APC Microbiome Ireland - Journal Articles
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Item Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies(Springer Nature Ltd., 2023-01-25) Kennedy, Katherine M.; de Goffau, Marcus C.; Perez-Muñoz, Maria Elisa; Arrieta, Marie-Claire; Bäckhed, Fredrik; Bork, Peer; Braun, Thorsten; Bushman, Frederic D.; Dore, Joel; de Vos, Willem M.; Earl, Ashlee M.; Eisen, Jonathan A.; Elovitz, Michal A.; Ganal-Vonarburg, Stephanie C.; Gänzle, Michael G.; Garrett, Wendy S.; Hall, Lindsay J.; Hornef, Mathias W.; Huttenhower, Curtis; Konnikova, Liza; Lebeer, Sarah; Macpherson, Andrew J.; Massey, Ruth C.; Carolyn McHardy, Alice; Koren, Omry; Lawley, Trevor D.; Ley, Ruth E.; O’Mahony, Liam; O’Toole, Paul W.; Pamer, Eric G.; Parkhill, Julian; Raes, Jeroen; Rattei, Thomas; Salonen, Anne; Segal, Eran; Segata, Nicola; Shanahan, Fergus; Sloboda, Deborah M.; Smith, Gordon C. S.; Sokol, Harry; Spector, Tim D.; Surette, Michael G.; Tannock, Gerald W.; Walker, Alan W.; Yassour, Moran; Walter, Jens; Science Foundation IrelandWhether the human fetus and the prenatal intrauterine environment (amniotic fluid and placenta) are stably colonized by microbial communities in a healthy pregnancy remains a subject of debate. Here we evaluate recent studies that characterized microbial populations in human fetuses from the perspectives of reproductive biology, microbial ecology, bioinformatics, immunology, clinical microbiology and gnotobiology, and assess possible mechanisms by which the fetus might interact with microorganisms. Our analysis indicates that the detected microbial signals are likely the result of contamination during the clinical procedures to obtain fetal samples or during DNA extraction and DNA sequencing. Furthermore, the existence of live and replicating microbial populations in healthy fetal tissues is not compatible with fundamental concepts of immunology, clinical microbiology and the derivation of germ-free mammals. These conclusions are important to our understanding of human immune development and illustrate common pitfalls in the microbial analyses of many other low-biomass environments. The pursuit of a fetal microbiome serves as a cautionary example of the challenges of sequence-based microbiome studies when biomass is low or absent, and emphasizes the need for a trans-disciplinary approach that goes beyond contamination controls by also incorporating biological, ecological and mechanistic concepts.Item Isolation and characterization of Septuagintavirus ; a novel clade of Escherichia coli phages within the subfamily Vequintavirinae(American Society for Microbiology, 2024) Cortés-Martín, Adrián; Buttimer, Colin; Pozhydaieva, Nadiia; Hille, Frank; Shareefdeen, Hiba; Bolocan, Andrei Sorin; Draper, Lorraine A.; Shkoporov, Andrey N.; Franz, Charles M. A. P.; Höfer, Katharina; Ross, R. Paul; Hill, Colin; Science Foundation Ireland; Janssen Biotech; Max Planck Society; Deutsche ForschungsgemeinschaftEscherichia coli is a commensal inhabitant of the mammalian gut microbiota, frequently associated with various gastrointestinal diseases. There is increasing interest in comprehending the variety of bacteriophages (phages) that target this bacterium, as such insights could pave the way for their potential use in therapeutic applications. Here, we report the isolation and characterization of four newly identified E. coli infecting tailed phages (W70, A7-1, A5-4, and A73) that were found to constitute a novel genus, Septuagintavirus, within the subfamily Vequintavirinae. Genomes of these phages ranged from 137 kbp to 145 kbp, with a GC content of 41 mol%. They possess a maximum nucleotide similarity of 30% with phages of the closest phylogenetic genus, Certrevirus, while displaying limited homology to other genera of the Vequintavirinae family. Host range analysis showed that these phages have limited activity against a panel of E. coli strains, infecting 6 out of 16 tested isolates, regardless of their phylotype. Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) was performed on the virion of phage W70, allowing the identification of 28 structural proteins, 19 of which were shared with phages of other genera of Vequintavirinae family. The greatest diversity was identified with proteins forming tail fiber structures, likely indicating the adaptation of virions of each phage genus of this subfamily for the recognition of their target receptor on host cells. The findings of this study provide greater insights into the phages of the subfamily Vequintavirinae, contributing to the pool of knowledge currently known about these phages.Item Akkermansia muciniphila in infectious disease: A new target for this next-generation probiotic?(SAGE Publishing, 2024-03-15) Keane, Jonathan M.; Cazzaniga, Monica; Gahan, Cormac G. M.; Science Foundation Ireland; Horizon 2020The common gastrointestinal commensal Akkermansia muciniphila is a mucin-degrading bacterium that is greatly reduced in individuals consuming a high-fat diet. Increasing evidence from a variety of clinical and pre-clinical studies suggests that oral supplementation with Akkermansia can improve metabolic health and moderate systemic inflammation. We and others have demonstrated a role for Akkermansia administration in protection against infectious disease and the outcome from sepsis. Very recent studies have indicated the molecular mechanisms by which A. muciniphila may interact with the host to influence systemic immune-regulation and control of microbial pathogenesis. Here we consider recent studies which demonstrate the efficacy of this potential next-generation probiotic in animal models of Salmonella Typhimurium, Listeria monocytogenes and Clostridioides difficile as well as influenza virus and phlebovirus. The potential mechanisms by which A. muciniphila may influence local and systemic immune responses are discussed.Item Artificial intelligence and endo-histo-omics: new dimensions of precision endoscopy and histology in inflammatory bowel disease(Elsevier Ltd., 2024-07-03) Iacucci, Marietta; Santacroce, Giovanni; Zammarchi, Irene; Maeda, Yasuharu; Del Amor, Rocío; Meseguer, Pablo; Kolawole, Bisi Bode; Chaudhari, Ujwala; Di Sabatino, Antonio; Danese, Silvio; Mori, Yuichi; Grisan, Enrico; Naranjo, Valery; Ghosh, SubrataIntegrating artificial intelligence into inflammatory bowel disease (IBD) has the potential to revolutionise clinical practice and research. Artificial intelligence harnesses advanced algorithms to deliver accurate assessments of IBD endoscopy and histology, offering precise evaluations of disease activity, standardised scoring, and outcome prediction. Furthermore, artificial intelligence offers the potential for a holistic endo-histo-omics approach by interlacing and harmonising endoscopy, histology, and omics data towards precision medicine. The emerging applications of artificial intelligence could pave the way for personalised medicine in IBD, offering patient stratification for the most beneficial therapy with minimal risk. Although artificial intelligence holds promise, challenges remain, including data quality, standardisation, reproducibility, scarcity of randomised controlled trials, clinical implementation, ethical concerns, legal liability, and regulatory issues. The development of standardised guidelines and interdisciplinary collaboration, including policy makers and regulatory agencies, is crucial for addressing these challenges and advancing artificial intelligence in IBD clinical practice and trials.Item In vitro digestibility of bioprocessed brewer’s spent yeast: Demonstrating protein quality and gut microbiome modulation potential(Elsevier Ltd., 2025-01-23) Jaeger, Alice; Nyhan, Laura; Sahin, Aylin W.; Zannini, Emanuele; Meehan, Dara; Li, Junhui; O’Toole, Paul W.; Arendt, Elke K.; Horizon 2020; Science Foundation IrelandWith an ever-increasing global population and dwindling natural resources, a shift towards more sustainable food systems is required. Important aspects to aid in this transition are the reduction of food waste, and a movement towards non-animal protein sources. Brewers spent yeast (BSY) is an abundant by-product of the brewing industry, which is generally regarded as waste, despite its high nutritional value. Previous work has shown that fermentation of BSY with Lactobacillus amylovorus FST 2.11 resulted in changes in composition, functionality, and improved palatability of the processed raw material (PBSY). In this study, in vitro protein digestibility, amino acid bioaccessability, and protein quality of PBSY was explored using the static INFOGEST in vitro model. In vitro protein digestibility of PBSY (73.0 %) was almost two-fold higher than that of CBSY (40.0 %), while PBSY also displayed significantly higher in vitro bioaccessability values for all essential amino acids, except for tryptophan. Investigation of protein quality using the digestible indispensable amino acid score (DIAAS) values and the FAO recommended amino acid scoring pattern for individuals >3 years old showed that the protein quality for CBSY was low (DIAAS of 17.0 %), while PBSY was considered to be of “good” protein quality (DIAAS of 98.2 %). Investigation of the modulation potential of PBSY on the gut microbiome using an in vitro colon model system showed an increase in gut microbiome α-diversity indices and an abundance of beneficial Mediterranean diet-responsive taxa after 24 h. Overall, this study highlights the potential of BSY as raw material for the production of a high-quality food ingredient with potential prebiotic effects, aiding in the reduction food waste and supporting global food systems.
