We continued our screening assays in Year 2, incorporating a wider range of livestock bacteria and tests, to help us identify the microbiome species with the greatest inhibitory activity against pathogens. In total well over 100 microbiome species were tested, and our results demonstrated that a significant proportion of these species were able to inhibit at least one of the pathogens tested. Importantly, we also showed that inhibitory microbiome species were able to inhibit the growth of more than one type of each pathogen, including some strains that are resistant to multiple antibiotics.

We then began experiments that investigate the potential mechanisms of action that underpin antibacterial activities and allow us to assess suitability of some of our most active livestock gut bacteria as candidate novel therapeutic products. This includes generating genome sequences from the inhibitory microbiome and environmental species, which will allow us to mine these genomes for further clues to the mechanisms underpinning inhibition of pathogens.  The latter work will continue into Years 3 and 4.

Publications

• Links between Diet, Intestinal Anaerobes, Microbial Metabolites and Health (2023)  paper published in Biomedicines by Sylvia Duncan et al.
• Human microbiome myths and misconceptions (2023) article published in Nature Microbiology by Alan Walker and Lesley Hoyle

Knowledge exchange and other outputs

• Alan Walker was a speaker at a RANK Forum workshop in June 2023, discussing the impact of food security inequalities on health, with a focus on impacts mediated by the gut microbiome.
• Alan Walker and Sylvia Duncan were co-organisers of the 13^th biennial International Gut Microbiology Symposium (13-15^th June 2023) which included a scientific session on “Interactions between microbiota, pathogens and host”.
• Alan Walker carried out extensive press interviews (e.g. De Standaard, ZME Science, New Scientist, The Hindu, Neue Zurcher Zeitung) to advertise one of his articles, published in Nature Microbiology, illustrating myths and misconceptions about the microbiome. Several other news outlets from around the world picked up the news story and ran articles about it (https://nature.altmetric.com/details/152191319/news).
• Sylvia Duncan participated in Rowett Research Day, presenting a talk entitled: “Synergising one health solutions against pathogens and antimicrobial resistance”
• Alan Walker was a participant at a meeting at the House of Lords in November 2023, aimed at improving the visibility of UK microbiome research.
• Alan Walker was a guest on the "Inside Matters" podcast series, talking about gut health and microbiomes.
• Alan Walker was a speaker and session chair at a microbiome safety workshop in London, organised in January 2024 by the Microbiology Society, to assess the potential safety concerns around microbiome-targeted interventions.
• Sylvia Duncan participated in a discussion group meeting with Scottish farmers, food producers and an Aberdeenshire councillor (Industry support executive) on One Health and the environment
• Sylvia Duncan wrote an article for The Conversation on one of our gut microbiota species with inhibitory activity against multiple pathogens – Gut Microbiome: meet Ruminococcus bromii – the microbe that loves carbs.
• Alan Walker received ~£400k research funding from an industrial partner for a two-year research project to cultivate gut bacteria.

In Year 1 we successfully identified livestock gut-derived microbiome species with antimicrobial activity against the fungal pathogen Candida albicans. We also successfully developed overlay and supernatant assays to assess the ability of cattle and chicken microbiome species to inhibit the growth of bacterial pathogens linked to diarrhoeal disease and skin infections in livestock. From this initial work, we identified a number of promising livestock microbiome species with inhibitory activities against the pathogens Escherichia coli, Klebsiella oxytoca, Clostridium perfringens, Streptococcus uberis and Staphylococcus aureus. These highly encouraging results gave us promising candidates to take forward into subsequent years of the project. 

Key Outputs

Human microbiome myths and misconceptions (2023) paper published in Nature Microbiology by Alan Walker et al. 

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies (2023) paper published in Nature by Katherine Kennedy et al

Human gut bifidobacteria inhibit the growth of the opportunistic fungal pathogen Candida albicans (2022) paper published in FEMS Microbiology Ecology by Liviana Ricci et al. 

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Presentations, reports, non-Gateway blogs etc.,

• A blog was written by one of our previous PhD students, Liviana Ricci, for the FEMS Microbiology website, describing some of the work we have done to characterise the anti-fungal activities of gut bifidobacteria - https://fems-microbiology.org/femsmicroblog-fecal-bifidobacteria-inhibit-candida-albicans/
• We co-organised and hosted an International Gut Microbiology conference (13-15th June, 2023), featuring a dedicated session on the use of the microbiome to reduce infectious disease in animals. This conference attracted around 200 delegates from around the world.
• Alan Walker had extensive press interviews (e.g. De Standaard, ZME Science, New Scientist, The Hindu, Neue Zurcher Zeitung) in the 2^nd half of 2023 to advertise his article published in Nature Microbiology, illustrating myths and misconceptions about the microbiome.
• Alan Walker attended a Microbiome Policy Meeting at the House of Lords (Millbank House), London, in November 2023. This meeting discussed how we can increase the profile of UK-based microbiome research in a One Health context.
• Alan walker attended, spoke at, and chaired a session at, a Microbiome Safety Workshop in London in January 2024. This event brought together experts from academia, industry and beyond to discuss the current research landscape around the assessment of the safety of microbiome perturbations by chemicals and probiotics.