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Yap M, O'Sullivan O, O'Toole PW, Sheehan JJ, Fenelon MA, Cotter PD. Seasonal and geographical impact on the Irish raw milk microbiota correlates with chemical composition and climatic variables. mSystems 2024; 9:e0129023. [PMID: 38445870 PMCID: PMC11019797 DOI: 10.1128/msystems.01290-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/14/2024] [Indexed: 03/07/2024] Open
Abstract
Season and location have previously been shown to be associated with differences in the microbiota of raw milk, especially in milk from pasture-based systems. Here, we further advance research in this area by examining differences in the raw milk microbiota from several locations across Ireland over 12 months, and by investigating microbiota associations with climatic variables and chemical composition. Shotgun metagenomic sequencing was used to investigate the microbiota of raw milk collected from nine locations (n = 241). Concurrent chemical analysis of the protein, fat, lactose, total solids, nonprotein nitrogen contents, and titratable acidity (TA) of the same raw milk were performed. Although the raw milk microbiota was highly diverse, a core microbiota was found, with Pseudomonas_E, Lactococcus, Acinetobacter, and Leuconostoc present in all samples. Microbiota diversity significantly differed by season and location, with differences in seasonality and geography corresponding to 11.8% and 10.5% of the variation in the microbiota. Functional and antibiotic resistance profiles also varied across season and location. The analysis of other metadata revealed additional interactions, such as an association between mean daily air and grass temperatures with the abundance of spoilage taxa like Pseudomonas species. Correlations were identified between pathogenic, mastitis-related species, fat content, and the number of sun hours, suggesting a seasonal effect. Ultimately, this study expands our understanding of the interconnected nature of the microbiota, environment/climate variables, and chemical composition of raw milk and provides evidence of a season- and location-specific microbiota. IMPORTANCE The microbiota of raw milk is influenced by many factors that encourage or prevent the introduction and growth of both beneficial and undesirable microorganisms. The seasonal and geographical impacts on the microbial communities of raw milk have been previously seen, but the relationships with environmental factors and the chemical composition has yet to be investigated. In this year-long study, we found that while raw milk is highly diverse, a core microbiota was detected for Irish raw milk, with strong evidence of seasonal and geographical influence. We also found associations between groups of microorganisms, environmental factors, and milk composition, which expand current knowledge on the relationships between microbial and chemical composition and the climate. These results provide evidence for the development of a tool to allow for the prediction of raw milk quality and safety.
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Affiliation(s)
- Min Yap
- Teagasc Food Research Centre, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Orla O'Sullivan
- Teagasc Food Research Centre, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
- VistaMilk SFI Research Centre, Cork, Ireland
| | - Paul W. O'Toole
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Jeremiah J. Sheehan
- Teagasc Food Research Centre, Cork, Ireland
- VistaMilk SFI Research Centre, Cork, Ireland
- Dairy Processing Technology Centre (DPTC), Limerick, Ireland
| | - Mark A. Fenelon
- Teagasc Food Research Centre, Cork, Ireland
- VistaMilk SFI Research Centre, Cork, Ireland
- Dairy Processing Technology Centre (DPTC), Limerick, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
- VistaMilk SFI Research Centre, Cork, Ireland
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2
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Ortiz Sanjuán JM, Argüello H, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Ekhlas D, Burgess CM, Manzanilla EG. Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs. Anim Microbiome 2024; 6:18. [PMID: 38627869 PMCID: PMC11022352 DOI: 10.1186/s42523-024-00306-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 03/31/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Post weaning diarrhoea (PWD) causes piglet morbidity and mortality at weaning and is a major driver for antimicrobial use worldwide. New regulations in the EU limit the use of in-feed antibiotics (Ab) and therapeutic zinc oxide (ZnO) to prevent PWD. New approaches to control PWD are needed, and understanding the role of the microbiota in this context is key. In this study, shotgun metagenome sequencing was used to describe the taxonomic and functional evolution of the faecal microbiota of the piglet during the first two weeks post weaning within three experimental groups, Ab, ZnO and no medication, on commercial farms using antimicrobials regularly in the post weaning period. RESULTS Diversity was affected by day post weaning (dpw), treatment used and diarrhoea but not by the farm. Microbiota composition evolved towards the dominance of groups of species such as Prevotella spp. at day 14dpw. ZnO inhibited E. coli overgrowth, promoted higher abundance of the family Bacteroidaceae and decreased Megasphaera spp. Animals treated with Ab exhibited inconsistent taxonomic changes across time points, with an overall increase of Limosilactobacillus reuteri and Megasphaera elsdenii. Samples from non-medicated pigs showed virulence-related functions at 7dpw, and specific ETEC-related virulence factors were detected in all samples presenting diarrhoea. Differential microbiota functions of pigs treated with ZnO were related to sulphur and DNA metabolism, as well as mechanisms of antimicrobial and heavy metal resistance, whereas Ab treated animals exhibited functions related to antimicrobial resistance and virulence. CONCLUSION Ab and particularly ZnO maintained a stable microbiota composition and functionality during the two weeks post weaning, by limiting E. coli overgrowth, and ultimately preventing microbiota dysbiosis. Future approaches to support piglet health should be able to reproduce this stable gut microbiota transition during the post weaning period, in order to maintain optimal gut physiological and productive conditions.
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Affiliation(s)
- Juan M Ortiz Sanjuán
- Pig Development Department, Teagasc Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland.
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain.
| | - Héctor Argüello
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Raúl Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Institute, University College Cork, Co. Cork, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Institute, University College Cork, Co. Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Institute, University College Cork, Co. Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, Co. Cork, Ireland
| | - Juan J Garrido
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Daniel Ekhlas
- Pig Development Department, Teagasc Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland
- Department of Food Safety, Teagasc Food Research Centre, Ashtown, Dublin, Ireland
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Catherine M Burgess
- Department of Food Safety, Teagasc Food Research Centre, Ashtown, Dublin, Ireland
| | - Edgar G Manzanilla
- Pig Development Department, Teagasc Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
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Mukherjee A, Breselge S, Dimidi E, Marco ML, Cotter PD. Fermented foods and gastrointestinal health: underlying mechanisms. Nat Rev Gastroenterol Hepatol 2024; 21:248-266. [PMID: 38081933 DOI: 10.1038/s41575-023-00869-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/01/2023] [Indexed: 12/20/2023]
Abstract
Although fermentation probably originally developed as a means of preserving food substrates, many fermented foods (FFs), and components therein, are thought to have a beneficial effect on various aspects of human health, and gastrointestinal health in particular. It is important that any such perceived benefits are underpinned by rigorous scientific research to understand the associated mechanisms of action. Here, we review in vitro, ex vivo and in vivo studies that have provided insights into the ways in which the specific food components, including FF microorganisms and a variety of bioactives, can contribute to health-promoting activities. More specifically, we draw on representative examples of FFs to discuss the mechanisms through which functional components are produced or enriched during fermentation (such as bioactive peptides and exopolysaccharides), potentially toxic or harmful compounds (such as phytic acid, mycotoxins and lactose) are removed from the food substrate, and how the introduction of fermentation-associated live or dead microorganisms, or components thereof, to the gut can convey health benefits. These studies, combined with a deeper understanding of the microbial composition of a wider variety of modern and traditional FFs, can facilitate the future optimization of FFs, and associated microorganisms, to retain and maximize beneficial effects in the gut.
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Affiliation(s)
| | - Samuel Breselge
- Teagasc Food Research Centre, Moorepark, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Eirini Dimidi
- Department of Nutritional Sciences, King's College London, London, UK
| | - Maria L Marco
- Department of Food Science & Technology, University of California, Davis, CA, USA
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Cork, Ireland.
- APC Microbiome Ireland, Cork, Ireland.
- VistaMilk, Cork, Ireland.
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McDermott G, Walsh A, Crispie F, Frost S, Greally P, Cotter PD, O’Sullivan O, Renwick J. Insights into the Adolescent Cystic Fibrosis Airway Microbiome Using Shotgun Metagenomics. Int J Mol Sci 2024; 25:3893. [PMID: 38612702 PMCID: PMC11011389 DOI: 10.3390/ijms25073893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
Cystic fibrosis (CF) is an inherited genetic disorder which manifests primarily in airway disease. Recent advances in molecular technologies have unearthed the diverse polymicrobial nature of the CF airway. Numerous studies have characterised the genus-level composition of this airway community using targeted 16S rDNA sequencing. Here, we employed whole-genome shotgun metagenomics to provide a more comprehensive understanding of the early CF airway microbiome. We collected 48 sputum samples from 11 adolescents and children with CF over a 12-month period and performed shotgun metagenomics on the Illumina NextSeq platform. We carried out functional and taxonomic analysis of the lung microbiome at the species and strain levels. Correlations between microbial diversity measures and independent demographic and clinical variables were performed. Shotgun metagenomics detected a greater diversity of bacteria than culture-based methods. A large proportion of the top 25 most-dominant species were anaerobes. Samples dominated by Staphylococcus aureus and Prevotella melaninogenica had significantly higher microbiome diversity, while no CF pathogen was associated with reduced microbial diversity. There was a diverse resistome present in all samples in this study, with 57.8% agreement between shotgun metagenomics and culture-based methods for detection of resistance. Pathogenic sequence types (STs) of S. aureus, Pseudomonas aeruginosa, Haemophilus influenzae and Stenotrophomonas maltophilia were observed to persist in young CF patients, while STs of S. aureus were both persistent and shared between patients. This study provides new insight into the temporal changes in strain level composition of the microbiome and the landscape of the resistome in young people with CF. Shotgun metagenomics could provide a very useful one-stop assay for detecting pathogens, emergence of resistance and conversion to persistent colonisation in early CF disease.
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Affiliation(s)
- Gillian McDermott
- Trinity Centre for Health Science, Clinical Microbiology Department, School of Medicine, Faculty of Health Science, Trinity College Dublin, Tallaght University Hospital, D24 NR0A Dublin, Ireland;
| | - Aaron Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996 Co Cork, Ireland; (A.W.); (F.C.); (P.D.C.); (O.O.)
- APC Microbiome Ireland, University College Cork, T12 R229 Co Cork, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996 Co Cork, Ireland; (A.W.); (F.C.); (P.D.C.); (O.O.)
- APC Microbiome Ireland, University College Cork, T12 R229 Co Cork, Ireland
| | - Susanna Frost
- Tallaght University Hospital, Tallaght, D24 NR0 Dublin, Ireland (P.G.)
| | - Peter Greally
- Tallaght University Hospital, Tallaght, D24 NR0 Dublin, Ireland (P.G.)
- Hermitage Medical Clinic, Lucan, D20 W722 Dublin, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996 Co Cork, Ireland; (A.W.); (F.C.); (P.D.C.); (O.O.)
- APC Microbiome Ireland, University College Cork, T12 R229 Co Cork, Ireland
| | - Orla O’Sullivan
- Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996 Co Cork, Ireland; (A.W.); (F.C.); (P.D.C.); (O.O.)
- APC Microbiome Ireland, University College Cork, T12 R229 Co Cork, Ireland
| | - Julie Renwick
- Trinity Centre for Health Science, Clinical Microbiology Department, School of Medicine, Faculty of Health Science, Trinity College Dublin, Tallaght University Hospital, D24 NR0A Dublin, Ireland;
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Lordan C, Roche AK, Delsing D, Nauta A, Groeneveld A, MacSharry J, Cotter PD, van Sinderen D. Linking human milk oligosaccharide metabolism and early life gut microbiota: bifidobacteria and beyond. Microbiol Mol Biol Rev 2024; 88:e0009423. [PMID: 38206006 DOI: 10.1128/mmbr.00094-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024] Open
Abstract
SUMMARYHuman milk oligosaccharides (HMOs) are complex, multi-functional glycans present in human breast milk. They represent an intricate mix of heterogeneous structures which reach the infant intestine in an intact form as they resist gastrointestinal digestion. Therefore, they confer a multitude of benefits, directly and/or indirectly, to the developing neonate. Certain bifidobacterial species, being among the earliest gut colonizers of breast-fed infants, have an adapted functional capacity to metabolize various HMO structures. This ability is typically observed in infant-associated bifidobacteria, as opposed to bifidobacteria associated with a mature microbiota. In recent years, information has been gleaned regarding how these infant-associated bifidobacteria as well as certain other taxa are able to assimilate HMOs, including the mechanistic strategies enabling their acquisition and consumption. Additionally, complex metabolic interactions occur between microbes facilitated by HMOs, including the utilization of breakdown products released from HMO degradation. Interest in HMO-mediated changes in microbial composition and function has been the focal point of numerous studies, in recent times fueled by the availability of individual biosynthetic HMOs, some of which are now commonly included in infant formula. In this review, we outline the main HMO assimilatory and catabolic strategies employed by infant-associated bifidobacteria, discuss other taxa that exhibit breast milk glycan degradation capacity, and cover HMO-supported cross-feeding interactions and related metabolites that have been described thus far.
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Affiliation(s)
- Cathy Lordan
- Teagasc Food Research Centre, Fermoy, Co Cork, Ireland
| | - Aoife K Roche
- APC Microbiome Ireland, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | | | - Arjen Nauta
- FrieslandCampina, Amersfoort, the Netherlands
| | | | - John MacSharry
- APC Microbiome Ireland, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Fermoy, Co Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Douwe van Sinderen
- APC Microbiome Ireland, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
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6
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Balasubramanian R, Schneider E, Gunnigle E, Cotter PD, Cryan JF. Fermented foods: Harnessing their potential to modulate the microbiota-gut-brain axis for mental health. Neurosci Biobehav Rev 2024; 158:105562. [PMID: 38278378 DOI: 10.1016/j.neubiorev.2024.105562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/18/2024] [Accepted: 01/21/2024] [Indexed: 01/28/2024]
Abstract
Over the past two decades, whole food supplementation strategies have been leveraged to target mental health. In addition, there has been increasing attention on the ability of gut microbes, so called psychobiotics, to positively impact behaviour though the microbiota-gut-brain axis. Fermented foods offer themselves as a combined whole food microbiota modulating intervention. Indeed, they contain potentially beneficial microbes, microbial metabolites and other bioactives, which are being harnessed to target the microbiota-gut-brain axis for positive benefits. This review highlights the diverse nature of fermented foods in terms of the raw materials used and type of fermentation employed, and summarises their potential to shape composition of the gut microbiota, the gut to brain communication pathways including the immune system and, ultimately, modulate the microbiota-gut-brain axis. Throughout, we identify knowledge gaps and challenges faced in designing human studies for investigating the mental health-promoting potential of individual fermented foods or components thereof. Importantly, we also suggest solutions that can advance understanding of the therapeutic merit of fermented foods to modulate the microbiota-gut-brain axis.
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Affiliation(s)
- Ramya Balasubramanian
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, P61C996, County Cork, Ireland
| | | | - Eoin Gunnigle
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Paul D Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, P61C996, County Cork, Ireland.
| | - John F Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland.
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7
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Ortiz Sanjuán JM, Manzanilla EG, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Ekhlas D, O’Neill L, Argüello H. Fine-tuning of post-weaning pig microbiome structure and functionality by in-feed zinc oxide and antibiotics use. Front Cell Infect Microbiol 2024; 14:1354449. [PMID: 38384302 PMCID: PMC10879578 DOI: 10.3389/fcimb.2024.1354449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/22/2024] [Indexed: 02/23/2024] Open
Abstract
Introduction Post-weaning diarrhoea (PWD) is a multifactorial disease that affects piglets after weaning, contributing to productive and economic losses. Its control includes the use of in-feed prophylactic antibiotics and therapeutic zinc oxide (ZnO), treatments that, since 2022, are no longer permitted in the European Union due to spread of antimicrobial resistance genes and pollution of soil with heavy metals. A dysbiosis in the microbiota has been suggested as a potential risk factor of PWD onset. Understanding pig's microbiota development around weaning and its changes in response to ZnO and antibiotics is crucial to develop feasible alternatives to prophylactic and metaphylactic antimicrobial use. Methods This study used shotgun metagenomic sequencing to investigate the environmental and faecal microbiota on 10 farms using (Treated) or not using (ZnO-free) in-feed antibiotics and ZnO during the first 14 days post-weaning (dpw). Environmental samples from clean pens were collected at weaning day (0dpw), and faecal samples at 0, 7 and 14dpw. Diarrhoeic faecal samples were collected at 7dpw when available. Results The analysis of data revealed that the faecal microbiota composition and its functionality was impacted by the sampling time point (microbiota maturation after weaning) but not by the farm environment. Treatment with antibiotics and ZnO showed no effects on diversity indices while the analyses of microbiota taxonomic and functional profiles revealed increased abundance of taxa and metabolic functions associated with Phascolarctobacterium succinatutens or different species of Prevotella spp. on the Treated farms, and with Megasphaera elsdenii and Escherichia coli on the ZnO-free farms. The analysis of diarrhoea samples revealed that the treatment favoured the microbiota transition or maturation from 0dpw to 14dpw in Treated farms, resembling the composition of healthy animals, when compared to diarrhoea from ZnO-free farms, which were linked in composition to 0dpw samples. Discussion The results provide a comprehensive overview of the beneficial effects of ZnO and antibiotics in PWD in the microbiota transition after weaning, preventing the overgrowth of pathogens such as pathogenic E. coli and revealing the key aspects in microbiota maturation that antibiotics or ZnO alternatives should fulfil.
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Affiliation(s)
- Juan M. Ortiz Sanjuán
- Pig Development Department, Teagasc Grassland Research and Innovation Centre, Moorepark, Cork, Ireland
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Edgar G. Manzanilla
- Pig Development Department, Teagasc Grassland Research and Innovation Centre, Moorepark, Cork, Ireland
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Raúl Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Cork, Ireland
- APC Microbiome Institute Science Foundation Ireland (SFI) Research Centre, University College Cork, Cork, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Cork, Ireland
- APC Microbiome Institute Science Foundation Ireland (SFI) Research Centre, University College Cork, Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Cork, Ireland
- APC Microbiome Institute Science Foundation Ireland (SFI) Research Centre, University College Cork, Cork, Ireland
- VistaMilk Science Foundation Ireland (SFI) Research Centre, Cork, Ireland
| | - Juan J. Garrido
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Daniel Ekhlas
- Pig Development Department, Teagasc Grassland Research and Innovation Centre, Moorepark, Cork, Ireland
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Lorcan O’Neill
- Pig Development Department, Teagasc Grassland Research and Innovation Centre, Moorepark, Cork, Ireland
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Héctor Argüello
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, León, Spain
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Iyer A, Mukherjee A, Gómez-Sala B, O'Connor EM, Kenny JG, Cotter PD. The impact of live dietary microbes on health: A scoping review. J Food Sci 2024; 89:773-792. [PMID: 38174642 DOI: 10.1111/1750-3841.16893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/16/2023] [Accepted: 12/02/2023] [Indexed: 01/05/2024]
Abstract
A systematic approach to collect, peruse, and summarize the available information relating to the potential benefits of consuming dietary microbes was pursued in this scoping review. This review focused on the research endpoints, experimental designs, and microbial exposure in experimental as well as observational research work. Using a structured- set of keywords, scientific databases were systematically searched to retrieve publications reporting outcomes pertaining to the use of dietary microbes in healthy, nonpatient populations. Searches were further tailored to focus on eight different health categories, namely, "antibiotic associated diarrhoea" (AAD), "gastrointestinal health" (GIH), "immunological health" (ImH), "cardiovascular health and metabolic syndrome" (CvHMS), "cancer prevention" (CanPr), "respiratory health" (ReH), "weight management" (WtMgt), and "urogenital health" (UrGH). Quality of evidence available in each publication was assessed using the Jadad scoring system. The search yielded 228 relevant publications describing 282 experimental cases comprising 62 research endpoints overall. A microbial dose of≥ 2 × 10 9 $\ge 2\times 10^9$ CFU.day-1 was associated with non-negative reported outcomes. Older population groups with a median age of 39 years were associated with positive outcomes. More high-quality research is required investigating the role of dietary microbes in maintaining general health, particularly in the health categories of UrGH, WtMgt, and CanPr.
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Affiliation(s)
- Ajay Iyer
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
| | - Arghya Mukherjee
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
| | - Beatriz Gómez-Sala
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Eibhlís M O'Connor
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Biological Sciences, University of Limerick, Limerick, Ireland
- Health Research Institute, University of Limerick, Limerick, Ireland
| | - John G Kenny
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- VistaMilk SFI Research Centre, Cork, Ireland
| | - Paul D Cotter
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- VistaMilk SFI Research Centre, Cork, Ireland
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9
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Ritz NL, Draper LA, Bastiaanssen TFS, Turkington CJR, Peterson VL, van de Wouw M, Vlckova K, Fülling C, Guzzetta KE, Burokas A, Harris H, Dalmasso M, Crispie F, Cotter PD, Shkoporov AN, Moloney GM, Dinan TG, Hill C, Cryan JF. The gut virome is associated with stress-induced changes in behaviour and immune responses in mice. Nat Microbiol 2024; 9:359-376. [PMID: 38316929 PMCID: PMC10847049 DOI: 10.1038/s41564-023-01564-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 11/17/2023] [Indexed: 02/07/2024]
Abstract
The microbiota-gut-brain axis has been shown to play an important role in the stress response, but previous work has focused primarily on the role of the bacteriome. The gut virome constitutes a major portion of the microbiome, with bacteriophages having the potential to remodel bacteriome structure and activity. Here we use a mouse model of chronic social stress, and employ 16S rRNA and whole metagenomic sequencing on faecal pellets to determine how the virome is modulated by and contributes to the effects of stress. We found that chronic stress led to behavioural, immune and bacteriome alterations in mice that were associated with changes in the bacteriophage class Caudoviricetes and unassigned viral taxa. To determine whether these changes were causally related to stress-associated behavioural or physiological outcomes, we conducted a faecal virome transplant from mice before stress and autochthonously transferred it to mice undergoing chronic social stress. The transfer of the faecal virome protected against stress-associated behaviour sequelae and restored stress-induced changes in select circulating immune cell populations, cytokine release, bacteriome alterations and gene expression in the amygdala. These data provide evidence that the virome plays a role in the modulation of the microbiota-gut-brain axis during stress, indicating that these viral populations should be considered when designing future microbiome-directed therapies.
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Affiliation(s)
- Nathaniel L Ritz
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Lorraine A Draper
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Thomaz F S Bastiaanssen
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Christopher J R Turkington
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Veronica L Peterson
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Marcel van de Wouw
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- Department of Pediatrics, University of Calgary, Calgary, Canada
| | - Klara Vlckova
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Katherine E Guzzetta
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Aurelijus Burokas
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Biological Models, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Hugh Harris
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Marion Dalmasso
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- Normandie Univ, UNICAEN, UNIROUEN, ABTE, 14000, Caen, France
| | - Fiona Crispie
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
| | - Paul D Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
| | - Andrey N Shkoporov
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Gerard M Moloney
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Timothy G Dinan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Psychiatry and Neurobehavioural Science, University College Corke, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - John F Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland.
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10
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Killeen SL, Mealy G, Brennan K, Cotter PD, Yelverton C, Saldova R, Groeger D, VanSinderen D, Doyle S, McAuliffe FM. Impact of Bifidobacterium longum1714® on maternal cytokine response in peripheral blood mononuclear cells. Cytokine 2024; 174:156458. [PMID: 38071842 DOI: 10.1016/j.cyto.2023.156458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/17/2023] [Accepted: 11/27/2023] [Indexed: 01/01/2024]
Abstract
PURPOSE The maternal immune system is implicated in adverse pregnancy outcomes. Manipulation of maternal immune response by probiotics holds potential to reduce pregnancy complications. The MicrobeMom2 study investigates the impact of probiotic supplementation on maternal immune responses to pathogen associated molecular patterns (PAMPs) in peripheral blood mononuclear cells (PBMCs) during pregnancy. METHODS This double-blinded randomised-controlled trial involved oral supplementation of Bifidobacterium longum subsp. longum 1714® (B. longum 1714; daily ingestion of a minimum of 1x109 colony forming units) or placebo from 16 to 20-weeks' gestation until delivery in healthy pregnant women. The primary outcome was a change in IL-10 production, after stimulation with Lipopolysaccharide (LPS) or anti-CD3/28/2, in PBMCs isolated from blood samples taken at baseline (11-15 weeks' gestation) and late pregnancy (28-32 weeks' gestation) after 48 h incubation. 68 subjects were needed (34ineachgroup) for 80 % power at an alpha significance of 0.05 to detect differences in IL10. RESULTS 72 women (mean ± SD age 33.17 ± 4.53 years and median (25th, 75th centile) body mass index 24.93 (21.93, 27.57 kg/m2)) were recruited with primary outcome data. Using LPS, late pregnancy fold change in IL-10 in PBMCs after 48 h incubation was median (25th, 75th centile) 88.45 (4.88, 488.78) in the intervention, 24.18 (6.36, 141.17) in the control group, p = 0.183. Using anti-CD3/28/2, values were 189.69 (425.96, 866.57),148.74 (31.67, 887.03) in intervention and control groups, respectively, p = 0.506. No significant differences were observed between the two groups. CONCLUSION Maternal antenatal supplementation with B. longum 1714 did not alter cytokine production by maternal PBMCs in response to PAMPs or anti-CD3/28/2. TRIAL REGISTRATION NUMBER ISRCTN registry ISRCTN43013285.
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Affiliation(s)
- Sarah Louise Killeen
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Grace Mealy
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Kiva Brennan
- Department of Clinical Medicine, Trinity College Institute of Neuroscience, School of Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Paul D Cotter
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland; Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Cara Yelverton
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Radka Saldova
- The National Institute for Bioprocessing, Research, and Training (NIBRT), Dublin, Ireland; UCD School of Medicine, College of Health and Agricultural Science (CHAS), University College Dublin (UCD), Dublin, Ireland
| | - David Groeger
- PrecisionBiotics Group Ltd (Novozymes), Cork Airport Business Park, Kinsale Road, Cork, Ireland
| | - Douwe VanSinderen
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland
| | - Sarah Doyle
- Department of Clinical Medicine, Trinity College Institute of Neuroscience, School of Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Fionnuala M McAuliffe
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland.
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11
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Valentino V, Magliulo R, Farsi D, Cotter PD, O'Sullivan O, Ercolini D, De Filippis F. Fermented foods, their microbiome and its potential in boosting human health. Microb Biotechnol 2024; 17:e14428. [PMID: 38393607 PMCID: PMC10886436 DOI: 10.1111/1751-7915.14428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Fermented foods (FFs) are part of the cultural heritage of several populations, and their production dates back 8000 years. Over the last ~150 years, the microbial consortia of many of the most widespread FFs have been characterised, leading in some instances to the standardisation of their production. Nevertheless, limited knowledge exists about the microbial communities of local and traditional FFs and their possible effects on human health. Recent findings suggest they might be a valuable source of novel probiotic strains, enriched in nutrients and highly sustainable for the environment. Despite the increasing number of observational studies and randomised controlled trials, it still remains unclear whether and how regular FF consumption is linked with health outcomes and enrichment of the gut microbiome in health-associated species. This review aims to sum up the knowledge about traditional FFs and their associated microbiomes, outlining the role of fermentation with respect to boosting nutritional profiles and attempting to establish a link between FF consumption and health-beneficial outcomes.
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Affiliation(s)
- Vincenzo Valentino
- Department of Agricultural SciencesUniversity of Naples Federico IIPorticiItaly
| | - Raffaele Magliulo
- Department of Agricultural SciencesUniversity of Naples Federico IIPorticiItaly
- NBFC‐National Biodiversity Future CenterPalermoItaly
| | - Dominic Farsi
- Department of Food BiosciencesTeagasc Food Research CentreMooreparkFermoyIreland
| | - Paul D. Cotter
- Department of Food BiosciencesTeagasc Food Research CentreMooreparkFermoyIreland
- APC Microbiome IrelandNational University of IrelandCorkIreland
- VistaMilk, FermoyCorkIreland
| | - Orla O'Sullivan
- Department of Food BiosciencesTeagasc Food Research CentreMooreparkFermoyIreland
- APC Microbiome IrelandNational University of IrelandCorkIreland
- VistaMilk, FermoyCorkIreland
| | - Danilo Ercolini
- Department of Agricultural SciencesUniversity of Naples Federico IIPorticiItaly
- Task Force on Microbiome StudiesUniversity of Naples Federico IIPorticiItaly
| | - Francesca De Filippis
- Department of Agricultural SciencesUniversity of Naples Federico IIPorticiItaly
- NBFC‐National Biodiversity Future CenterPalermoItaly
- Task Force on Microbiome StudiesUniversity of Naples Federico IIPorticiItaly
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12
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Soriano-Lerma A, García-Burgos M, Barton W, M Alférez MJ, Crespo-Pérez JV, Soriano M, López-Aliaga I, Cotter PD, García-Salcedo JA. Comprehensive insight into the alterations in the gut microbiome and the intestinal barrier as a consequence of iron deficiency anaemia. Biomed J 2024:100701. [PMID: 38281699 DOI: 10.1016/j.bj.2024.100701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 11/09/2023] [Accepted: 01/19/2024] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Iron deficiency is the top leading cause of anaemia, whose treatment has been shown to deteriorate gut health. However, a comprehensive analysis of the intestinal barrier and the gut microbiome during IDA have not been performed to date. This study aims to delve further into the analysis of these two aspects, which will mean a step forward minimising the negative impact of iron supplements on intestinal health. METHODS IDA was experimentally induced in an animal model. Shotgun sequencing was used to analyse the gut microbiome in the colonic region, while the intestinal barrier was studied through histological analyses, mRNA sequencing (RNA-Seq), qPCR and immunofluorescence. Determinations of lipopolysaccharide (LPS) and bacteria-specific immunoglobulins were performed to assess microbial translocation. RESULTS Microbial metabolism in the colon shifted towards an increased production of certain amino acids, short chain fatty acids and nucleotides, with Clostridium species being enriched during IDA. Structural alterations of the colonic epithelium were shown by histological analysis. RNA-Seq revealed a downregulation of extracellular matrix-associated genes and proteins and an overall underdeveloped epithelium. Increased levels of serum LPS and an increased immune response against dysbiotic bacteria support an impairment in the integrity of the gut barrier during IDA. CONCLUSIONS IDA negatively impacts the gut microbiome and the intestinal barrier, triggering an increased microbial translocation. This study emphasizes the deterioration of gut health during IDA and the fact that it should be addressed when treating the disease.
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Affiliation(s)
- Ana Soriano-Lerma
- Department of Physiology (Faculty of Pharmacy, Campus Universitario de Cartuja), Institute of Nutrition and Food Technology "José Mataix Verdú", University of Granada, E-18071, Granada, Spain; GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government, PTS Granada, E-18016, Granada, Spain; Instituto de Investigación Biosanitaria ibs.GRANADA, E-18012, Granada, Spain
| | - María García-Burgos
- Department of Physiology (Faculty of Pharmacy, Campus Universitario de Cartuja), Institute of Nutrition and Food Technology "José Mataix Verdú", University of Granada, E-18071, Granada, Spain; GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government, PTS Granada, E-18016, Granada, Spain
| | - Wiley Barton
- VistaMilk, Ireland; Teagasc Food Research Centre, Moorepark, P61 C996, Fermoy, Cork, Ireland
| | - María José M Alférez
- Department of Physiology (Faculty of Pharmacy, Campus Universitario de Cartuja), Institute of Nutrition and Food Technology "José Mataix Verdú", University of Granada, E-18071, Granada, Spain
| | - Jorge Valentín Crespo-Pérez
- Service of Anatomical pathology, Intercenter Regional Unit Granada, University Hospital Virgen de las Nieves, E-18014, Granada, Spain
| | - Miguel Soriano
- Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04001, Almería, Spain.
| | - Inmaculada López-Aliaga
- Department of Physiology (Faculty of Pharmacy, Campus Universitario de Cartuja), Institute of Nutrition and Food Technology "José Mataix Verdú", University of Granada, E-18071, Granada, Spain.
| | - Paul D Cotter
- VistaMilk, Ireland; Teagasc Food Research Centre, Moorepark, P61 C996, Fermoy, Cork, Ireland; APC Microbiome Ireland, Cork, Ireland
| | - José A García-Salcedo
- GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government, PTS Granada, E-18016, Granada, Spain; Instituto de Investigación Biosanitaria ibs.GRANADA, E-18012, Granada, Spain; Microbiology Unit, University Hospital Virgen de las Nieves, E-18014, Granada, Spain
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13
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Barcenilla C, Cobo-Díaz JF, De Filippis F, Valentino V, Cabrera Rubio R, O'Neil D, Mahler de Sanchez L, Armanini F, Carlino N, Blanco-Míguez A, Pinto F, Calvete-Torre I, Sabater C, Delgado S, Ruas-Madiedo P, Quijada NM, Dzieciol M, Skírnisdóttir S, Knobloch S, Puente A, López M, Prieto M, Marteinsson VT, Wagner M, Margolles A, Segata N, Cotter PD, Ercolini D, Alvarez-Ordóñez A. Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments. Nat Protoc 2024:10.1038/s41596-023-00949-x. [PMID: 38267717 DOI: 10.1038/s41596-023-00949-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 11/09/2023] [Indexed: 01/26/2024]
Abstract
Deep investigation of the microbiome of food-production and food-processing environments through whole-metagenome sequencing (WMS) can provide detailed information on the taxonomic composition and functional potential of the microbial communities that inhabit them, with huge potential benefits for environmental monitoring programs. However, certain technical challenges jeopardize the application of WMS technologies with this aim, with the most relevant one being the recovery of a sufficient amount of DNA from the frequently low-biomass samples collected from the equipment, tools and surfaces of food-processing plants. Here, we present the first complete workflow, with optimized DNA-purification methodology, to obtain high-quality WMS sequencing results from samples taken from food-production and food-processing environments and reconstruct metagenome assembled genomes (MAGs). The protocol can yield DNA loads >10 ng in >98% of samples and >500 ng in 57.1% of samples and allows the collection of, on average, 12.2 MAGs per sample (with up to 62 MAGs in a single sample) in ~1 week, including both laboratory and computational work. This markedly improves on results previously obtained in studies performing WMS of processing environments and using other protocols not specifically developed to sequence these types of sample, in which <2 MAGs per sample were obtained. The full protocol has been developed and applied in the framework of the European Union project MASTER (Microbiome applications for sustainable food systems through technologies and enterprise) in 114 food-processing facilities from different production sectors.
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Affiliation(s)
- Coral Barcenilla
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - José F Cobo-Díaz
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Vincenzo Valentino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | | | | | | | - Federica Armanini
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Niccolò Carlino
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Aitor Blanco-Míguez
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Federica Pinto
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Inés Calvete-Torre
- Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Paseo Río Linares, Villaviciosa, Asturias, Spain
- Health Research Institute of Asturias (ISPA), Avenida Hospital Universitario, Oviedo, Asturias, Spain
| | - Carlos Sabater
- Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Paseo Río Linares, Villaviciosa, Asturias, Spain
- Health Research Institute of Asturias (ISPA), Avenida Hospital Universitario, Oviedo, Asturias, Spain
| | - Susana Delgado
- Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Paseo Río Linares, Villaviciosa, Asturias, Spain
- Health Research Institute of Asturias (ISPA), Avenida Hospital Universitario, Oviedo, Asturias, Spain
| | - Patricia Ruas-Madiedo
- Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Paseo Río Linares, Villaviciosa, Asturias, Spain
- Health Research Institute of Asturias (ISPA), Avenida Hospital Universitario, Oviedo, Asturias, Spain
| | - Narciso M Quijada
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria
- Department for Farm Animals and Veterinary Public Health, Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, Salamanca, Spain
| | - Monika Dzieciol
- Department for Farm Animals and Veterinary Public Health, Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | - Stephen Knobloch
- Microbiology Research Group, Matís ohf., Reykjavík, Iceland
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany
| | - Alba Puente
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Mercedes López
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Miguel Prieto
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Viggó Thór Marteinsson
- Microbiology Research Group, Matís ohf., Reykjavík, Iceland
- Faculty of Food Science and Nutrition, University of Iceland, Reykjavik, Iceland
| | - Martin Wagner
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria
- Department for Farm Animals and Veterinary Public Health, Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Abelardo Margolles
- Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Paseo Río Linares, Villaviciosa, Asturias, Spain
- Health Research Institute of Asturias (ISPA), Avenida Hospital Universitario, Oviedo, Asturias, Spain
| | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Cork, Ireland
- APC Microbiome Ireland and VistaMilk Research Centres, Cork, Ireland
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Avelino Alvarez-Ordóñez
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain.
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14
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Sabino YNV, Araújo Domingues KCD, Mathur H, Gómez-Mascaraque LG, Drouin G, Martínez-Abad A, Tótola MR, Abreu LM, Cotter PD, Mantovani HC. Exopolysaccharides produced by Bacillus spp. inhibit biofilm formation by Staphylococcus aureus strains associated with bovine mastitis. Int J Biol Macromol 2023; 253:126689. [PMID: 37678679 DOI: 10.1016/j.ijbiomac.2023.126689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/22/2023] [Accepted: 09/02/2023] [Indexed: 09/09/2023]
Abstract
Bovine mastitis is a costly disease in the dairy sector worldwide. Here the objective was to identify and characterize anti-biofilm compounds produced by Bacillus spp. against S. aureus associated with bovine mastitis. Results showed that cell-free supernatants of three Bacillus strains (out of 33 analysed) reduced S. aureus biofilm formation by approximately 40 % without affecting bacterial growth. The anti-biofilm activity was associated with exopolysaccharides (EPS) secreted by Bacillus spp. The EPS decreased S. aureus biofilm formation in a dose-dependent manner, inhibiting biofilm formation by 83 % at 1 mg/mL. The EPS also showed some biofilm disruption activity (up to 36.4 %), which may be partially mediated by increased expression of the aur gene. The characterization of EPS produced by Bacillus velezensis 87 and B. velezensis TR47II revealed macromolecules with molecular weights of 31.2 and 33.7 kDa, respectively. These macromolecules were composed mainly of glucose (mean = 218.5 μg/mg) and mannose (mean = 241.5 μg/mg) and had similar functional groups (pyranose ring, beta-type glycosidic linkage, and alkynes) as revealed by FT-IR. In conclusion, this study shows the potential applications of EPS produced by B. velezensis as an anti-biofilm compound that could contribute to the treatment of bovine mastitis caused by S. aureus.
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Affiliation(s)
| | | | - Harsh Mathur
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | | | - Gaetan Drouin
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | | | - Marcos Rogério Tótola
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Lucas Magalhães Abreu
- Department of Phytopathology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; APC Microbiome Ireland, Cork, Ireland
| | - Hilario Cuquetto Mantovani
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil; Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA.
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15
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Lawrence K, Fibert P, Hobbs J, Myrissa K, Toribio-Mateas MA, Quadt F, Cotter PD, Gregory AM. Randomised controlled trial of the effects of kefir on behaviour, sleep and the microbiome in children with ADHD: a study protocol. BMJ Open 2023; 13:e071063. [PMID: 38149413 PMCID: PMC10711914 DOI: 10.1136/bmjopen-2022-071063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 11/07/2023] [Indexed: 12/28/2023] Open
Abstract
INTRODUCTION Current interventions for children with attention-deficit/hyperactivity disorder (ADHD) are primarily medication, behavioural therapy and parent training. However, research suggests dietary manipulations may provide therapeutic benefit for some. There is accumulating evidence that the gut microbiome may be atypical in ADHD, and therefore, manipulating gut bacteria in such individuals may help alleviate some of the symptoms of this condition. The aim of this study is to explore the effects of supplementation with kefir (a fermented dairy drink) on ADHD symptomatology, sleep, attention and the gut microbiome in children diagnosed with ADHD. METHODS AND ANALYSIS A 6-week randomised, double-blind, placebo-controlled trial in 70 children aged 8-13 years diagnosed with ADHD. Participants will be recruited throughout the UK, through support groups, community groups, schools, social media and word of mouth. Children will be randomised to consume daily either dairy kefir or a placebo dairy drink for 6 weeks. The primary outcome, ADHD symptomatology, will be measured by The Strengths and Weakness of ADHD-symptoms and Normal-behaviour scale. Secondary outcomes will include gut microbiota composition (using shotgun metagenomic microbiome sequencing), gut symptomatology (The Gastrointestinal Severity Index questionnaire), sleep (using 7-day actigraphy recordings, The Child's Sleep Habits Questionnaire and Sleep Self Report questionnaire), inattention and impulsivity (with a computerised Go/NoGo test). Assessments will be conducted prior to the intervention and at the end of the intervention. Interaction between time (preintervention/postintervention) and group (probiotic/placebo) is to be analysed using a Mixed Model Analysis of Variances. ETHICS AND DISSEMINATION Ethical approval for the study was granted by St Mary's University Ethics Committee. Results will be disseminated through peer-reviewed publications, presentations to the scientific community and support groups. TRIAL REGISTRATION NUMBER NCT05155696.
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Affiliation(s)
- Kate Lawrence
- School of Allied Health & Life Sciences, St Mary's University, Twickenham, UK
| | - Philippa Fibert
- School of Allied Health & Life Sciences, St Mary's University, Twickenham, UK
| | - Jemima Hobbs
- School of Allied Health & Life Sciences, St Mary's University, Twickenham, UK
| | - Kyriaki Myrissa
- School of Allied Health & Life Sciences, St Mary's University, Twickenham, UK
| | | | - Frits Quadt
- Quadt Consultancy B.V, Oostvoorne, The Netherlands
| | - Paul D Cotter
- SeqBiome Ltd, Cork, Ireland
- University College Cork APC Microbiome Institute, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Cork, Ireland
| | - Alice M Gregory
- Department of Psychology, Goldsmiths University of London, London, UK
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16
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Garcia-Gutierrez E, Walsh LH, Cotter PD. Six areas of consideration when designing and conducting online surveys in microbiology for facilitating improved scientific communication. Front Microbiol 2023; 14:1288822. [PMID: 38116523 PMCID: PMC10728466 DOI: 10.3389/fmicb.2023.1288822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/17/2023] [Indexed: 12/21/2023] Open
Affiliation(s)
- Enriqueta Garcia-Gutierrez
- Food Bioscience Department, Teagasc Food Research Centre Moorepark, County Cork, Ireland
- APC Microbiome Ireland, University College Cork, County Cork, Ireland
- VistaMilk SFI Research Centre, Moorepark, County Cork, Ireland
| | - Liam H. Walsh
- Food Bioscience Department, Teagasc Food Research Centre Moorepark, County Cork, Ireland
- School of Microbiology, University College Cork, County Cork, Ireland
| | - Paul D. Cotter
- Food Bioscience Department, Teagasc Food Research Centre Moorepark, County Cork, Ireland
- APC Microbiome Ireland, University College Cork, County Cork, Ireland
- VistaMilk SFI Research Centre, Moorepark, County Cork, Ireland
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17
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Mathur H, Mechoud MA, Matthews C, Lordan C, FitzGerald JA, Beresford T, Cotter PD. Methods to mitigate Escherichia coli blooms in human ex vivo colon model experiments using the high throughput micro-Matrix bioreactor fermentation system. MethodsX 2023; 11:102393. [PMID: 37846356 PMCID: PMC10577065 DOI: 10.1016/j.mex.2023.102393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/22/2023] [Indexed: 10/18/2023] Open
Abstract
Ex vivo colon model experiments are frequently employed as a means to assess the gut microbiome modulating potential of different foods, food ingredients and dietary supplements. A number of useful models already exist; however, they tend to be relatively low in terms of throughput (3-4 samples per experiment) with a long experiment duration of one to a number of weeks. Therefore, a need for a high-throughput system with a short duration time is required to enable screening of large numbers of samples. Therefore, we report here on the development of a system based on the Applikon micro-Matrix bioreactor which has the capacity to run 24 samples with an experiment duration of 48 h. However, Escherichia coli blooms are a common problem encountered in this model. Here, we describe the factors that contribute to such blooms and provide approaches to address them, providing:•Step by step optimisation of processes involved in conducting ex vivo distal colon experiments using the micro-Matrix bioreactor fermentation platform•Recommended steps for users on how to attenuate E. coli blooms in such ex vivo colon model experiments.
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Affiliation(s)
- Harsh Mathur
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- Food for Health Ireland, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Monica A. Mechoud
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- Food for Health Ireland, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Chloe Matthews
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- Food for Health Ireland, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Cathy Lordan
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- Food for Health Ireland, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Jamie A. FitzGerald
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- Food for Health Ireland, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Tom Beresford
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- Food for Health Ireland, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- Food for Health Ireland, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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18
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Nori SRC, McGuire TK, Lawton EM, McAuliffe FM, Sinderen DV, Walsh CJ, Cotter PD, Feehily C. Profiling of vaginal Lactobacillus jensenii isolated from preterm and full-term pregnancies reveals strain-specific factors relating to host interaction. Microb Genom 2023; 9. [PMID: 38010361 DOI: 10.1099/mgen.0.001137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Abstract
Each year, 15 million infants are born preterm (<37 weeks gestation), representing the leading cause of mortality for children under the age of five. Whilst there is no single cause, factors such as maternal genetics, environmental interactions, and the vaginal microbiome have been associated with an increased risk of preterm birth. Previous studies show that a vaginal microbiota dominated by Lactobacillus is, in contrast to communities containing a mixture of genera, associated with full-term birth. However, this binary principle does not fully consider more nuanced interactions between bacterial strains and the host. Here, through a combination of analyses involving genome-sequenced isolates and strain-resolved metagenomics, we identify that L. jensenii strains from preterm pregnancies are phylogenetically distinct from strains from full-term pregnancies. Detailed analysis reveals several genetic signatures that distinguish preterm birth strains, including genes predicted to be involved in cell wall synthesis, and lactate and acetate metabolism. Notably, we identify a distinct gene cluster involved in cell surface protein synthesis in our preterm strains, and profiling the prevalence of this gene cluster in publicly available genomes revealed it to be predominantly present in the preterm-associated clade. This study contributes to the ongoing search for molecular biomarkers linked to preterm birth and opens up new avenues for exploring strain-level variations and mechanisms that may contribute to preterm birth.
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Affiliation(s)
- Sai Ravi Chandra Nori
- Teagasc Food Research Centre, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- SFI Centre for Research Training in Genomics Data Science, School of Mathematics, Statistics & Applied Mathematics, University of Galway, Galway, Ireland
| | | | | | - Fionnuala M McAuliffe
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Douwe Van Sinderen
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Calum J Walsh
- Department of Microbiology & Immunology, Peter Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Australia
| | - Paul D Cotter
- Teagasc Food Research Centre, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Conor Feehily
- Teagasc Food Research Centre, Fermoy, Co. Cork, Ireland
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
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19
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Moore SG, Feehily C, Doyle RC, Buckley F, Lonergan P, Cotter PD, Butler ST. Associations between the postpartum uterine and vaginal microbiota and the subsequent development of purulent vaginal discharge vary with dairy cow breed and parity. J Dairy Sci 2023; 106:8133-8151. [PMID: 37641353 DOI: 10.3168/jds.2022-22720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 05/26/2023] [Indexed: 08/31/2023]
Abstract
The objective of this study was to characterize the species composition and functional potential of the vaginal and uterine microbiota at 1 wk postpartum in dairy cows diagnosed with or without purulent vaginal discharge (PVD) at 3 wk postpartum. The hypothesis was that differences in the vaginal and uterine microbiota between cows diagnosed with (PVD+) or without (PVD-) PVD were dependent on parity and breed. Cytobrush samples of the vagina and uterus were collected at 1 wk postpartum from 36 Holstein-Friesian (7 primiparous and 29 multiparous) and 29 Jersey (10 primiparous and 19 multiparous) cows. Microbial DNA was isolated from each sample and processed for shotgun metagenomic sequencing. The odds of multiparous cows being diagnosed as PVD+ was less compared with primiparous cows (OR = 0.21). Neither the α-diversity nor β-diversity of the uterine and vaginal microbiota were associated with PVD but the β-diversity was different between breeds and between parities. In the vagina of primiparous cows, differences in the microbiota of PVD- and PVD+ cows were minor, but the microbiota of multiparous PVD+ cows had greater relative abundance of Fusobacterium necrophorum, Trueperella pyogenes, Porphyromonas levii, and greater functional potential for amino acid and protein synthesis, energy metabolism, and growth compared with PVD- cows. The uterus of primiparous PVD+ cows had lesser relative abundance of Bacteroides heparinolyticus compared with PVD- cows. In the uterine microbiota, differences included greater functional potential for cellulose biosynthesis and fucose catabolism in multiparous PVD+ cows compared with PVD- cows. In the uterine microbiota of primiparous PVD+ cows, the functional potential for gram-negative cell wall synthesis and for negative regulation of tumor necrosis factor signaling was lesser compared with multiparous PVD+ cows. In the vagina of Holstein-Friesian PVD+ cows, the relative abundance of Caviibacter abscessus was greater whereas in the vagina of Jersey PVD+ cows the relative abundance of Catenibacterium mitsuokai, Finegoldia magna, Klebsiella variicola, and Streptococcus anginosus was greater compared with PVD- cows. In the uterine microbiota of Holstein-Friesian cows, the functional potential for spermidine biosynthesis was reduced compared with PVD- cows. In summary, differences in the species composition and functional potential of the vaginal and uterine microbiota between PVD- and PVD+ cows were dependent on parity and breed. The findings suggest that alternative strategies may be required to treat PVD for different parities and breeds of dairy cow.
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Affiliation(s)
- S G Moore
- Animal & Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland P61 P302.
| | - C Feehily
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland P61 C996
| | - R C Doyle
- Animal & Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland P61 P302
| | - F Buckley
- Animal & Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland P61 P302
| | - P Lonergan
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland D04 N2E5
| | - P D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland P61 C996
| | - S T Butler
- Animal & Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland P61 P302
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20
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Bourrie BCT, Diether N, Dias RP, Nam SL, de la Mata AP, Forgie AJ, Gaur G, Harynuk JJ, Gänzle M, Cotter PD, Willing BP. Use of reconstituted kefir consortia to determine the impact of microbial composition on kefir metabolite profiles. Food Res Int 2023; 173:113467. [PMID: 37803789 DOI: 10.1016/j.foodres.2023.113467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/29/2023] [Accepted: 09/10/2023] [Indexed: 10/08/2023]
Abstract
Kefir is fermented traditionally with kefir grains, but commercial kefir production often relies on fermentation with planktonic cultures. Kefir has been associated with many health benefits, however, the utilization of kefir grains to facilitate large industrial production of kefir is challenging and makes to difficult to ensure consistent product quality and consistency. Notably, the microbial composition of kefir fermentations has been shown to impact kefir associated health benefits. This study aimed to compare volatile compounds, organic acids, and sugar composition of kefir produced through a traditional grain fermentation and through a reconstituted kefir consortium fermentation. Additionally, the impact of two key microbial communities on metabolite production in kefir was assessed using two modified versions of the consortium, with either yeasts or lactobacilli removed. We hypothesized that the complete kefir consortium would closely resemble traditional kefir, while the consortia without yeasts or lactobacilli would differ significantly from both traditional kefir and the complete consortium fermentation. Kefir fermentations were examined after 12 and 18 h using two-dimensional gas chromatography-time-of-flight mass spectrometry (GC × GC-TOFMS) to identify volatile compounds and high performance liquid chromatography (HPLC) to identify organic acid and sugar composition. The traditional kefir differed significantly from the kefir consortium fermentation with the traditional kefir having 15-20 log2(fold change) higher levels of esters and the consortium fermented kefir having between 1 and 3 log2(fold change) higher organic acids including lactate and acetate. The use of a version of kefir consortium that lacked lactobacilli resulted in between 2 and 20 log2(fold change) lower levels of organic acids, ethanol, and butanoic acid ethyl ester, while the absence of yeast from the consortium resulted in minimal change. In summary, the kefir consortium fermentation is significantly different from traditional grain fermented kefir with respect to the profile of metabolites present, and seems to be driven by lactobacilli, as evidenced by the significant decrease in multiple metabolites when the lactobacilli were removed from the fermentation and minimal differences observed upon the removal of yeast.
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Affiliation(s)
- Benjamin C T Bourrie
- Department of Agricultural, Food, and Nutrition Sciences, University of Alberta, Edmonton, AB, Canada
| | - Natalie Diether
- Department of Agricultural, Food, and Nutrition Sciences, University of Alberta, Edmonton, AB, Canada
| | - Ryan P Dias
- The Metabolomics Innovation Centre (TMIC), University of Alberta, Edmonton, AB, Canada; Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Seo Lin Nam
- The Metabolomics Innovation Centre (TMIC), University of Alberta, Edmonton, AB, Canada; Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - A Paulina de la Mata
- The Metabolomics Innovation Centre (TMIC), University of Alberta, Edmonton, AB, Canada; Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Andrew J Forgie
- Department of Agricultural, Food, and Nutrition Sciences, University of Alberta, Edmonton, AB, Canada
| | - Gautam Gaur
- Department of Agricultural, Food, and Nutrition Sciences, University of Alberta, Edmonton, AB, Canada
| | - James J Harynuk
- The Metabolomics Innovation Centre (TMIC), University of Alberta, Edmonton, AB, Canada; Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Michael Gänzle
- Department of Agricultural, Food, and Nutrition Sciences, University of Alberta, Edmonton, AB, Canada
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; APC Microbiome Ireland, Cork, Ireland; VistaMilk, Ireland
| | - Benjamin P Willing
- Department of Agricultural, Food, and Nutrition Sciences, University of Alberta, Edmonton, AB, Canada.
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21
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Alvarez-Molina A, Cobo-Díaz JF, Alexa EA, Crispie F, Prieto M, López M, Cotter PD, Alvarez-Ordóñez A. Sequencing-based analysis of the microbiomes of Spanish food processing facilities reveals environment-specific variation in the dominant taxa and antibiotic resistance genes. Food Res Int 2023; 173:113442. [PMID: 37803768 DOI: 10.1016/j.foodres.2023.113442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 07/11/2023] [Accepted: 09/09/2023] [Indexed: 10/08/2023]
Abstract
In the last years, advances in high throughput sequencing technologies have opened the possibility to broaden environmental monitoring activities in facilities processing food, offering expanded opportunities for characterizing in an untargeted manner the microbiome and resistome of foods and food processing environments (FPE) with huge potential benefits in food safety management systems. Here the microbiome and resistome of FPE from slaughterhouses (n = 3), dairy (n = 12) and meat (n = 10) processing plants were assessed through whole metagenome sequencing of 2 composite samples for each facility, comprising 10 FPE swabs taken from food contact surfaces and 10 FPE samples from non-food contact surfaces, respectively. FPE from slaughterhouses had more diverse microbiomes and resistomes, while FPE from dairy processing plants showed the highest β-dispersion, consistent with a more heterogeneous microbiome and resistome composition. The predominant bacterial genera depended on the industry type, with Pseudomonas and Psychrobacter being highly dominant in surfaces from slaughterhouses and meat industries, while different lactic acid bacteria predominated in dairy industries. The most abundant antimicrobial resistance genes (ARG) found were associated with resistance to aminoglycosides, tetracyclines and quaternary ammonium compounds (QAC). ARGs relating to resistance to aminoglycosides and tetracyclines were significantly more prevalent in slaughterhouses than in food processing plants, while QAC resistance genes were particularly abundant in some food contact surfaces from dairy and meat processing plants, suggesting that daily sanitation under suboptimal conditions may be selecting for persistent microbiota tolerant to these biocides in some facilities. The taxonomic mapping of ARG pointed to specific bacterial genera, such as Escherichia, Bacillus, or Staphylococcus, as carriers of the most relevant resistance determinants. About 63% of all ARG reads were assigned to contigs classified as plasmid-associated, indicating that the resistome of FPE may be strongly shaped through the spread of mobile genetic elements. Overall, the relevance of FPE as reservoirs of ARG was confirmed and it was demonstrated that next generation sequencing technologies allowing a deep characterisation of sources and routes of spread of microorganisms and antimicrobial resistance determinants in food industry settings hold promise to be integrated in monitoring and food safety management programmes.
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Affiliation(s)
| | - José F Cobo-Díaz
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Elena A Alexa
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Fiona Crispie
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Teagasc Food Research Centre, Fermoy, Co. Cork, Ireland
| | - Miguel Prieto
- Department of Food Hygiene and Technology, Universidad de León, León, Spain; Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Mercedes López
- Department of Food Hygiene and Technology, Universidad de León, León, Spain; Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Paul D Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Teagasc Food Research Centre, Fermoy, Co. Cork, Ireland
| | - Avelino Alvarez-Ordóñez
- Department of Food Hygiene and Technology, Universidad de León, León, Spain; Institute of Food Science and Technology, Universidad de León, León, Spain.
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22
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Walsh LH, Coakley M, Walsh AM, O'Toole PW, Cotter PD. Bioinformatic approaches for studying the microbiome of fermented food. Crit Rev Microbiol 2023; 49:693-725. [PMID: 36287644 DOI: 10.1080/1040841x.2022.2132850] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/11/2022] [Accepted: 09/28/2022] [Indexed: 11/03/2022]
Abstract
High-throughput DNA sequencing-based approaches continue to revolutionise our understanding of microbial ecosystems, including those associated with fermented foods. Metagenomic and metatranscriptomic approaches are state-of-the-art biological profiling methods and are employed to investigate a wide variety of characteristics of microbial communities, such as taxonomic membership, gene content and the range and level at which these genes are expressed. Individual groups and consortia of researchers are utilising these approaches to produce increasingly large and complex datasets, representing vast populations of microorganisms. There is a corresponding requirement for the development and application of appropriate bioinformatic tools and pipelines to interpret this data. This review critically analyses the tools and pipelines that have been used or that could be applied to the analysis of metagenomic and metatranscriptomic data from fermented foods. In addition, we critically analyse a number of studies of fermented foods in which these tools have previously been applied, to highlight the insights that these approaches can provide.
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Affiliation(s)
- Liam H Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- School of Microbiology, University College Cork, Ireland
| | - Mairéad Coakley
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Aaron M Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Paul W O'Toole
- School of Microbiology, University College Cork, Ireland
- APC Microbiome Ireland, University College Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Ireland
- VistaMilk SFI Research Centre, Teagasc, Moorepark, Fermoy, Cork, Ireland
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23
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Nilaweera KN, Cotter PD. Can dietary proteins selectively reduce either the visceral or subcutaneous adipose tissues? Obes Rev 2023; 24:e13613. [PMID: 37548066 DOI: 10.1111/obr.13613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 06/22/2023] [Accepted: 07/12/2023] [Indexed: 08/08/2023]
Abstract
There is a considerable appeal for interventions that can selectively reduce either the visceral or subcutaneous white adipose tissues in humans and other species because of their associated impact on outcomes related to metabolic health. Here, we reviewed the data related to the specificity of five interventions to affect the two depots in humans and rodents. The interventions relate to the use of dietary proteins, monounsaturated fatty acids, polyunsaturated fatty acids, calorie restriction, or bariatric surgery. The available data show that calorie restriction and bariatric surgery reduce both visceral and subcutaneous tissues, whereas there is no consistency in the effect of monounsaturated or polyunsaturated fatty acids. Dietary proteins, more specifically, whey proteins show efficacy to reduce one or both depots based on how the proteins interact with other macronutrients in the diet. We provide evidence that this specificity is related to changes in the composition and the functional potential of the gut microbiota and the resulting metabolites produced by these microorganisms. The effect of the sex of the host is also discussed. This knowledge may help to develop nutritional approaches to deplete either the visceral or subcutaneous adipose tissues and improve metabolic health in humans and other species.
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Affiliation(s)
- Kanishka N Nilaweera
- Food Biosciences Department, Teagasc Food Research Centre, Fermoy, County Cork, Ireland
- VistaMilk Research Centre, Teagasc, Fermoy, County Cork, Ireland
| | - Paul D Cotter
- Food Biosciences Department, Teagasc Food Research Centre, Fermoy, County Cork, Ireland
- VistaMilk Research Centre, Teagasc, Fermoy, County Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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24
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Arenas-Gómez CM, Garcia-Gutierrez E, Escobar JS, Cotter PD. Human gut homeostasis and regeneration: the role of the gut microbiota and its metabolites. Crit Rev Microbiol 2023; 49:764-785. [PMID: 36369718 DOI: 10.1080/1040841x.2022.2142088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 08/18/2022] [Accepted: 10/26/2022] [Indexed: 11/13/2022]
Abstract
The healthy human gut is a balanced ecosystem where host cells and representatives of the gut microbiota interact and communicate in a bidirectional manner at the gut epithelium. As a result of these interactions, many local and systemic processes necessary for host functionality, and ultimately health, take place. Impairment of the integrity of the gut epithelium diminishes its ability to act as an effective gut barrier, can contribute to conditions associated to inflammation processes and can have other negative consequences. Pathogens and pathobionts have been linked with damage of the integrity of the gut epithelium, but other components of the gut microbiota and some of their metabolites can contribute to its repair and regeneration. Here, we review what is known about the effect of bacterial metabolites on the gut epithelium and, more specifically, on the regulation of repair by intestinal stem cells and the regulation of the immune system in the gut. Additionally, we explore the potential therapeutic use of targeted modulation of the gut microbiota to maintain and improve gut homeostasis as a mean to improve health outcomes.
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Affiliation(s)
- Claudia Marcela Arenas-Gómez
- Vidarium-Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
- Dirección Académica, Universidad Nacional de Colombia, Sede de La Paz, La Paz 202017, Colombia
| | - Enriqueta Garcia-Gutierrez
- Teagasc Food Research Centre Moorepark, Fermoy, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- VistaMilk SFI Research Centre, Moorepark, Fermoy, Ireland
| | - Juan S Escobar
- Vidarium-Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
| | - Paul D Cotter
- Teagasc Food Research Centre Moorepark, Fermoy, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- VistaMilk SFI Research Centre, Moorepark, Fermoy, Ireland
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25
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Walsh LH, Coakley M, Walsh AM, Crispie F, O’Toole PW, Cotter PD. Analysis of the milk kefir pan-metagenome reveals four community types, core species, and associated metabolic pathways. iScience 2023; 26:108004. [PMID: 37841598 PMCID: PMC10568436 DOI: 10.1016/j.isci.2023.108004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/14/2023] [Accepted: 09/18/2023] [Indexed: 10/17/2023] Open
Abstract
A comprehensive metagenomics-based investigation of the microorganisms present within milk kefir communities from across the globe was carried out with a view to defining the milk kefir pan-metagenome, including details relating to core and non-core components. Milk kefir samples, generated by inoculating full fat, pasteurized cow's milk with 64 kefir grains sourced from 25 different countries, were analyzed. We identified core features, including a consistent pattern of domination by representatives from the species Lactobacillus helveticus or the sub-species Lactobacillus kefiranofaciens subsp. kefiranofaciens, Lactococcus lactis subsp. lactis or Lla. cremoris subsp. cremoris in each kefir. Notably, even in kefirs where the lactococci did not dominate, they and 51 associated metabolic pathways were identified across all metagenomes. These insights can contribute to future efforts to create tailored kefir-based microbial communities for different applications and assist regulators and producers to ensure that kefir products have a microbial composition that reflects the artisanal beverage.
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Affiliation(s)
- Liam H. Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- School of Microbiology, University College Cork, Ireland
| | - Mairéad Coakley
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Aaron M. Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Paul W. O’Toole
- School of Microbiology, University College Cork, Ireland
- APC Microbiome Ireland SFI Research Centre, University College Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland SFI Research Centre, University College Cork, Ireland
- VistaMilk SFI Research Centre, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland
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26
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Barcenilla C, Puente A, Cobo-Díaz JF, Alexa EA, Garcia-Gutierrez E, O'Connor PM, Cotter PD, González-Raurich M, López M, Prieto M, Álvarez-Ordóñez A. Selection of lactic acid bacteria as biopreservation agents and optimization of their mode of application for the control of Listeria monocytogenes in ready-to-eat cooked meat products. Int J Food Microbiol 2023; 403:110341. [PMID: 37543003 DOI: 10.1016/j.ijfoodmicro.2023.110341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 08/07/2023]
Abstract
In order to meet consumers´ demands for more natural foods and to find new methods to control foodborne pathogens in them, research is currently being focused on alternative preservation approaches, such as biopreservation with lactic acid bacteria (LAB). Here, a collection of lactic acid bacteria (LAB) isolates was characterized to identify potential biopreservative agents. Six isolates (one Lactococcus lactis, one Lacticaseibacillus paracasei and four Lactiplantibacillus plantarum) were selected based on their antimicrobial activity in in vitro assays. Whole genome sequencing showed that none of the six LAB isolates carried known virulence factors or acquired antimicrobial resistance genes, and that the L. lactis isolate was potentially a nisin Z producer. Growth of L. monocytogenes was successfully limited by L. lactis ULE383, L. paracasei ULE721 and L. plantarum ULE1599 throughout the shelf-life of cooked ham, meatloaf and roasted pork shoulder. These LAB isolates were also applied individually or as a cocktail at different inoculum concentrations (4, 6 and 8 log10 CFU/g) in challenge test studies involving cooked ham, showing a stronger anti-Listerial activity when a cocktail was used at 8 log10 CFU/g. Thus, a reduction of up to ~5.0 log10 CFU/g in L. monocytogenes growth potential was attained in cooked ham packaged under vacuum, modified atmosphere packaging or vacuum followed by high pressure processing (HPP). Only minor changes in color and texture were induced, although there was a significant acidification of the product when the LAB cultures were applied. Remarkably, this acidification was delayed when HPP was applied to the LAB inoculated batches. Metataxonomic analyses showed that the LAB cocktail was able to grow in the cooked ham and outcompete the indigenous microbiota, including spoilage microorganisms such as Brochothrix. Moreover, none of the batches were considered unacceptable in a sensory evaluation. Overall, this study shows the favourable antilisterial activity of the cocktail of LAB employed, with the combination of HPP and LAB achieving a complete inhibition of the pathogen with no detrimental effects in physico-chemical or sensorial evaluations, highlighting the usefulness of biopreservation approaches involving LAB for enhancing the safety of cooked meat products.
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Affiliation(s)
- Coral Barcenilla
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Alba Puente
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - José F Cobo-Díaz
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Elena-Alexandra Alexa
- Department of Food Hygiene and Technology, Universidad de León, León, Spain; Food Safety Department, Teagasc Food Research Centre, Ashtown, Dublin, Ireland
| | - Enriqueta Garcia-Gutierrez
- Food Bioscience Department, Teagasc Food Research Centre, Moorepark, Fermoy, Ireland; APC Microbiome Ireland, Cork, Ireland
| | - Paula M O'Connor
- Food Bioscience Department, Teagasc Food Research Centre, Moorepark, Fermoy, Ireland; APC Microbiome Ireland, Cork, Ireland
| | - Paul D Cotter
- Food Bioscience Department, Teagasc Food Research Centre, Moorepark, Fermoy, Ireland; APC Microbiome Ireland, Cork, Ireland
| | - Montserrat González-Raurich
- Department of Food Hygiene and Technology, Universidad de León, León, Spain; Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Mercedes López
- Department of Food Hygiene and Technology, Universidad de León, León, Spain; Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Miguel Prieto
- Department of Food Hygiene and Technology, Universidad de León, León, Spain; Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Avelino Álvarez-Ordóñez
- Department of Food Hygiene and Technology, Universidad de León, León, Spain; Institute of Food Science and Technology, Universidad de León, León, Spain.
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27
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Sessitsch A, Wakelin S, Schloter M, Maguin E, Cernava T, Champomier-Verges MC, Charles TC, Cotter PD, Ferrocino I, Kriaa A, Lebre P, Cowan D, Lange L, Kiran S, Markiewicz L, Meisner A, Olivares M, Sarand I, Schelkle B, Selvin J, Smidt H, van Overbeek L, Berg G, Cocolin L, Sanz Y, Fernandes WL, Liu SJ, Ryan M, Singh B, Kostic T. Microbiome Interconnectedness throughout Environments with Major Consequences for Healthy People and a Healthy Planet. Microbiol Mol Biol Rev 2023; 87:e0021222. [PMID: 37367231 PMCID: PMC10521359 DOI: 10.1128/mmbr.00212-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023] Open
Abstract
Microbiomes have highly important roles for ecosystem functioning and carry out key functions that support planetary health, including nutrient cycling, climate regulation, and water filtration. Microbiomes are also intimately associated with complex multicellular organisms such as humans, other animals, plants, and insects and perform crucial roles for the health of their hosts. Although we are starting to understand that microbiomes in different systems are interconnected, there is still a poor understanding of microbiome transfer and connectivity. In this review we show how microbiomes are connected within and transferred between different habitats and discuss the functional consequences of these connections. Microbiome transfer occurs between and within abiotic (e.g., air, soil, and water) and biotic environments, and can either be mediated through different vectors (e.g., insects or food) or direct interactions. Such transfer processes may also include the transmission of pathogens or antibiotic resistance genes. However, here, we highlight the fact that microbiome transmission can have positive effects on planetary and human health, where transmitted microorganisms potentially providing novel functions may be important for the adaptation of ecosystems.
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Affiliation(s)
| | | | | | - Emmanuelle Maguin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Tomislav Cernava
- University of Southampton, Faculty of Environmental and Life Sciences, Southampton, United Kingdom
| | | | | | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, APC Microbiome Ireland and VistaMilk, Cork, Ireland
| | | | - Aicha Kriaa
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Pedro Lebre
- University of Pretoria, Pretoria, South Africa
| | - Don Cowan
- University of Pretoria, Pretoria, South Africa
| | - Lene Lange
- LL-BioEconomy, Valby, Copenhagen, Denmark
| | | | - Lidia Markiewicz
- Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Department of Immunology and Food Microbiology, Olsztyn, Poland
| | - Annelein Meisner
- Wageningen University and Research, Wageningen Research, Wageningen, The Netherlands
| | - Marta Olivares
- Institute of Agrochemistry and Food Technology, Excellence Center Severo Ochoa – Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Inga Sarand
- Tallinn University of Technology, Department of Chemistry and Biotechnology, Tallinn, Estonia
| | | | | | - Hauke Smidt
- Wageningen University and Research, Laboratory of Microbiology, Wageningen, The Netherlands
| | - Leo van Overbeek
- Wageningen University and Research, Wageningen Research, Wageningen, The Netherlands
| | | | | | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology, Excellence Center Severo Ochoa – Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | | | - S. J. Liu
- Chinese Academy of Sciences, Institute of Microbiology, Beijing, China
| | - Matthew Ryan
- Genetic Resources Collection, CABI, Egham, United Kingdom
| | - Brajesh Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Tanja Kostic
- AIT Austrian Institute of Technology GmbH, Tulln, Austria
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28
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Bourrie BCT, Forgie AJ, Makarowski A, Cotter PD, Richard C, Willing BP. Consumption of kefir made with traditional microorganisms resulted in greater improvements in LDL cholesterol and plasma markers of inflammation in males when compared to a commercial kefir: a randomized pilot study. Appl Physiol Nutr Metab 2023; 48:668-677. [PMID: 37224566 DOI: 10.1139/apnm-2022-0463] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Kefir has long been associated with health benefits; however, recent evidence suggests that these benefits are dependent on the specific microbial composition of the kefir consumed. This study aimed to compare how consumption of a commercial kefir without traditional kefir organisms and a pitched kefir containing traditional organisms affected plasma lipid levels, glucose homeostasis, and markers of endothelial function and inflammation in males with elevated LDL cholesterol. We utilized a crossover design in n = 21 participants consisting of two treatments of 4 weeks each in random order separated by a 4-week washout. Participants received either commercial kefir or pitched kefir containing traditional kefir organisms for each treatment period. Participants consumed 2 servings of kefir (350 g) per day. Plasma lipid profile, glucose, insulin, markers of endothelial function, and inflammation were measured in the fasting state before and after each treatment period. Differences within each treatment period and comparison of treatment delta values were performed using paired t tests and Wilcoxon signed-rank test, respectively. When compared to baseline, pitched kefir consumption reduced LDL-C, ICAM-1, and VCAM-1, while commercial kefir consumption increased TNF-α. Pitched kefir consumption resulted in greater reductions in IL-8, CRP, VCAM-1, and TNF-α when compared to commercial kefir consumption. These findings provide strong evidence that microbial composition is an important factor in the metabolic health benefits associated with kefir consumption. They also provide support for larger studies examining these to assess whether traditional kefir organisms are necessary to confer health benefits to individuals at risk of developing cardiovascular disease.
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Affiliation(s)
- Benjamin C T Bourrie
- Agricultural Food and Nutritional Science, Agriculture/Forestry Center, University of Alberta, Edmonton, AB, Canada
| | - Andrew J Forgie
- Agricultural Food and Nutritional Science, Agriculture/Forestry Center, University of Alberta, Edmonton, AB, Canada
| | - Alexander Makarowski
- Agricultural Food and Nutritional Science, Agriculture/Forestry Center, University of Alberta, Edmonton, AB, Canada
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
- VistaMilk, Fermoy, Co. Cork, Ireland
| | - Caroline Richard
- Agricultural Food and Nutritional Science, Agriculture/Forestry Center, University of Alberta, Edmonton, AB, Canada
| | - Benjamin P Willing
- Agricultural Food and Nutritional Science, Agriculture/Forestry Center, University of Alberta, Edmonton, AB, Canada
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29
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Pant KJ, Cotter PD, Wilkinson MG, Sheehan JJ. Towards sustainable Cleaning-in-Place (CIP) in dairy processing: Exploring enzyme-based approaches to cleaning in the Cheese industry. Compr Rev Food Sci Food Saf 2023; 22:3602-3619. [PMID: 37458296 DOI: 10.1111/1541-4337.13206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 09/13/2023]
Abstract
Cleaning-in-place (CIP) is the most commonly used cleaning and sanitation system for processing lines, equipment, and storage facilities such as milk silos in the global dairy processing industry. CIP employs thermal treatments and nonbiodegradable chemicals (acids and alkalis), requiring appropriate neutralization before disposal, resulting in sustainability challenges. In addition, biofilms are a major source of contamination and spoilage in dairy industries, and it is believed that current chemical CIP protocols do not entirely destroy biofilms. Use of enzymes as effective agents for CIP and as a more sustainable alternative to chemicals and thermal treatments is gaining interest. Enzymes offer several advantages when used for CIP, such as reduced water usage (less rinsing), lower operating temperatures resulting in energy savings, shorter cleaning times, and lower costs for wastewater treatment. Additionally, they are typically derived from natural sources, are easy to neutralize, and do not produce hazardous waste products. However, even with such advantages, enzymes for CIP within the dairy processing industry remain focused mainly on membrane cleaning. Greater adoption of enzyme-based CIP for cheese industries is projected pending a greater knowledge relating to cost, control of the process (inactivation kinetics), reusability of enzyme solutions, and the potential for residual activity, including possible effects on the subsequent product batches. Such studies are essential for the cheese industry to move toward more energy-efficient and sustainable cleaning solutions.
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Affiliation(s)
- Karan J Pant
- Department of Food Chemistry and Technology, Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- Department of Biological Sciences, University of Limerick, Castletroy, Limerick, Ireland
| | - Paul D Cotter
- Department of Food Chemistry and Technology, Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
| | - Martin G Wilkinson
- Department of Biological Sciences, University of Limerick, Castletroy, Limerick, Ireland
| | - Jeremiah J Sheehan
- Department of Food Chemistry and Technology, Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
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30
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Yelverton CA, Killeen SL, Feehily C, Moore RL, Callaghan SL, Geraghty AA, Byrne DF, Walsh CJ, Lawton EM, Murphy EF, Van Sinderen D, Cotter PD, McAuliffe FM. Maternal breastfeeding is associated with offspring microbiome diversity; a secondary analysis of the MicrobeMom randomized control trial. Front Microbiol 2023; 14:1154114. [PMID: 37720155 PMCID: PMC10502216 DOI: 10.3389/fmicb.2023.1154114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 08/10/2023] [Indexed: 09/19/2023] Open
Abstract
Background Microbial dysbiosis in infancy can influence long-term health outcomes such as childhood obesity. The aim of this study is to explore relationships among maternal well-being during pregnancy, breastfeeding, and the infant gut microbiome. Methods This is a secondary analysis of healthy pregnant women from the MicrobeMom study, a double-blind randomized control trial of maternal probiotic supplementation (Bifidobacterium breve 702258) versus placebo antenatally and up to 3 months postpartum. Maternal well-being was assessed using the WHO-5 well-being index at 16 weeks' and 34 weeks' gestation. Breastfeeding practices were recorded at discharge from hospital and at 1 month postpartum. Infant stool samples were obtained at 1 month of age. Next generation shotgun sequencing determined infant microbial diversity. Independent sample t-tests and Mann-Whitney U tests informed adjusted regression analysis, which was adjusted for delivery mode, antibiotics during delivery, maternal age and body mass index (BMI), and probiotic vs. control study group. Results Women (n = 118) with at least one measure of well-being were on average 33 years (SD 3.93) of age and 25.09 kg/m2 (SD 3.28) BMI. Exclusive breastfeeding was initiated by 65% (n = 74). Any breastfeeding was continued by 69% (n = 81) after 1 month. In early and late pregnancy, 87% (n = 97/111) and 94% (n = 107/114) had high well-being scores. Well-being was not associated with infant microbial diversity at 1 month. In adjusted analysis, exclusive breastfeeding at discharge from hospital was associated with infant microbial beta diversity (PC2; 0.254, 95% CI 0.006, 0.038). At 1 month postpartum, any breastfeeding was associated with infant microbial alpha diversity (Shannon index; -0.241, 95% CI -0.498, -0.060) and observed species; (-0.325, 95% CI -0.307, -0.060), and infant microbial beta diversity (PC2; 0.319, 95% CI 0.013, 0.045). Exclusive breastfeeding at 1 month postpartum was associated with infant alpha diversity (Shannon index -0.364, 95% CI -0.573, -0.194; Simpson index 0.339, 95% CI 0.027, 0.091), and infant's number of observed microbial species (-0.271, 95% CI -0.172, -0.037). Conclusion Breastfeeding practices at 1 month postpartum were associated with lower microbial diversity and observed species in infants at 1 month postpartum, which is potentially beneficial to allow greater abundance of Bifidobacterium. Clinical trial registration ISRCTN53023014.
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Affiliation(s)
- Cara A. Yelverton
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Sarah Louise Killeen
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Conor Feehily
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Rebecca L. Moore
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Shauna L. Callaghan
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Aisling A. Geraghty
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
- UCD Institute of Food and Health, School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - David F. Byrne
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Calum J. Walsh
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Elaine M. Lawton
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | | | - Douwe Van Sinderen
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Paul D. Cotter
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Fionnuala M. McAuliffe
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
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31
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Walsh LH, Walsh AM, Garcia-Perez I, Crispie F, Costabile A, Ellis R, Finlayson J, Finnegan LA, Claesson MJ, Holmes E, Cotter PD. Comparison of the relative impacts of acute consumption of an inulin-enriched diet, milk kefir or a commercial probiotic product on the human gut microbiome and metabolome. NPJ Sci Food 2023; 7:41. [PMID: 37587110 PMCID: PMC10432396 DOI: 10.1038/s41538-023-00216-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/17/2023] [Indexed: 08/18/2023] Open
Abstract
It has been established that the human gut microbiota is central to health, and, consequently, there has been a growing desire to positively modulate its composition and/or function through, for example, the use of fermented foods, prebiotics or probiotics. Here, we compare the relative impact of the daily consumption of an inulin-enriched diet (n = 10), a commercial probiotic-containing fermented milk product (FMP) (n = 10), or a traditional kefir FMP (n = 9), over a 28-day period on the gut microbiome and urine metabolome of healthy human adults. None of the treatments resulted in significant changes to clinical parameters or biomarkers tested. However, shotgun metagenomic analysis revealed that kefir consumption resulted in a significant change in taxonomy, in the form of an increased abundance of the sub-dominant FMP-associated species Lactococcus raffinolactis, which further corresponded to shifts in the urine metabolome. Overall, our results indicated that daily consumption of a single portion of kefir alone resulted in detectable changes to the gut microbiota and metabolome of consumers.
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Affiliation(s)
- Liam H Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Co, Cork, Ireland
- School of Microbiology Department, University College Cork, Co, Cork, Ireland
| | - Aaron M Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Co, Cork, Ireland
- School of Microbiology Department, University College Cork, Co, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Co, Cork, Ireland
| | - Isabel Garcia-Perez
- Section of Biomolecular Medicine, Division of Computational Systems Medicine, Imperial College London, London, UK
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, Co, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Co, Cork, Ireland
| | - Adele Costabile
- School of Life and Health Sciences, University of Roehampton London, London, UK
| | - Richard Ellis
- Surveillance and Laboratory Services Department, APHA, Addlestone, UK
| | - Jim Finlayson
- NHS Highland, Highland Clinical Research Facility, University of the Highlands & Islands, Centre for Health Science, Inverness, UK
| | - Laura A Finnegan
- Teagasc Food Research Centre, Moorepark, Fermoy, Co, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Co, Cork, Ireland
| | - Marcus J Claesson
- School of Microbiology Department, University College Cork, Co, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Co, Cork, Ireland
| | - Elaine Holmes
- Section of Biomolecular Medicine, Division of Computational Systems Medicine, Imperial College London, London, UK
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Co, Cork, Ireland.
- School of Microbiology Department, University College Cork, Co, Cork, Ireland.
- VistaMilk SFI Research Centre, Teagasc, Moorepark, Fermoy, Co, Cork, Ireland.
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32
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Moore RL, Feehily C, Killeen SL, Yelverton CA, Geraghty AA, Walsh CJ, O'Neill IJ, Nielsan IB, Lawton EM, Sanchez-Gallardo R, Nori SRC, Shanahan F, Murphy EF, Van Sinderen D, Cotter PD, McAuliffe FM. Ability of Bifidobacterium breve 702258 to transfer from mother to infant: the MicrobeMom randomized controlled trial. Am J Obstet Gynecol MFM 2023; 5:100994. [PMID: 37142190 DOI: 10.1016/j.ajogmf.2023.100994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023]
Abstract
BACKGROUND The composition of the infant microbiome can have a variety of short- and long-term implications for health. It is unclear if maternal probiotic supplementation in pregnancy can affect the infant gut microbiome. OBJECTIVE This study aimed to investigate if maternal supplementation of a formulation of Bifidobacterium breve 702258 from early pregnancy until 3 months postpartum could transfer to the infant gut. STUDY DESIGN This was a double-blinded, placebo-controlled, randomized controlled trial of B breve 702258 (minimum 1 × 109 colony-forming units) or placebo taken orally from 16 weeks' gestation until 3 months postpartum in healthy pregnant women. The primary outcome was presence of the supplemented strain in infant stool up to 3 months of life, detected by at least 2 of 3 methods: strain-specific polymerase chain reaction, shotgun metagenomic sequencing, or genome sequencing of cultured B breve. A total of 120 individual infants' stool samples were required for 80% power to detect a difference in strain transfer between groups. Rates of detection were compared using the Fisher exact test. RESULTS A total of 160 pregnant women with average age of 33.6 (3.9) years and mean body mass index of 24.3 (22.5-26.5) kg/m2, of whom 43% were nulliparous (n=58), were recruited from September 2016 to July 2019. Neonatal stool samples were obtained from 135 infants (65 in intervention and 70 in control group). The presence of the supplemented strain was detected through at least 2 methods (polymerase chain reaction and culture) in 2 infants in the intervention group (n=2/65; 3.1%) and none in the control group (n=0; 0%; P=.230). CONCLUSION Direct mother-to-infant strain transfer of B breve 702258 occurred, albeit infrequently. This study highlights the potential for maternal supplementation to introduce microbial strains into the infant microbiome.
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Affiliation(s)
- Rebecca L Moore
- UCD Perinatal Research Centre, UCD School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland (Drs Moore, Killeen, Yelverton, Geraghty, and McAuliffe)
| | - Conor Feehily
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland (Drs Feehily, Walsh, and O'Neill, Mses Nielsan, Lawton, and Sanchez-Gallardo, Mr Nori, and Drs Shanahan and Cotter); Teagasc Food Research Centre, Moorepark, Fermoy, Ireland (Drs Feehily and Walsh, Ms Lawton, Mr Nori, and Drs Sinderen and Cotter); Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, United Kingdom (Dr Feehily)
| | - Sarah Louise Killeen
- UCD Perinatal Research Centre, UCD School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland (Drs Moore, Killeen, Yelverton, Geraghty, and McAuliffe)
| | - Cara A Yelverton
- UCD Perinatal Research Centre, UCD School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland (Drs Moore, Killeen, Yelverton, Geraghty, and McAuliffe)
| | - Aisling A Geraghty
- UCD Perinatal Research Centre, UCD School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland (Drs Moore, Killeen, Yelverton, Geraghty, and McAuliffe); Institute of Food and Health, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland (Dr Geraghty)
| | - Calum J Walsh
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland (Drs Feehily, Walsh, and O'Neill, Mses Nielsan, Lawton, and Sanchez-Gallardo, Mr Nori, and Drs Shanahan and Cotter); Teagasc Food Research Centre, Moorepark, Fermoy, Ireland (Drs Feehily and Walsh, Ms Lawton, Mr Nori, and Drs Sinderen and Cotter)
| | - Ian J O'Neill
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland (Drs Feehily, Walsh, and O'Neill, Mses Nielsan, Lawton, and Sanchez-Gallardo, Mr Nori, and Drs Shanahan and Cotter); School of Microbiology, University College Cork, Cork, Ireland (Dr O'Neill, Mses Nielsan and Sanchez-Gallardo, and Dr Van Sinderen)
| | - Ida Busch Nielsan
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland (Drs Feehily, Walsh, and O'Neill, Mses Nielsan, Lawton, and Sanchez-Gallardo, Mr Nori, and Drs Shanahan and Cotter); School of Microbiology, University College Cork, Cork, Ireland (Dr O'Neill, Mses Nielsan and Sanchez-Gallardo, and Dr Van Sinderen)
| | - Elaine M Lawton
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland (Drs Feehily, Walsh, and O'Neill, Mses Nielsan, Lawton, and Sanchez-Gallardo, Mr Nori, and Drs Shanahan and Cotter); Teagasc Food Research Centre, Moorepark, Fermoy, Ireland (Drs Feehily and Walsh, Ms Lawton, Mr Nori, and Drs Sinderen and Cotter)
| | - Rocio Sanchez-Gallardo
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland (Drs Feehily, Walsh, and O'Neill, Mses Nielsan, Lawton, and Sanchez-Gallardo, Mr Nori, and Drs Shanahan and Cotter); School of Microbiology, University College Cork, Cork, Ireland (Dr O'Neill, Mses Nielsan and Sanchez-Gallardo, and Dr Van Sinderen)
| | - Sai Ravi Chandra Nori
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland (Drs Feehily, Walsh, and O'Neill, Mses Nielsan, Lawton, and Sanchez-Gallardo, Mr Nori, and Drs Shanahan and Cotter); Teagasc Food Research Centre, Moorepark, Fermoy, Ireland (Drs Feehily and Walsh, Ms Lawton, Mr Nori, and Drs Sinderen and Cotter); Science Foundation Ireland Centre for Research Training in Genomics Data Science, School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland (Mr Nori)
| | - Fergus Shanahan
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland (Drs Feehily, Walsh, and O'Neill, Mses Nielsan, Lawton, and Sanchez-Gallardo, Mr Nori, and Drs Shanahan and Cotter); Department of Medicine, University College Cork, National University of Ireland, Cork, Ireland (Dr Shanahan)
| | - Eileen F Murphy
- PrecisionBiotics Group Ltd, Novozymes, Cork, Ireland (Dr Murphy)
| | - Douwe Van Sinderen
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland (Drs Feehily and Walsh, Ms Lawton, Mr Nori, and Drs Sinderen and Cotter); School of Microbiology, University College Cork, Cork, Ireland (Dr O'Neill, Mses Nielsan and Sanchez-Gallardo, and Dr Van Sinderen)
| | - Paul D Cotter
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland (Drs Feehily, Walsh, and O'Neill, Mses Nielsan, Lawton, and Sanchez-Gallardo, Mr Nori, and Drs Shanahan and Cotter); Teagasc Food Research Centre, Moorepark, Fermoy, Ireland (Drs Feehily and Walsh, Ms Lawton, Mr Nori, and Drs Sinderen and Cotter)
| | - Fionnuala M McAuliffe
- UCD Perinatal Research Centre, UCD School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland (Drs Moore, Killeen, Yelverton, Geraghty, and McAuliffe).
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Bester A, O'Brien M, Cotter PD, Dam S, Civai C. Shotgun Metagenomic Sequencing Revealed the Prebiotic Potential of a Fruit Juice Drink with Fermentable Fibres in Healthy Humans. Foods 2023; 12:2480. [PMID: 37444219 DOI: 10.3390/foods12132480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/13/2023] [Accepted: 06/08/2023] [Indexed: 07/15/2023] Open
Abstract
Fibre-based dietary interventions are at the forefront of gut microbiome modulation research, with a wealth of 16S rRNA information to demonstrate the prebiotic effects of isolated fibres. However, there is a distinct lack of data relating to the effect of a combination of soluble and insoluble fibres in a convenient-to-consume fruit juice food matrix on gut microbiota structure, diversity, and function. Here, we aimed to determine the impact of the MOJU Prebiotic Shot, an apple, lemon, ginger, and raspberry fruit juice drink blend containing chicory inulin, baobab, golden kiwi, and green banana powders, on gut microbiota structure and function. Healthy adults (n = 20) were included in a randomised, double-blind, placebo-controlled, cross-over study, receiving 60 mL MOJU Prebiotic Shot or placebo (without the fibre mix) for 3 weeks with a 3-week washout period between interventions. Shotgun metagenomics revealed significant between-group differences in alpha and beta diversity. In addition, the relative abundance of the phyla Actinobacteria and Desulfobacteria was significantly increased as a result of the prebiotic intervention. Nine species were observed to be differentially abundant (uncorrected p-value of <0.05) as a result of the prebiotic treatment. Of these, Bifidobacterium adolescentis and CAG-81 sp900066785 (Lachnospiraceae) were present at increased abundance relative to baseline. Additionally, KEGG analysis showed an increased abundance in pathways associated with arginine biosynthesis and phenylacetate degradation during the prebiotic treatment. Our results show the effects of the daily consumption of 60 mL MOJU Prebiotic Shot for 3 weeks and provide insight into the functional potential of B. adolescentis.
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Affiliation(s)
- Adri Bester
- London Agri Food Innovation Clinic (LAFIC), School of Applied Sciences, London South Bank University, London SE1 0AA, UK
| | | | | | | | - Claudia Civai
- London Agri Food Innovation Clinic (LAFIC), School of Applied Sciences, London South Bank University, London SE1 0AA, UK
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Feehily C, O'Neill IJ, Walsh CJ, Moore RL, Killeen SL, Geraghty AA, Lawton EM, Byrne D, Sanchez-Gallardo R, Nori SRC, Nielsen IB, Wortmann E, Matthews E, O'Flaherty R, Rudd PM, Groeger D, Shanahan F, Saldova R, McAuliffe FM, Van Sinderen D, Cotter PD. Detailed mapping of Bifidobacterium strain transmission from mother to infant via a dual culture-based and metagenomic approach. Nat Commun 2023; 14:3015. [PMID: 37230981 DOI: 10.1038/s41467-023-38694-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 05/10/2023] [Indexed: 05/27/2023] Open
Abstract
A significant proportion of the infant gut microbiome is considered to be acquired from the mother during and after birth. Thus begins a lifelong and dynamic relationship with microbes that has an enduring impact on host health. Based on a cohort of 135 mother-infant (F = 72, M = 63) dyads (MicrobeMom: ISRCTN53023014), we investigated the phenomenon of microbial strain transfer, with a particular emphasis on the use of a combined metagenomic-culture-based approach to determine the frequency of strain transfer involving members of the genus Bifidobacterium, including species/strains present at low relative abundance. From the isolation and genome sequencing of over 449 bifidobacterial strains, we validate and augment metagenomics-based evidence to reveal strain transfer in almost 50% of dyads. Factors important in strain transfer include vaginal birth, spontaneous rupture of amniotic membranes, and avoidance of intrapartum antibiotics. Importantly, we reveal that several transfer events are uniquely detected employing either cultivation or metagenomic sequencing, highlighting the requirement for a dual approach to obtain an in-depth insight into this transfer process.
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Affiliation(s)
- Conor Feehily
- Teagasc Food Research Centre, Fermoy, Co, Cork, Ireland
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, United Kingdom
| | - Ian J O'Neill
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Calum J Walsh
- Teagasc Food Research Centre, Fermoy, Co, Cork, Ireland
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland
| | - Rebecca L Moore
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Sarah Louise Killeen
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Aisling A Geraghty
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Elaine M Lawton
- Teagasc Food Research Centre, Fermoy, Co, Cork, Ireland
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland
| | - David Byrne
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Rocio Sanchez-Gallardo
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Sai Ravi Chandra Nori
- Teagasc Food Research Centre, Fermoy, Co, Cork, Ireland
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland
- SFI Centre for Research Training in Genomics Data Science, School of Mathematics, Statistics & Applied Mathematics, University of Galway, Galway, Ireland
| | - Ida Busch Nielsen
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Esther Wortmann
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Elizabeth Matthews
- NIBRT GlycoScience Group, National Institute for Bioprocessing Research and Training, Co, Dublin, Ireland
| | - Roisin O'Flaherty
- NIBRT GlycoScience Group, National Institute for Bioprocessing Research and Training, Co, Dublin, Ireland
- Department of Chemistry, Maynooth University, Maynooth, Co, Kildare, Ireland
| | - Pauline M Rudd
- NIBRT GlycoScience Group, National Institute for Bioprocessing Research and Training, Co, Dublin, Ireland
- Bioprocessing Technology Institute, AStar, Singapore, Singapore
| | - David Groeger
- PrecisionBiotics Group Ltd. (Novozymes Cork), Cork Airport Business Park, Kinsale Road, Cork, Ireland
| | - Fergus Shanahan
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland
| | - Radka Saldova
- NIBRT GlycoScience Group, National Institute for Bioprocessing Research and Training, Co, Dublin, Ireland
- UCD School of Medicine, College of Health and Agricultural Science (CHAS), University College Dublin (UCD), Dublin, Ireland
| | - Fionnuala M McAuliffe
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Douwe Van Sinderen
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland.
- School of Microbiology, University College Cork, Cork, Ireland.
| | - Paul D Cotter
- Teagasc Food Research Centre, Fermoy, Co, Cork, Ireland
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland
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Mukherjee A, Iyer A, Gómez-Sala B, O'Connor E, Kenny JG, Cotter PD. Mapping the available evidence on the impact of ingested live microbes on health: a scoping review protocol. BMJ Open 2023; 13:e067766. [PMID: 37197820 DOI: 10.1136/bmjopen-2022-067766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/19/2023] Open
Abstract
INTRODUCTION It has been hypothesised that the regular consumption of safe, live microbes confers health-promoting attributes, including the prevention of disease. To address this hypothesis, we propose a scoping review approach that will systematically assess the large corpus of relevant literature that is now available on this research topic. This article outlines a protocol for a scoping review of published studies on interventions with live microbes in non-patient populations across eight health categories. The scoping review aims to catalogue types of interventions, measured outcomes, dosages, effectiveness, as well as current research gaps. METHODS AND ANALYSIS The scoping review will follow the six-staged protocol as proposed by Arksey and O'Malley and will include the following stages: defining the research questions (stage 1); defining the eligibility criteria and finalising search strategy (stage 2); selection of studies based on the eligibility criteria (stage 3); development of a data extraction framework and charting of data (stage 4); aggregation of results and summarisation of findings (stage 5); and the optional consultation with stakeholders (stage 6), which will not be performed. ETHICS AND DISSEMINATION Since the scoping review synthesises information from existing literature, no separate ethical approval is required. The findings of the scoping review will be communicated for publication to an open-access, peer-reviewed scientific journal, presented at relevant conferences, and disseminated at future workshops with all relevant data and documents being available online through the Open Science Framework (https://osf.io/kvhe7).
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Affiliation(s)
- Arghya Mukherjee
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Ajay Iyer
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Beatriz Gómez-Sala
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, County Cork, Ireland
| | - Eibhlis O'Connor
- APC Microbiome Ireland, University College Cork, Cork, County Cork, Ireland
- Department of Biological Sciences, University of Limerick, Limerick, Ireland
| | - John G Kenny
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, County Cork, Ireland
| | - Paul D Cotter
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, County Cork, Ireland
- Vistamilk, Cork, Ireland
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36
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O'Reilly C, Grimaud GM, Coakley M, O'Connor PM, Mathur H, Peterson VL, O'Donovan CM, Lawlor PG, Cotter PD, Stanton C, Rea MC, Hill C, Ross RP. Modulation of the gut microbiome with nisin. Sci Rep 2023; 13:7899. [PMID: 37193715 DOI: 10.1038/s41598-023-34586-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/03/2023] [Indexed: 05/18/2023] Open
Abstract
Nisin is a broad spectrum bacteriocin used extensively as a food preservative that was identified in Lactococcus lactis nearly a century ago. We show that orally-ingested nisin survives transit through the porcine gastrointestinal tract intact (as evidenced by activity and molecular weight determination) where it impacts both the composition and functioning of the microbiota. Specifically, nisin treatment caused a reversible decrease in Gram positive bacteria, resulting in a reshaping of the Firmicutes and a corresponding relative increase in Gram negative Proteobacteria. These changes were mirrored by the modification in relative abundance of pathways involved in acetate, butyrate (decreased) and propionate (increased) synthesis which correlated with overall reductions in short chain fatty acid levels in stool. These reversible changes that occur as a result of nisin ingestion demonstrate the potential of bacteriocins like nisin to shape mammalian microbiomes and impact on the functionality of the community.
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Affiliation(s)
- Catherine O'Reilly
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- Microbiology Department, University College Cork, Co. Cork, Ireland
| | - Ghjuvan M Grimaud
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Mairéad Coakley
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Paula M O'Connor
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- Microbiology Department, University College Cork, Co. Cork, Ireland
| | - Harsh Mathur
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Veronica L Peterson
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Ciara M O'Donovan
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Peadar G Lawlor
- Pig Development Department, Teagasc Animal & Grassland Research & Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Paul D Cotter
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Mary C Rea
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Microbiology Department, University College Cork, Co. Cork, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland.
- Microbiology Department, University College Cork, Co. Cork, Ireland.
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Matthews C, Walsh AM, Gordon SV, Markey B, Cotter PD, O' Mahony J. Differences in Faecal Microbiome Taxonomy, Diversity and Functional Potential in a Bovine Cohort Experimentally Challenged with Mycobacterium avium subsp. paratuberculosis (MAP). Animals (Basel) 2023; 13:ani13101652. [PMID: 37238082 DOI: 10.3390/ani13101652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/01/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Mycobacterium avium subspecies paratuberculosis (MAP) is the causative agent of Johne's disease in ruminants, a chronic enteritis which results in emaciation and eventual loss of the animal. Recent advances in metagenomics have allowed a more in-depth study of complex microbiomes, including that of gastrointestinal tracts, and have the potential to provide insights into consequences of the exposure of an animal to MAP or other pathogens. This study aimed to investigate taxonomic diversity and compositional changes of the faecal microbiome of cattle experimentally challenged with MAP compared to an unexposed control group. Faecal swab samples were collected from a total of 55 animals [exposed group (n = 35) and a control group (n = 20)], across three time points (months 3, 6 and 9 post-inoculation). The composition and functional potential of the faecal microbiota differed across time and between the groups (p < 0.05), with the primary differences, from both a taxonomic and functional perspective, occurring at 3 months post inoculation. These included significant differences in the relative abundance of the genera Methanobrevibacter and Bifidobacterium and also of 11 other species (4 at a higher relative abundance in the exposed group and 7 at a higher relative abundance in the control group). Correlations were made between microbiome data and immunopathology measurements and it was noted that changes in the microbial composition correlated with miRNA-155, miR-146b and IFN-ɣ. In summary, this study illustrates the impact of exposure to MAP on the ruminant faecal microbiome with a number of species that may have relevance in veterinary medicine for tracking exposure to MAP.
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Affiliation(s)
- Chloe Matthews
- Department of Biological Sciences, Munster Technological University, Bishopstown, T12 P928 Cork, Ireland
- Teagasc Food Research Centre, Moorepark, P61 C996 Fermoy, Ireland
| | - Aaron M Walsh
- Teagasc Food Research Centre, Moorepark, P61 C996 Fermoy, Ireland
| | - Stephen V Gordon
- School of Veterinary Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Bryan Markey
- School of Veterinary Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, P61 C996 Fermoy, Ireland
- APC Microbiome Ireland, University College Cork, T12 R229 Cork, Ireland
| | - Jim O' Mahony
- Department of Biological Sciences, Munster Technological University, Bishopstown, T12 P928 Cork, Ireland
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Vinderola G, Cotter PD, Freitas M, Gueimonde M, Holscher HD, Ruas-Madiedo P, Salminen S, Swanson KS, Sanders ME, Cifelli CJ. Fermented foods: a perspective on their role in delivering biotics. Front Microbiol 2023; 14:1196239. [PMID: 37250040 PMCID: PMC10213265 DOI: 10.3389/fmicb.2023.1196239] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 04/13/2023] [Indexed: 05/31/2023] Open
Abstract
Fermented foods are often erroneously equated with probiotics. Although they might act as delivery vehicles for probiotics, or other 'biotic' substances, including prebiotics, synbiotics, and postbiotics, stringent criteria must be met for a fermented food to be considered a 'biotic'. Those criteria include documented health benefit, sufficient product characterization (for probiotics to the strain level) and testing. Similar to other functional ingredients, the health benefits must go beyond that of the product's nutritional components and food matrix. Therefore, the 'fermented food' and 'probiotic' terms may not be used interchangeably. This concept would apply to the other biotics as well. In this context, the capacity of fermented foods to deliver one, several, or all biotics defined so far will depend on the microbiological and chemical level of characterization, the reproducibility of the technological process used to produce the fermented foods, the evidence for health benefits conferred by the biotics, as well as the type and amount of testing carried out to show the probiotic, prebiotic, synbiotic, and postbiotic capacity of that fermented food.
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Affiliation(s)
- Gabriel Vinderola
- Instituto de Lactología Industrial (CONICET-UNL), Faculty of Chemical Engineering, National University of Litoral, Santa Fe, Argentina
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark and APC Microbiome Ireland, Cork, Ireland
| | - Miguel Freitas
- Health and Scientific Affairs, Danone North America, White Plains, NY, United States
| | - Miguel Gueimonde
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias—Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Asturias, Spain
| | - Hannah D. Holscher
- Department of Food Science and Human Nutrition, Division of Nutritional Sciences, 260 Edward R. Madigan Laboratory, University of Illinois, Urbana, IL, United States
| | - Patricia Ruas-Madiedo
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias—Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Asturias, Spain
| | - Seppo Salminen
- Functional Foods Forum, Faculty of Medicine, University of Turku, Turku, Finland
| | - Kelly S. Swanson
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Mary Ellen Sanders
- International Scientific Association for Probiotics and Prebiotics, Centennial, CO, United States
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Fitzpatrick AH, Rupnik A, O'Shea H, Crispie F, Cotter PD, Keaveney S. Amplicon-Based High-Throughput Sequencing Method for Genotypic Characterization of Norovirus in Oysters. Appl Environ Microbiol 2023; 89:e0216522. [PMID: 37071010 DOI: 10.1128/aem.02165-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023] Open
Abstract
Norovirus is a highly diverse RNA virus often implicated in foodborne outbreaks, particularly those associated with shellfish. Shellfish are filter feeders, and when harvested in bays exposed to wastewater overflow or storm overflows, they can harbor various pathogens, including human-pathogenic viruses. The application of Sanger or amplicon-based high-throughput sequencing (HTS) technologies to identify human pathogens in shellfish faces two main challenges: (i) distinguishing multiple genotypes/variants in a single sample and (ii) low concentrations of norovirus RNA. Here, we assessed the performance of a novel norovirus capsid amplicon HTS method. We generated a panel of spiked oysters containing various norovirus concentrations with different genotypic compositions. Several DNA polymerases and reverse transcriptases (RTs) were compared, and performance was evaluated based on (i) the number of reads passing quality filters per sample, (ii) the number of correct genotypes identified, and (iii) the sequence identity of outputs compared to Sanger-derived sequences. A combination of the reverse transcriptase LunaScript and the DNA polymerase AmpliTaq Gold provided the best results. The method was then employed, and compared with Sanger sequencing, to characterize norovirus populations in naturally contaminated oysters. IMPORTANCE While foodborne outbreaks account for approximately 14% of norovirus cases (L. Verhoef, J. Hewitt, L. Barclay, S. Ahmed, R. Lake, A. J. Hall, B. Lopman, A. Kroneman, H. Vennema, J. Vinjé, and M. Koopmans, Emerg Infect Dis 21:592-599, 2015), we do not have standardized high-throughput sequencing methods for genotypic characterization in foodstuffs. Here, we present an optimized amplicon high-throughput sequencing method for the genotypic characterization of norovirus in oysters. This method can accurately detect and characterize norovirus at concentrations found in oysters grown in production areas impacted by human wastewater discharges. It will permit the investigation of norovirus genetic diversity in complex matrices and contribute to ongoing surveillance of norovirus in the environment.
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Affiliation(s)
- Amy H Fitzpatrick
- Department of Food Biosciences, Teagasc Food Research Centre, Fermoy, Ireland
- Department of Shellfish Microbiology, Marine Institute, Oranmore, Ireland
- Department of Biological Sciences, Munster Technological University, Cork, Ireland
| | - Agnieszka Rupnik
- Department of Shellfish Microbiology, Marine Institute, Oranmore, Ireland
| | - Helen O'Shea
- Department of Biological Sciences, Munster Technological University, Cork, Ireland
| | - Fiona Crispie
- Department of Food Biosciences, Teagasc Food Research Centre, Fermoy, Ireland
| | - Paul D Cotter
- Department of Food Biosciences, Teagasc Food Research Centre, Fermoy, Ireland
| | - Sinéad Keaveney
- Department of Shellfish Microbiology, Marine Institute, Oranmore, Ireland
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Martin JGP, Cotter PD. Filamentous fungi in artisanal cheeses: A problem to be avoided or a market opportunity? Heliyon 2023; 9:e15110. [PMID: 37151695 PMCID: PMC10161367 DOI: 10.1016/j.heliyon.2023.e15110] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 02/24/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
The microbial diversity of artisanal cheeses has been ever more extensively explored over recent years. Many new studies have been particularly focused on the detection and identification of fungi associated with cheese rinds. This is not surprising given that the composition and abundance of fungi on the cheese surface can significantly contribute to desirable sensory qualities, while also contributing to defects, particularly during ripening, and risks associated with the production of mycotoxins. Here we critically review the impact of fungi on the quality of artisanal cheeses, as well as the risks associated with the presence of particular species or strains with specific phenotypes. Ultimately, we address the question; should fungi be predominantly considered villains when it comes to artisanal cheese safety or could their presence be better exploited by producers in order to generate innovative products with greater added value? Such discussions will be increasingly important from the perspective of the future commercialization and regulation of artisanal cheeses that frequently contain a high abundance of moulds.
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Affiliation(s)
- José Guilherme Prado Martin
- Microbiology of Fermented Products Laboratory (FERMICRO), Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Corresponding author.
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- APC Microbiome Ireland and VistaMilk, Ireland
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41
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Malesevic M, Gardijan L, Miljkovic M, O'Connor PM, Mirkovic N, Jovcic B, Cotter PD, Jovanovic G, Kojic M. Exploring the antibacterial potential of Lactococcus lactis subsp. lactis bv. diacetylactis BGBU1-4 by genome mining, bacteriocin gene overexpression, and chemical protein synthesis of lactolisterin BU variants. Lett Appl Microbiol 2023; 76:6986262. [PMID: 36695436 DOI: 10.1093/lambio/ovad004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/09/2022] [Accepted: 01/11/2023] [Indexed: 01/15/2023]
Abstract
Lactic acid bacterium Lactococcus lactis BGBU1-4 produces 43 amino acids (aa) long bacteriocin, lactolisterin BU (LBU), a 5.161 kDa peptide with potent antibacterial activity against many Gram-positive pathogens. In addition, BGBU1-4 produces an additional unknown product of 3.642 kDa with antibacterial activity. Here, we determined that the significant amount of naturally produced LBU breaks down to create a 3.642 kDa truncated form of LBU bacteriocin consisting of 31 N-terminal aa (LBU1-31) that exhibits 12.5% the antibacterial activity of the full-length LBU. We showed that chemically synthesized LBU is stable and 50% less active than native LBU, and so we used the synthetic peptides of LBU and its variants to further study their activities and antibacterial potential. Deletion analysis of LBU revealed that the 24 N-terminal aa of LBU (LBU1-24) are responsible for antibacterial activity, while downstream aa (25-43) determine the species-specific effectiveness of LBU. Although LBU1-31 contains aa 1-24, the truncation at position 31 is predicted to change the structure within aa 15-31 and might impact on antibacterial activity. Intriguingly, whole genome sequencing and genome mining established that BGBU1-4 is abundant in genes that encode potential antibacterials, but produces LBU and its breakdown product LBU1-31 exclusively.
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Affiliation(s)
- Milka Malesevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 444a Vojvode Stepe, Belgrade, Serbia
| | - Lazar Gardijan
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 444a Vojvode Stepe, Belgrade, Serbia
| | - Marija Miljkovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 444a Vojvode Stepe, Belgrade, Serbia
| | - Paula M O'Connor
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, P61 C996, Ireland.,APC Microbiome Ireland, Cork D03 E5R6, Ireland
| | - Nemanja Mirkovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 444a Vojvode Stepe, Belgrade, Serbia
| | - Branko Jovcic
- Faculty of Biology, University of Belgrade, Beograd 11000, Serbia.,Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 444a Vojvode Stepe, Belgrade, Serbia
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, P61 C996, Ireland.,APC Microbiome Ireland, Cork D03 E5R6, Ireland
| | - Goran Jovanovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 444a Vojvode Stepe, Belgrade, Serbia
| | - Milan Kojic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 444a Vojvode Stepe, Belgrade, Serbia
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Martin JGP, Silva JMM, César ICDR, da Silva M, Santana SA, Veloso TGR, Silva JGE, Ferreira CLDLF, Leech J, Cotter PD. Seasonal variation in the Canastra cheese mycobiota. Front Microbiol 2023; 13:1076672. [PMID: 36817100 PMCID: PMC9936976 DOI: 10.3389/fmicb.2022.1076672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/28/2022] [Indexed: 02/05/2023] Open
Abstract
Canastra cheese is the most well-known artisanal cheese produced in Brazil. Although its production includes a step to remove fungi from the cheese surface, in recent years some cheesemakers have preserved the autochthonous fungi grown during ripening due to an interest in the sensory characteristics attributed to these microorganisms. In this work, the mycobiota of artisanal cheeses produced in the Canastra region was characterized based on ITS marker gene analysis. A total of 96 artisanal cheeses from 16 different farms across 9 cities were collected during two different periods (dry and wet seasons). The Canastra cheese mycobiota was significantly impacted by the season, the city of production and the farm but altitude did not affect the fungal community of the cheeses analyzed. Debaryomyces prosopidis was most abundant in the majority of samples across both seasons. During the wet season, Trichosporon asahii, Kluyveromyces lactis and Fusarium solani were the next most abundant species, followed by Torulaspora delbrueckii and Acremonium citrinum. These results highlight the importance of manufacturing practices and seasonality on the fungal composition of Canastra cheeses. These insights are particularly important in light of recent new regulation in Brazil, removing previous obstacles for surface fungi to persist on cheese. These new regulations will allow new approaches to cheese production, and ultimately, novel products.
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Affiliation(s)
- José Guilherme Prado Martin
- Microbiology of Fermented Products Laboratory (FERMICRO), Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Brazil,*Correspondence: José Guilherme Prado Martin,
| | - João Marcos Maia Silva
- Microbiology of Fermented Products Laboratory (FERMICRO), Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Isabel Cristina da Rocha César
- Microbiology of Fermented Products Laboratory (FERMICRO), Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Meiriele da Silva
- Laboratory of Mycorrhizae (LAMIC), Department of Microbiology, Universidade Federal de Viçosa (UFV), Viçosa, Brazil
| | - Samara Aparecida Santana
- Microbiology of Fermented Products Laboratory (FERMICRO), Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Tomás Gomes Reis Veloso
- Laboratory of Mycorrhizae (LAMIC), Department of Microbiology, Universidade Federal de Viçosa (UFV), Viçosa, Brazil
| | | | | | - John Leech
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland,APC Microbiome Ireland and VistaMilk, Fermoy, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland,APC Microbiome Ireland and VistaMilk, Fermoy, Ireland
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43
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Keane JM, Walsh CJ, Cronin P, Baker K, Melgar S, Cotter PD, Joyce SA, Gahan CGM, Houston A, Hyland NP. Investigation of the gut microbiome, bile acid composition and host immunoinflammatory response in a model of azoxymethane-induced colon cancer at discrete timepoints. Br J Cancer 2023; 128:528-536. [PMID: 36418894 PMCID: PMC9938136 DOI: 10.1038/s41416-022-02062-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 11/03/2022] [Accepted: 11/08/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Distinct sets of microbes contribute to colorectal cancer (CRC) initiation and progression. Some occur due to the evolving intestinal environment but may not contribute to disease. In contrast, others may play an important role at particular times during the tumorigenic process. Here, we describe changes in the microbiota and host over the course of azoxymethane (AOM)-induced tumorigenesis. METHODS Mice were administered AOM or PBS and were euthanised 8, 12, 24 and 48 weeks later. Samples were analysed using 16S rRNA gene sequencing, UPLC-MS and qRT-PCR. RESULTS The microbiota and bile acid profile showed distinct changes at each timepoint. The inflammatory response became apparent at weeks 12 and 24. Moreover, significant correlations between individual taxa, cytokines and bile acids were detected. One co-abundance group (CAG) differed significantly between PBS- and AOM-treated mice at week 24. Correlation analysis also revealed significant associations between CAGs, bile acids and the bile acid transporter, ASBT. Aberrant crypt foci and adenomas were first detectable at weeks 24 and 48, respectively. CONCLUSION The observed changes precede host hyperplastic transformation and may represent early therapeutic targets for the prevention or management of CRC at specific timepoints in the tumorigenic process.
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Affiliation(s)
- J M Keane
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- Department of Medicine, University College Cork, Cork, Ireland
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
- Department of Physiology, University College Cork, Cork, Ireland
| | - C J Walsh
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - P Cronin
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - K Baker
- Department of Medicine, University College Cork, Cork, Ireland
- Department of Pathology, University College Cork, Cork, Ireland
| | - S Melgar
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - P D Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - S A Joyce
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - C G M Gahan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- School of Pharmacy, University College Cork, Cork, Ireland
| | - A Houston
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
- Department of Medicine, University College Cork, Cork, Ireland.
| | - N P Hyland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Physiology, University College Cork, Cork, Ireland
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44
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Keane JM, Las Heras V, Pinheiro J, FitzGerald JA, Núñez-Sánchez MA, Hueston CM, O'Mahony L, Cotter PD, Hill C, Melgar S, Gahan CGM. Akkermansia muciniphila reduces susceptibility to Listeria monocytogenes infection in mice fed a high-fat diet. Gut Microbes 2023; 15:2229948. [PMID: 37424323 DOI: 10.1080/19490976.2023.2229948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/11/2023] Open
Abstract
A high-fat (HF) diet reduces resistance to the foodborne pathogen Listeria monocytogenes. We demonstrate that short-term gavage with A. muciniphila increases resistance to oral and systemic L. monocytogenes infection in mice fed a HF diet. A. muciniphila reduced inflammation in the gut and liver of mice fed a high-fat diet prior to infection and reduced inflammatory cell infiltration in the ileum to levels similar to mice fed a low-fat (LF) diet. Akkermansia administration had minimal impacts upon the microbiota and microbial metabolites and did not affect individual taxa or impact the Bacteroidetes to Firmicutes ratio. In summary, A. muciniphila increased resistance to L. monocytogenes infection in mice fed a HF diet by moderating immune/physiological effects through specific interaction between A. muciniphila and the host gut.
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Affiliation(s)
- Jonathan M Keane
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Vanessa Las Heras
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Jorge Pinheiro
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Jamie A FitzGerald
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Ireland
| | - María A Núñez-Sánchez
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Obesity and Metabolism Laboratory, Biomedical Research Institute of Murcia (IMIB-Arrixaca), Murcia, Spain
| | - Cara M Hueston
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Liam O'Mahony
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- Department of Medicine, University College Cork, Cork, Ireland
| | - Paul D Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Silvia Melgar
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Cormac G M Gahan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- School of Pharmacy, University College Cork, Cork, Ireland
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45
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Falà AK, Álvarez-Ordóñez A, Filloux A, Gahan CGM, Cotter PD. Quorum sensing in human gut and food microbiomes: Significance and potential for therapeutic targeting. Front Microbiol 2022; 13:1002185. [PMID: 36504831 PMCID: PMC9733432 DOI: 10.3389/fmicb.2022.1002185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 10/17/2022] [Indexed: 11/27/2022] Open
Abstract
Human gut and food microbiomes interact during digestion. The outcome of these interactions influences the taxonomical composition and functional capacity of the resident human gut microbiome, with potential consequential impacts on health and disease. Microbe-microbe interactions between the resident and introduced microbiomes, which likely influence host colonisation, are orchestrated by environmental conditions, elements of the food matrix, host-associated factors as well as social cues from other microorganisms. Quorum sensing is one example of a social cue that allows bacterial communities to regulate genetic expression based on their respective population density and has emerged as an attractive target for therapeutic intervention. By interfering with bacterial quorum sensing, for instance, enzymatic degradation of signalling molecules (quorum quenching) or the application of quorum sensing inhibitory compounds, it may be possible to modulate the microbial composition of communities of interest without incurring negative effects associated with traditional antimicrobial approaches. In this review, we summarise and critically discuss the literature relating to quorum sensing from the perspective of the interactions between the food and human gut microbiome, providing a general overview of the current understanding of the prevalence and influence of quorum sensing in this context, and assessing the potential for therapeutic targeting of quorum sensing mechanisms.
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Affiliation(s)
- A. Kate Falà
- APC Microbiome Ireland, University College Cork, Cork, Ireland,School of Microbiology, University College Cork, Cork, Ireland,Food Bioscience Department, Teagasc Food Research Centre, Fermoy, Ireland
| | - Avelino Álvarez-Ordóñez
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Cormac G. M. Gahan
- APC Microbiome Ireland, University College Cork, Cork, Ireland,School of Microbiology, University College Cork, Cork, Ireland,School of Pharmacy, University College Cork, Cork, Ireland
| | - Paul D. Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland,Food Bioscience Department, Teagasc Food Research Centre, Fermoy, Ireland,*Correspondence: Paul D. Cotter,
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46
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Bourrie BCT, Forgie AJ, Ju T, Richard C, Cotter PD, Willing BP. Consumption of the cell-free or heat-treated fractions of a pitched kefir confers some but not all positive impacts of the corresponding whole kefir. Front Microbiol 2022; 13:1056526. [PMID: 36504827 PMCID: PMC9730713 DOI: 10.3389/fmicb.2022.1056526] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/31/2022] [Indexed: 11/25/2022] Open
Abstract
Introduction Kefir consumption can have many metabolic health benefits, including, in the case of specific kefirs, improvements in plasma and liver lipid profiles. Our group has previously shown that these health benefits are dependent on the microbial composition of the kefir fermentation, and that a pitched kefir (PK1) containing specific traditional microbes can recapitulate the health benefits of a traditional kefir. In this study we investigated how different preparations of kefir impact cholesterol and lipid metabolism and circulating markers of cardiovascular disease risk and determine if freeze-drying impacts health benefits relative to past studies. Materials and methods Eight-week-old male and female C57Bl/6 mice were fed a high fat diet (40% kcal from fat) supplemented with one of 3 freeze-dried kefir preparations (whole kefir, cell-free kefir, or heat-treated kefir) for 8 weeks prior to analysis of plasma and liver lipid profiles, circulating cardiovascular disease (CVD) biomarkers, cecal microbiome composition, and cecal short-chain fatty acid levels. These groups of mice were compared to others that were fed a control low-fat diet, control high fat diet or high fat diet supplemented with milk, respectively. Results All kefir preparations lowered plasma cholesterol in both male and female mice, while only whole kefir lowered liver cholesterol and triglycerides. Plasma vascular cell adhesion molecule 1 (VCAM-1) was lowered by both whole kefir and heat-treated kefir in male mice but not females, while c-reactive protein (CRP) was unchanged across all high fat diet fed groups in males and females. Conclusion These results indicate that some of the metabolic benefits of consumption of this kefir do not require whole kefir while also indicating that there are multiple compounds or components responsible for the different benefits observed.
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Affiliation(s)
- Benjamin C. T. Bourrie
- Agricultural Food and Nutritional Science, Agriculture/Forestry Center, University of Alberta, Edmonton, AB, Canada
| | - Andrew J. Forgie
- Agricultural Food and Nutritional Science, Agriculture/Forestry Center, University of Alberta, Edmonton, AB, Canada
| | - Tingting Ju
- Agricultural Food and Nutritional Science, Agriculture/Forestry Center, University of Alberta, Edmonton, AB, Canada
| | - Caroline Richard
- Agricultural Food and Nutritional Science, Agriculture/Forestry Center, University of Alberta, Edmonton, AB, Canada
| | - Paul D. Cotter
- Teagasc Food Research Centre, Fermoy, Ireland,APC Microbiome Ireland, Cork, Ireland,VistaMilk, Cork, Ireland
| | - Benjamin P. Willing
- Agricultural Food and Nutritional Science, Agriculture/Forestry Center, University of Alberta, Edmonton, AB, Canada,*Correspondence: Benjamin P. Willing,
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47
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Yap M, O’Sullivan O, O’Toole PW, Cotter PD. Development of sequencing-based methodologies to distinguish viable from non-viable cells in a bovine milk matrix: A pilot study. Front Microbiol 2022; 13:1036643. [PMID: 36466696 PMCID: PMC9713316 DOI: 10.3389/fmicb.2022.1036643] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 10/28/2022] [Indexed: 04/22/2024] Open
Abstract
Although high-throughput DNA sequencing-based methods have been of great value for determining the composition of microbial communities in various environments, there is the potential for inaccuracies arising from the sequencing of DNA from dead microorganisms. In this pilot study, we compared different sequencing-based methods to assess their relative accuracy with respect to distinguishing between viable and non-viable cells, using a live and heat-inactivated model community spiked into bovine milk. The methods used were shotgun metagenomics with and without propidium monoazide (PMA) treatment, RNA-based 16S rRNA sequencing and metatranscriptomics. The results showed that methods were generally accurate, though significant differences were found depending on the library types and sequencing technologies. Different molecular targets were the basis for variations in the results generated using different library types, while differences in the derived composition data from Oxford Nanopore Technologies-and Illumina-based sequencing likely reflect a combination of different sequencing depths, error rates and bioinformatics pipelines. Although PMA was successfully applied in this study, further optimisation is required before it can be applied in a more universal context for complex microbiomes. Overall, these methods show promise and represent another important step towards the ultimate establishment of approaches that can be applied to accurately identify live microorganisms in milk and other food niches.
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Affiliation(s)
- Min Yap
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Orla O’Sullivan
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Paul W. O’Toole
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- APC Microbiome Ireland, Cork, Ireland
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48
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Gahan J, O’Sullivan O, Cotter PD, Schmalenberger A. Arbuscular Mycorrhiza Support Plant Sulfur Supply through Organosulfur Mobilizing Bacteria in the Hypho- and Rhizosphere. Plants (Basel) 2022; 11:3050. [PMID: 36432779 PMCID: PMC9694294 DOI: 10.3390/plants11223050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
This study aimed to elucidate the role of bacteria colonising mycorrhizal hyphae in organically bound sulfur mobilisation, the dominant soil sulfur source that is not directly plant available. The effect of an intact mycorrhizal symbiosis with access to stable isotope organo-34S enriched soils encased in 35 µm mesh cores was tested in microcosms with Agrostis stolonifera and Plantago lanceolata. Hyphae and associated soil were sampled from static mesh cores with mycorrhizal ingrowth and rotating mesh cores that exclude mycorrhizal ingrowth as well as corresponding rhizosphere soil, while plant shoots were analysed for 34S uptake. Static cores increased uptake of 34S at early stages of plant growth when sulfur demand appeared to be high and harboured significantly larger populations of sulfonate mobilising bacteria. Bacterial and fungal communities were significantly different in the hyphospheres of static cores when compared to rotating cores, not associated with plant hosts. Shifts in bacterial and fungal communities occurred not only in rotated cores but also in the rhizosphere. Arylsulfatase activity was significantly higher in the rhizosphere when cores stayed static, while atsA and asfA gene diversity was distinct in the microcosms with static and rotating cores. This study demonstrated that AM symbioses can promote organo-S mobilization and plant uptake through interactions with hyphospheric bacteria, enabling AM fungal ingrowth into static cores creating a positive feedback-loop, detectable in the microbial rhizosphere communities.
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Affiliation(s)
- Jacinta Gahan
- Department of Biological Sciences, School of Natural Sciences, University of Limerick, V94 T9PX Limerick, Ireland
| | - Orla O’Sullivan
- Teagasc Food Research Centre, Moorepark, Fermoy, and APC Microbiome Ireland, P61 C996 Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, and APC Microbiome Ireland, P61 C996 Cork, Ireland
| | - Achim Schmalenberger
- Department of Biological Sciences, School of Natural Sciences, University of Limerick, V94 T9PX Limerick, Ireland
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49
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Killeen SL, Byrne DF, Geraghty AA, Yelverton CA, van Sinderen D, Cotter PD, Murphy EF, O’Reilly SL, McAuliffe FM. Recruiting and Engaging Women of Reproductive Age with Obesity: Insights from A Mixed-Methods Study within A Trial. Int J Environ Res Public Health 2022; 19:13832. [PMID: 36360712 PMCID: PMC9658053 DOI: 10.3390/ijerph192113832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Engaging women with obesity in health-related studies during preconception is challenging. Limited data exists relating to their participation. The aim of this study is to explore the experiences and opinions of women participating in a weight-related, preconception trial. This is an explanatory sequential (quan-QUAL) mixed-methods Study Within A Trial, embedded in the GetGutsy randomized controlled trial (ISRCTN11295995). Screened participants completed an online survey of eight questions (single or multiple choice and Likert scale) on recruitment, motivations and opinions on study activities. Participants with abdominal obesity (waist circumference ≥ 80 cm) were invited to a subsequent semi-structured, online focus group (n = 2, 9 participants) that was transcribed and analyzed using inductive thematic analysis, with a pragmatic epistemological approach. The survey (n = 102) showed the main research participation motivations were supporting health research (n = 38, 37.3%) and wanting health screening (n = 30, 29.4%). Most participants were recruited via email (n = 35, 34.7%) or social media (n = 15, 14.7%). In the FGs, participants valued flexibility, convenience and. research methods that aligned with their lifestyles. Participants had an expanded view of health that considered emotional well-being and balance alongside more traditional medical assessments. Clinical trialists should consider well-being, addressing the interconnectedness of health and incorporate a variety of research activities to engage women of reproductive age with obesity.
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Affiliation(s)
- Sarah Louise Killeen
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, D02 YH21 Dublin, Ireland
| | - David F. Byrne
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, D02 YH21 Dublin, Ireland
| | - Aisling A. Geraghty
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, D02 YH21 Dublin, Ireland
- UCD Institute of Food and Health, School of Agriculture and Food Science, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Cara A. Yelverton
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, D02 YH21 Dublin, Ireland
| | - Douwe van Sinderen
- APC Microbiome Ireland, Biosciences Research Institute, National University of Ireland, T12 K8AF Cork, Ireland
- School of Microbiology, National University of Ireland, T12 K8AF Cork, Ireland
| | - Paul D. Cotter
- APC Microbiome Ireland, Biosciences Research Institute, National University of Ireland, T12 K8AF Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996 Cork, Ireland
| | - Eileen F. Murphy
- Precision Biotics Ltd. (Novozymes Cork), Cork Airport Business Park, Kinsale Road, T12 D292 Cork, Ireland
| | - Sharleen L. O’Reilly
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, D02 YH21 Dublin, Ireland
- UCD Institute of Food and Health, School of Agriculture and Food Science, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Fionnuala M. McAuliffe
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, D02 YH21 Dublin, Ireland
- APC Microbiome Ireland, Biosciences Research Institute, National University of Ireland, T12 K8AF Cork, Ireland
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50
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Srinivas M, O’Sullivan O, Cotter PD, van Sinderen D, Kenny JG. The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods. Foods 2022; 11:3297. [PMCID: PMC9601669 DOI: 10.3390/foods11203297] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The microbial communities present within fermented foods are diverse and dynamic, producing a variety of metabolites responsible for the fermentation processes, imparting characteristic organoleptic qualities and health-promoting traits, and maintaining microbiological safety of fermented foods. In this context, it is crucial to study these microbial communities to characterise fermented foods and the production processes involved. High Throughput Sequencing (HTS)-based methods such as metagenomics enable microbial community studies through amplicon and shotgun sequencing approaches. As the field constantly develops, sequencing technologies are becoming more accessible, affordable and accurate with a further shift from short read to long read sequencing being observed. Metagenomics is enjoying wide-spread application in fermented food studies and in recent years is also being employed in concert with synthetic biology techniques to help tackle problems with the large amounts of waste generated in the food sector. This review presents an introduction to current sequencing technologies and the benefits of their application in fermented foods.
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Affiliation(s)
- Meghana Srinivas
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- School of Microbiology, University College Cork, T12 CY82 Cork, Ireland
| | - Orla O’Sullivan
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, P61 C996 Cork, Ireland
| | - Paul D. Cotter
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, P61 C996 Cork, Ireland
| | - Douwe van Sinderen
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- School of Microbiology, University College Cork, T12 CY82 Cork, Ireland
| | - John G. Kenny
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, P61 C996 Cork, Ireland
- Correspondence:
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