Meeting summary & highlights by Dr. Radhika Bongoni & Ms. Jolanta Szkodon

On October 29, 2020 BaseClear had organised an online experts meeting on Microbiome & Animal Health and Performance. With 135 registrations, this open event was successfully organised in 2 sessions: morning session dedicated to explore “Microbiome link to animal health” and afternoon session dedicated to understand “Modulating the animal microbiome” topics.

The event discussed results from various studies on gut microbiome of different animal species and their link to health, nutrition, immune response and thus performance, finishing the day with study design for clinical trials and regulatory approval of feed additives. The event was hosted by Dr. Radhika Bongoni and Dr. Derek Butler from BaseClear. The speakers included:

  • KEYNOTE Dr. Nicola Walker, EMEA Principal Scientist at DSM Animal Nutrition & Health
  • Dr. Aleksandrina Patyshakuliyeva, Product Manager Animal Microbiome at BaseClear
  • Dr. Frédérick Bussy, Algo-Ceutical Product Specialist at Olmix
  • Dr. Richard Murphy, Research Director at Alltech
  • Dr. Tadele Kiros, Swine Global R&D manager and coordinator at Phileo, Lesaffre
  • DI(FH) Karin Schöndorfer, Regulatory Affairs Manager at Biomin

Detailed programme can be found here:

The panel discussions were most interactive sessions mostly with questions directly addressed to the speakers by the participants, as well as between speakers. Some of the topics that covered input and discussions by multiple speakers and participants are:

Could microbiome data ever be a tool or biomarker for pathogen detection & animal health?

Microbiome data or footprint can be a good indicator of pathogen in the animal. However,  pathogen in the initial hours or days are at insignificant abundance. With the already diverse microbial community, these pathogens go undetected. However, linking metabolites to specific microbial data & transcriptome data can shed light towards setting pathogen detection with accuracy.

Guidance on the number of animals per pen or per fieldtrial to establish the safety of a feed additive for regulatory bodies:

There is no official guidance. The variability will be judged between the pens (i.e. using the standard deviation within the *group*), rather than within the pens (the replicate within the group).  The number of animals within a pen will often *depend* (there we go again 😉 ) on, e.g.

  1. animal welfare considerations (e.g. pen floor size)
  2. sampling considerations (e.g. pooling of samples or sacrifice of animals before trial end…)
  3. experience with variability for the parameters in question

These are considerations to be taken by the applicant.

Is microbiome data a primary or secondary endpoint? Will this change in due course of time by regulatory bodies like EFSA?

Microbiome measurements are gaining importance and are becoming a datapoint among others for any field/clinical trials. However the microbiome data points is not yet a standard and must-have point per regulatory dossiers. This mindset is changing rather fast and in the very near future, with the flexibility of EFSA, microbiome datapoints can take a key role. For the moment, microbiome parameters are still considered secondary endpoints if an additive claims to affect animal production and performance. The current guidance, for example already states that for additives affecting animal welfare or additives affecting the characteristics of food of animal origin or “other additives”,  “the selection of the endpoints should be properly justified”. This already encourages innovations. Some of the guidelines are referred on page 9-10 of EFSA’s current Efficacy Guidance; items 2.4.1 – 2.4.5; and “Endpoints” (page 19), which give an indication about requirements EFSA really wants to see as well as possibilities.

With the next update on the guidance, more proactive input is expected on findings, endpoints and study designs during product evaluations.

Could phages be an alternative to functional feed additives like methanogen inhibitors or feed efficiency promotors or immune-modulators?

Regulations around phages is a challenge. There are no clear guidelines on assessing & establishing the safety of phages. Though phages clearly show potential to use in the industry. Assessing the antimicrobial resistance of Phages is also ambiguous and study-dependent.

What is expected from culturomics versus shotgun metagenomics?

Culturomics offers the possibility to enrich and discover novel strains and genes encoding enzymes & biomarkers. Culturomics is a laborious process, cost inefficient, applicable for live microbial communities only and culture media dependent. However, outcomes often payoff the efforts! Shotgun metagenomics is a robust method, sensitive to minutest microbial DNA present in the sample giving a full scope of microbial communities and for taxonomically-assigned of novel species. In that sense, Culturomics and Shotgun metagenomics are complementary to each other and is the way forward for discovery!

Can microbiome take a role in sustainable farming?

By now we know (gut) microbiome plays a key role in the health and performance of the animal. Animal husbandry and fishery can gain a lot with this microbial information and bring along sustainability aspects and contribute to the SDGs and environment. An example is to link microbial biomarker genes to feed efficiency, methane production,  and thus cater ways to modulate these biomarker genes. The industry is not there yet with this analysis!

Could incentivising farmers for feed additives for (environmental) sustainability make a difference?

Consumers MAY be more willing to pay for a “greener” product, but ARE FARMERS WILLING to invest in additives or other measures to reduce GHG emissions?


Dr. Nicola Walker, EMEA Principal Scientist at DSM Animal Nutrition & Health, kicked off the meeting. In her keynote talk, “Ruminations on sustainability: Reducing methane emissions by targeting the rumen microbiome”, she viewed the animal microbiome through the lens of climate change. Although there is a trend to reduce meat consumption in Western countries, ruminants remain a major food source. Livestock production is a major emitter of Green House Gases (GHG), and within this sector, beef and dairy cattle production account for a majority of emissions. What gives cows such a high hoofprint? As cows process feed, methanogens living in their gut microbiomes produce methane, a GHG. Strategies in animal management, breeding, genetics, and nutrition exist to reduce ruminant methane emissions. For the remainder of the talk, Dr. Walker focused on a strategy to inhibit target methanogens. 3- Nitrooxypropanol (3-NOP) inhibits an enzyme that catalyzes the final step of methanogenesis. Although the effects of 3-NOP are dependent on dose rate and diet, studies using dairy and beef cows showed promising decreases in methane emissions. Using pure cultures, qPCR, Illumina MiSeq sequencing, and metabolomics, these studies concluded that: different methanogenic species have different sensitivities to 3-NOP, 3-NOP does not seem to affect key rumen microbes, microbial abundance of some methanogens significantly decreases in abundance when 3-NOP is used, and methane emissions do decrease but changes in short change fatty acids and other metabolites are also observed. Dr. Walker concluded her talk with the reminder that future efforts to reduce methane emissions will have to consider the very complex rumen microbial system.

Dr. Aleksandrina Patyshakuliyeva, Product Manager Animal Microbiome at BaseClear, presented on “how culturomics can be used to reveal microbial diversity”. Culturomics is a high scale culturing technique that takes the unculturable gut microbiota and makes it culturable. The benefit is an increase in the number of species that can be isolated and identified and thus, the improvement of reference databases and better characterization of metabolic activities. To perform culturomics and reveal more microbial diversity, there have to be large variations in culture conditions. Variations in media, pH range, pre-treatments and enrichments, dilutions, aerobic/anaerobic conditions, and temperature can all be altered to create a number of diverse conditions. Sequencing the cultures from different conditions will reveal different microorganisms in a way that one culture condition cannot. However, it is still difficult to determine ideal culture conditions. The process is also very labor, time, and space-intensive and more, there is no current standardization of the technique. Dr. Patyshakuliyeva is confident that culture dependent and independent methods are complimentary and will continue to be used to learn about microbial diversity.

Dr. Frédérick Bussy, Algo-Ceutical Product Specialist at Olmix  spoke on, “Effect of immuno-modulating algae extract on monogastric animal”, outlined the role of algae in improving gut health. In chickens, immunoglobin is transferred through the yolk in eggs. Piglets, however, are born without an immune system and begin to acquire immune protection through milk. At weaning (3-4 weeks), they haven’t acquired enough protection from milk and also do not have enough protection from their own immune system. This puts them in an immunodepressive window that can leave them vulnerable to infection. Multicellular eukaryotic algae, termed “macroalgae”, contain carbohydrates that can be beneficial to the immune system. Sulfated polysaccharides from the macroalgae are used in marine sulfated polysaccharide (MSP), a patented technology that has been found to modulate immunity. When administered orally to male broilers, MSP activates heterophils and monocytes. In monocytes, MSP increases nitric oxide enough to kill pathogens but does not damage healthy cells in the process. Moreover, there is an increase in transcription of immune mediators (cytokines) and pattern recognition receptors. In gilts, the administration of MSP leads to a better transduction of serum from the blood to the colostrum and also benefits the transfer of IgA precursors in the mammary glands. These result in a better transfer of immune protection to the piglet during lactation and improve the innate immunity. Future research should focus on the potential use of algae to improve the gut health of pigs and chickens.

Dr. Richard Murphy, Research Director from Alltech, talked about “Modulation of Microbial Diversity – Opportunities for Health and Wellbeing”. Dr. Murphy explained that high microbial diversity is critical for health and performance because it is correlated to an increased resistance to pathogens. There are many products that combat pathogens and create a better condition for healthy microbiomes. One product uses mannan rich fractions (MRF), derived from the cell wall of yeast. MRF’s are similar to binding sites for pathogens and act as decoys by reducing the number of pathogens that bind to the intestinal receptors in animals. When added to the diet of birds, MRF showed changes in cecum microbial diversity. Specifically, an increase in Bacteroidetes and a decrease in Firmicutes was seen. Moreover, MRF reduces pathogen load by binding to bacteria with Type 1 fimbriae, such as Salmonella and E. coli. These bacteria are recognized by the immune system and a decrease in the microbial abundance of these pathogens decreases inflammatory cytokine expression. By increasing the microbial diversity and decreasing pathogen load, MRF also reduces the need for antibiotics. MRF should be further explored in the rehabilitation of the microbiome to result in healthy animals with diverse microflora.

Dr. Tadele Kiros, Swine Global R&D manager and coordinator at Phileo, a Lesaffre company, discussed “the effect of a live probiotic yeast supplement on the microbiota of suckling and weanling piglets”. The development of the microbiome begins in early life. Originally, the “sterile womb” hypothesis posed that the infant microbiome is sterile until birth, when the infant inherits the mother’s microbiota. However, new findings suggest that colonization starts in the uterus and fluctuations in microbial composition are seen until after weaning. The period before weaning is seen as a window of opportunity for microbial manipulation.Dr. Kiros works to understand this window of opportunity in piglets. He discussed two studies that explored the effects of a yeast supplement in suckling and weanling piglets. In both studies, supplementation with yeast showed a different microbial composition when compared to the control group. In the weanling study, the cecum microbiome of the yeast supplemented piglets had more positively interacting bacteria than piglets who were given sterile water without yeast. Lastly, yeast supplementation was correlated with an increased performance in both suckling and weanling piglets. These studies show that yeast supplementation has an effect on the microbiome of piglets.

Dr. Karin Schöndorfer, Regulatory Affairs Manager at Biomin gave an excellent overview & understanding on “the design process for efficacy trials that require EU feed additive authorization”. All trials have to consider a number of factors as they attempt to show the efficacy of the additive. First, choosing between in vitro and in vivo study design will depend on the type of additive and its function. Next, the duration of the study will depend on the claim. A shorter study is needed for some colorant or flavoring additives, while a long term study may be necessary for performance additives. The timing of the study will depend on the type of animal that is used. The number of studies and locations depend on the number of species being used and their categories (poultry for fattening, birds used for egg production, ruminants for dairy, etc.). If the additive will be extrapolated for use in other animals, there are further rules to follow as to which animal groups must be tested. The minimum proposed dose and endpoints of the studies also depend on animal species. All animals must collect endpoint information about feed intake, initial and final body weight, body weight gain, and feed to gain ratios. Other specific animal claims require further data. To make claims about laying hens, for example, the study must collect data on laying and egg parameters. Lastly, the number of replicates has to comply with a statistical power calculation, and depends on the differences between and within groups. Dr. Schöndorfer emphasized the importance of Knowing the product, the claim and target animals, and the effect you wish to show before starting any efficacy trials.



Register now for our next online experts meeting on “Discovery of Novel Microbial Strains and the Impact of the Nagoya protocol“ on November 24th, 2020. In this meeting experts from the Centre for Genetic Resources, DSM Nutritional Products, WUR, SINTEF and BaseClear will share their knowledge and insights on how the Nagoya protocol influences the discovery and industrial use of microbial strains. In addition the reclassification of the genus Lactobacillus is discussed, including the impact this has on commercial use and regulatory aspects of these strains.

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