.? How often? Is the sampling done by a BIOMIN technician, or by farm personnel?
[Raj Murugesan] The number of sampling time points and which analyses to be performed are entirely dependent on what the producer wants to know, but also of course dependent on the target animal/bird. We are also flexible in regards to where and how the sampling and lab work is performed. We can visit a producer’s facility to collect samples, but we are also open to receive samples collected by producer’s staff and veterinarians if they prefer to do so for biosecurity reasons.
Usually blood, feces samples and gut content samples are collected for analysis. When investigating the source or spread of certain microbes, we also collect samples of the litter material, feed, drinking water, or even insects.
We can than measure the concentrations of our target biomarkers in these samples. The most important aspect about these biomarkers is not the actual measurement in the lab though, but the statistical evaluation, just as with the DNA sequencing.
[Feedinfo] What kinds of interventions generally follow a gut indicator analysis? How has the tie-up with DSM broadened the categories of solutions that you can offer the market once a gut health problem is identified?
[Franz Waxenecker] Based on the results of the analyses, a set of recommendations are provided by a BIOMIN technical representative who can advise on the effective intervention strategies spanning management, nutrition, and application of feed or drinking water additives. Our gut performance portfolio includes probiotics, acidifiers, and phytogenics.
While BIOMIN customers already have a wide range of proprietary technologies to choose from to mitigate the presence of mycotoxins and support gut performance and health, the variety of options available has expanded –e.g. enzymes and novel feed additives—now that we are a part of DSM. It is our ambition to bring our data-driven microbiome analytical service to DSM customers worldwide.
[Feedinfo] To what extent does the area of gut indicator analysis remain a priority for BIOMIN’s R&D teams going forward? What are some of the white spaces in our understanding that your teams are looking to fill? What should we expect out of the company going forward?
[Franz Waxenecker] We plan to continue our focus on gut indicator analysis. We see a clear opportunity to use the insights gained from these methods and the continuous collection of commercial data to eventually predict the performance and health status of animals and the likelihood of disease outbreaks. Identifying and mitigating potential problems before they arise in this way means that producers will see better results while end consumers benefit from safe, affordable, and nutritious products that are produced more sustainably. It’s how we intend to unlock the promise of precision animal farming by making it a reality.
Published in association with BIOMIN
