The gut microbiome plays a crucial role in the health of animals. It helps to control digestion of feeds and it’s benefiting the immune system, among many other aspects of health. An imbalance of healthy and unhealthy microbes in the digestive tract contributes to digestive disorders, other health constrains and impaired performance.

Microbiota is a key pilar for Phileo by Lesaffre as we believe that gut microbiota is infinitely promising when it comes to performance, well being prevention of pathogens. By organizing these microbiota days, Phileo builds a bridge between scientific knowledge from academics and the feed industry and primary producers. With the ambition to reduce antibiotics in animal husbandry, we hope to give new insights in how gut microbiota can be a great target. Understanding the factors that influence the microbiota helps to focus on prevention to limit diseases instead of ‘treat and cure’ strategies.

With the knowledge and experience of all participating speakers, Phileo by Lesaffre aims to create collective inspiration and generate new ideas that could contribute to a more sustainable animal production.

During the Microbiota Days, a wide variety of insights will be shared. New tools and methodologies to better understand microbiota and its interactions with the host, links between gut microbiota, diets and animal performance and health, and the relationship between immunity, intestinal mucosa and pathogen prevention are amongst the topics being discussed.

Around the world, the poultry industry aims to reduce the need for antibiotics. With a stronger focus on a resilient and healthy microbiome, many health disorders can be prevented. Markers to monitor microbiome homeostasis, nutrient digestion and performance contribute to further progress in sustainable poultry production.

This document provides an overview of poultry related work that has been presented during the Microbiota Days. An overview of all speakers and contributions can be found on the dedicated webpage.

Prof. Richard Ducatelle
Emeritus Professor in Ghent University, Belgium

Pr Ducatelle is veterinarian, graduated from Ghent University in 1978, then gra- duated for a PhD in 1983. He was scientific advisor for the Belgian government from 1985 till 1989, and professor of veterinary pathology at Ghent University from 1989 till 2020, when he became emeritus professor. Pr Ducatelle is diplomate of the European College of Veterinary Pathologists and the European College of Poultry Veterinary Science. He’s president of the WVPA Belgian branch since 1991 and past-president of the European Society of Veterinary Pathology. He’s author or coauthor of more than 700 scientific publications listed in the Web of Science (h-index = 61) and more than 400 abstracts in proceedings of international congresses.He has been invited speaker at more than 200 national and international congresses.

Overview of poultry microbiome

Under standard industry conditions, chicks hatch in the clean environment of a hatchery, wit- hout contact with the mother hen. As a consequence, the colonization of their gastro-intestinal tract by bacteria and the establishment of a mature microbiome is delayed. Not surprisingly, the earliest colonizers are members of the spore forming Clostridium cluster I and of the en- terobacteriaceae family, which includes a.o. Escherichia coli. Both of these groups of bacteria can survive in the environment of the broiler house and include commensal as well as pa- thogenic strains. Whenever a chick is first colonized by such pathogenic strain, neonatal sep- ticemia may ensue. If, hopefully, this is not the case, then a second wave of colonization takes place after 3 to 4 days, with predominantly lactobacilli. By virtue of their facultative anaerobic nature, both the lactobacilli and the enterobacteriaceae, contribute to the creation of a strictly anaerobic environment in the caeca, which then allows the final colonization of this unique en- vironment by the strictly anaerobic butyrate producers. It is only after week 3 that a balanced microbiome, comprising approximately 109 bacteria in the ileum and 1011 in the caeca, can be found. Ideally, the ileal microbiome should be dominated by members of the genus Lactobacil- lus, whereas the cecal microbiome should be dominated by members of the Lachnospiraceae and Ruminococcaceae families, both of which are essentially butyrate producers. Whether or not broilers will carry members of the phylum Bacteroidetes in their caeca seems highly unpredictable. During the lecture, examples will be given of different conditions where this delicate balance of cross-feeding micro-organisms can be disturbed, leading to dysbiosis and leaky gut, and how to control such microbial imbalance.

Dr. Lisa Williams

Lecturer in Animal Science, Hartpury University, Gloucester, UK

Lisa Williams is a lecturer in Animal science, with a specialism in zoonotic diseases in animals. She ob- tained a BSc in Food, Nutrition and Consumer Protection from BathSpa University College (2001), a MSc in Meat Science and Technology (2003) and a PhD in Microbiology (2009) from the University of Bristol. Prior to her PhD, she worked for the Health Protection Agency. Post PhD, she undertook Postdoctoral positions at the University of Bristol (2009-2015) and Swansea University (2015-2020) before taking a lectureship at Hartpury University in 2020. Her research focuses on the foodborne pathogen Campylobacter species.

She’s interested in host-pathogen interactions including the immune response, interventions particularly dietary addi- tives as a method of control, extra-intestinal spread and whether or not Campylobacter is a commensal or pathogen of broiler chickens. She also has an interest in gut health of chickens and other animals including the microbiota as well as any microbial animal disease. In addition, she has supervised many Undergraduate, Master’s and PhD students’ projects to completion. She’s currently supervising 3 PhD students, 2 of whom are funded by industry.

Microbiota and food safety (Salmonella and Campylobacter)

Campylobacter and Salmonella spp. are the most commonly reported foodborne illness in humans  worldwide. Most cases of Campylobacter spp. can be linked back to chickens and there is an established long-term relationship with chickens and Cam- pylobacter spp, it is ideally suited to the chicken niche and can survive at 42oC which is body temperature of chickens. Despite having a lower number of reported cases in humans Salmonella spp. is still important and is of concern due to its association with a variety of food producing animals. In the UK, in the poultry industry Salmonella spp. is still routinely tested for prior to processing, despite widespread and successful vaccination programmes. Controlling and reducing these pathogens is a high prio- rity, certainly for the UK livestock industry. There have been many attempts to control these pathogens through improvements to biosecurity, dietary and water additives, bacteriophage, the use of pre- and pro-biotics and vaccination. There have been li- mited success with these depending on the species of animal and bacterial target, whilst vaccination has been very successful in some animal species for Salmonella spp., control of Campylobacter spp. in any animal species has not yet been achieved using vaccines. Host-pathogen interactions are known to be very important in the sur- vival of the bacteria within the host and there are many factors that can influence these interactions including the microbiota. Manipulating the microbiota so that it is less enticing to these bacteria without having an impact on the animal could be one way to control these pathogens. This talk will look at the role the microbiota could play in improving food safety worldwide and the feasibility of this as a control measure, with a focus on Salmonella and Campylobacter spp.

Dr. Rodrigo Guabiraba
INRAE Centre Val de Loire, UMR ISP, équipe 3IMo, France

I am an immunopharmacologist (PhD) and senior research scientist at the IN- RAE (Tours). My research focuses on identifying and characterizing mediators of inflammation and the role of the intestinal microbiota in the chicken innate immune response to influenza virus along the “gutlung axis”. Host’s effector mechanisms necessary to deal with infection are not necessarily the same that will exa- cerbate inflammation and drive disease. We thus aim to provide solid rationale on how mediators of inflammation and metabolites produced by the gut microbiota regulates im- mune functions at mucosal sites, therefore contributing to optimal viral clearance or to unwanted inflammation.

Uncovering the core principles of the gut-lung axis to enhance mucosal immunity in the chicken

The gut microbiota (GM) and its metabolites are central regulators of mucosal immunity in both the gut and the airways – a concept dubbed ‘gut-lung axis’. Likewise, changes in GM composition (dysbiosis) may facilitate respiratory di- seases and infections. The rearing environment profoundly influences the de- velopment of the chicken GM. However, in modern poultry hatcheries, with egg surface disinfection and absence of chick-hen contacts, this GM transfer is hampered, with potentially negative consequences for poultry health. Since the majority of pathogens causing high impact infectious diseases in poultry target the respiratory and/or gastrointestinal tract, understanding the contribution of the ‘gut-lung-axis’ to the chicken immune system is crucial for implementing measures to improve animal robustness in commercial poultry production. Ne- vertheless, birds have a different repertoire of organs, cells, molecules and ge- nes of the immune system compared to mammals. The concept of the ‘gut-lung axis’ in birds remain largely undefined amidst increasing societal demands for economically viable and environmentally responsible health solutions in lives- tock.

Breno Beirao, PhD, DVM
Lecturer at Federal University of Paraná UFPR, Brazil

Breno Beirao has been graduated in Veterinary Medicine at UFPR and did a MSc in Immunology at the same institution, evaluating cellular immune parameters in avian diseases. He obtained his PhD from the Roslin Institute/University of Edinburgh, in Scotland in animal immunity as well. Breno Beirao is partner at Imunova Análises Biológicas LTDA, which is a Contract Research Organization in Veteri- nary Sciences in Brazil, working especially with aviculture and swine products. Currently, Breno is lecturer at UFPR, in Brazil, on Veterinary Vaccinology and Microbiology.

Relationship between microbiota and gut integrity in broilers

Numerous cells are interconnected within the digestive system to create a condition that we recognize a homeostasis. Enterocytes, immune cells, neurons, and microbiological cells (bacteria and fungi) work alongside each other in the intestine. Not only do they coexist, but they cooperate for mutual benefit. As could be expected, disbalances in any of these cellular systems also have widespread negative effects on the other cell types. Since bacteria are the most numerous cell type within the gut, they have a significant role in local health and disease, either directly or indirectly (allowing or blocking the entrance of primarily pathogenic bacteria, for instance). Bacteria can produce hormones, neurotransmitters and nutri- tious substances that overlap with host cell functions, in a direct interac- tion between ´self´ and ´non-self´, microbial cells. Here we will review several aspects of the interactions between the intestinal microbiota and the gut, and how can we modulate them with the goal of improving animal health, welfare and productivity.

Dr. Alain Riggi
DVM, Global Species Manager Poultry, Phileo by Lesaffre, France

Dr Alain Riggi has rich field working experiences as Chief Veterinarian with diffe- rent poultry production companies before joining MSD Animal Health in 2010 where he held different positions including Poultry Technical Director for Europe and North & West Africa. Currently, Dr Riggi is Global Species Manager – Poultry at Phileo by Lesaffre. As poultry veterinarian, one of Dr Riggi’s core missions at Phileo by Lesaffre is to help large poultry producers in the world (US, China, EU, Brazil, Thailand, etc.) to identify the issues in their farms and provide solutions. Dr Riggi’s functions is also to deve- lop and support the implementation of worldwide strategy related to the poultry market via close collaboration with the other departments of Phileo by Lesaffre.

Relationship between microbiota and performances in turkeys The dietary administration of a postbiotic compound like Safmannan® is thought to positively affect productive efficiency and health of poultry by modulating the gut microbiota composi- tion. The aim of this study was to investigate the effects of the dietary administration of a yeast fraction rich in mannan-oligosaccharides and β-glucans (1,3 and 1,6) on productive perfor- mance and faecal microbiota of turkeys. Despite the fact that TRT group reached a lower body weight at slaughter (9,508 vs. 9,658 g; P<0.05) due to slightly worsen productive performance during the last feeding phase (92-106 d), these results indicate that the dietary supplemen- tation of the yeast fraction determines positive effects on faecal microbiota composition of turkeys promoting healthy gut conditions, but also highlight the importance of the dosage of the product to optimize performance. It is why a second study has been conducted in the same facility and under the same conditions, except the dose Safmannan® which has been adjusted (500 g/T from 0 to 37 d, 250 g/T from 38 to 72 d and 125 g/T from 73 to 107 d). Indeed this trial showed a better feed efficiency (FCR) on the supplemented group than the control (2,272 vs 2,313 respectively; p=0,014) and a numerically better body weight (10,516 kg vs 10,437 kg respectively; NS). The microbiota was also analysed in this second trial at 21 and 85 days. The results suggested that the faeces of the turkeys belonging to both groups CONT and TRT at 21 days were mainly colonized by microorganisms belonging to the order of Lactobacillales, Enterobacteriales and Clostridiales, while at 85 days the Lactobacillales alone represented the most abundant order in both groups. At genus and species level, statistically significant increase was highlighted in groups TRT with respect to group CONT at 21 days for Faecalibac- terium and specifically for F. praustnizii that is a producer of short-chain fatty acids, such as butyric acid, having an important function in both growth performance and protection against pathogens.

Dr. Ruth Raspoet
R&D Manager Poultry, Phileo by Lesaffre, Belgium

Dr Ruth Raspoet received a master’s in Biomedical Sciences and Molecular Biotechnology at Ghent University. In 2014 she obtained a PhD in Veterinary Medical Science at Ghent University, studying the survival mechanisms of Salmonella Enteritidis in egg white. After contributing on studies for Salmonella vaccine development with Ghent Uni- versity, she joined Phileo in April 2015 as Poultry R&D manager. Ruth’s core function is to develop and new products, services and solutions for the poultry industry.

Metagenomic distribution of antibiotic resistance genes in poultry microbiota

It is becoming more and more clear that animal health and performance are closely linked to gut health, which in turn is very dependent on the composition and especially the function of the gut microbiota. To bet- ter understand the complex host-bacteria interactions, metagenomic approaches are indispensable tools that help with the finetuning of the definition of what is a health microbiota at functional level. By using these methodologies, the metachick consortium coordinated by INRAE has created a reference gene catalogue for the assessment of the biodi- versity of the caecal microbiota in poultry species. Up till now, the study has verified the influence of the farm and production type but also the animals’ age and host genetics on the caecal microbiota diversity. The study also showed a higher abundance of antibiotic resistance genes in the broiler production, most likely due to higher use of antibiotics in this rearing system. Finally, later this gene catalogue can also be used to study the influence of nutritional modulations on the gut microbiota.

Laurant Debarbieux, PhD
Research Director, Institut Pasteur, France

Laurent DEBARBIEUX is molecular microbiologist who holds a PhD from Lille University, France. After a Post-Doc in Harvard Medical School he got a position at Institut Pasteur. Laurent DEBAR- BIEUX is the head of a research team studying bacteriophages and their application to target bacterial pathogens, namely phage therapy. One of the main research activity is dedicated to understand the factors affecting the dynamic interactions between bacteriophages and bacteria in the gut of mammals, using murine models. Laurent DEBARBIEUX has published over 50 articles on this topic and is an international leading scientist in the field. He is currently a Trustee of the International Society for Viruses of Microorganisms and the President of the non for profit association P.H.A.G.E. that is lobbying for the development of phage therapy in Europe.

The challenges that face intestinal bacteriophages to kill bacteria

Bacteriophages, viruses infecting bacteria, have attracted considerable attention as a possible solution to fight against bacterial pathogens resistant to antibiotics. They have also been proposed to precisely en- gineer the intestinal microbiota. However, these two applications neces- sitate bacteriophages to reach and kill their bacterial target within the gut environment. Interestingly, the most abundant viruses of the gut are bacteriophages, and several studies suggest that they play a role in gut homeostasis, but no molecular mechanism has yet been clearly iden- tified. In particular, it remains unclear to which extent the induction of resident prophages influences the overall dynamics of bacteriophages and bacteria in the gut. In this talk, I will illustrate with experimental data what are the physical and biological challenges that bacteriophages face when targeting intestinal bacteria. I will also discuss the benefit of using semi-complex systems to tease apart the net contribution of bac- teriophages to intestinal homeostasis.

Dr. Elliot mathieu
INRAE, MetaGenoPolis, France

After obtaining a Master of Science degree from Robert Gordon University (Scotland), Elliot joined the INRAE MICALIS Institute as an engineer where he worked on pro- jects focusing on the interactions between microbiomes (intestinal and pulmonary) and the host. In 2017, Elliot started a PhD at the MICALIS Institute on the isolation of bacterial strains from the oral cavity and the characterization of their effects on respiratory health. Af- ter graduating from Sorbonne University in June 2020, Elliot joined the METAFUN plat- form of MetaGenoPolis as Production Manager in Functional Metagenomics in July 2020. As an INRAE-Tranfert collaborator, he is in charge of the industrial partnerships and supports companies through research projects.

MetaFun, a high-throughput platform to decipher host-microbiota interactions

The presentation will focus on the offers of the high-throughput scree- ning platform MetaFun of MetaGenoPolis. MetaFun explore mechanisms/ interactions between gut bacteria and human cells through innovative approaches such as functional metagenomics. Elliot will highlight the screening tools and the targeted functions (inflammation and immunity, metabolism, barrier, …). We support academics and companies to identify genes of interest for your products (probiotics, commensal bacteria…) and molecules of interest (metabolites, proteins…) for drug discovery or nutri- tion optimization.