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Aziz G, Zaidi A, Sullivan DJO'. Insights from metagenome-assembled genomes on the genetic stability and safety of over-the-counter probiotic products. Curr Genet 2023; 69:213-234. [PMID: 37237157 DOI: 10.1007/s00294-023-01271-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 04/04/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023]
Abstract
The demand for and acceptance of probiotics is determined by their quality and safety. Illumina NGS sequencing and analytics were used to examine eight marketed probiotics. Up to the species level, sequenced DNA was taxonomically identified, and relative abundances were determined using Kaiju. The genomes were constructed using GTDB and validated through PATRICK and TYGS. A FastTree 2 phylogenetic tree was constructed using several type strain sequences from relevant species. Bacteriocin and ribosomally synthesized polypeptide (RiPP) genes were discovered, and a safety check was performed to test for toxins, antibiotic resistance, and genetic drift genes. Except for two products with unclaimed species, the labeling was taxonomically correct. In three product formulations, Lactobacillus acidophilus, Limosilactobacillus reuteri, Lacticaseibacillus paracasei, and Bifidobacterium animalis exhibited two to three genomic alterations, while Streptococcus equinus was found in one. TYGS and GDTB discovered E. faecium and L. paracasei in distinctly different ways. All the bacteria tested had the genetic repertoire to tolerate GIT transit, although some exhibited antibiotic resistance, and one strain had two virulence genes. Except for Bifidobacterium strains, the others revealed a variety of bacteriocins and ribosomally synthesized polypeptides (RiPP), 92% of which were unique and non-homologous to known ones. Plasmids and mobile genetic elements are present in strains of L. reuteri (NPLps01.et_L.r and NPLps02.uf_L.r), Lactobacillus delbrueckii (NPLps01.et_L.d), Streptococcus thermophilus (NPLps06.ab_S.t), and E. faecium (NPLps07.nf_E.f). Our findings support the use of metagenomics to build better and efficient production and post-production practices for probiotic quality and safety assessment.
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Affiliation(s)
- Ghazal Aziz
- National Probiotic Laboratory, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Punjab, 38000, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, 45650, Islamabad (ICT), Pakistan
- Department of Food Science and Nutrition, Center for Microbial and Plant Genomics, University of Minnesota, 1500 Gortner Ave, St. Paul, MN, 55108, USA
| | - Arsalan Zaidi
- National Probiotic Laboratory, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Punjab, 38000, Faisalabad, Pakistan.
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, 45650, Islamabad (ICT), Pakistan.
| | - Daniel J O ' Sullivan
- Department of Food Science and Nutrition, Center for Microbial and Plant Genomics, University of Minnesota, 1500 Gortner Ave, St. Paul, MN, 55108, USA
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Webberley TS, Bevan RJ, Kerry-Smith J, Dally J, Michael DR, Thomas S, Rees M, Morgan JE, Marchesi JR, Good MA, Plummer SF, Wang D, Hughes TR. Assessment of Lab4P Probiotic Effects on Cognition in 3xTg-AD Alzheimer's Disease Model Mice and the SH-SY5Y Neuronal Cell Line. Int J Mol Sci 2023; 24:ijms24054683. [PMID: 36902113 PMCID: PMC10003662 DOI: 10.3390/ijms24054683] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 02/20/2023] [Accepted: 02/23/2023] [Indexed: 03/04/2023] Open
Abstract
Aging and metabolic syndrome are associated with neurodegenerative pathologies including Alzheimer's disease (AD) and there is growing interest in the prophylactic potential of probiotic bacteria in this area. In this study, we assessed the neuroprotective potential of the Lab4P probiotic consortium in both age and metabolically challenged 3xTg-AD mice and in human SH-SY5Y cell culture models of neurodegeneration. In mice, supplementation prevented disease-associated deteriorations in novel object recognition, hippocampal neurone spine density (particularly thin spines) and mRNA expression in hippocampal tissue implying an anti-inflammatory impact of the probiotic, more notably in the metabolically challenged setting. In differentiated human SH-SY5Y neurones challenged with β-Amyloid, probiotic metabolites elicited a neuroprotective capability. Taken together, the results highlight Lab4P as a potential neuroprotective agent and provide compelling support for additional studies in animal models of other neurodegenerative conditions and human studies.
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Affiliation(s)
- Thomas S. Webberley
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XW, UK
- Cultech Limited, Unit 2 Christchurch Road, Baglan Industrial Park, Port Talbot SA12 7BZ, UK
- Correspondence:
| | - Ryan J. Bevan
- UK Dementia Research Institute, Cardiff University, Maindy Road, Cardiff CF24 4HQ, UK
- School of Optometry and Vision Sciences, Cardiff University, Maindy Road, Cardiff CF10 4HQ, UK
| | - Joshua Kerry-Smith
- Cultech Limited, Unit 2 Christchurch Road, Baglan Industrial Park, Port Talbot SA12 7BZ, UK
| | - Jordanna Dally
- Cultech Limited, Unit 2 Christchurch Road, Baglan Industrial Park, Port Talbot SA12 7BZ, UK
| | - Daryn R. Michael
- Cultech Limited, Unit 2 Christchurch Road, Baglan Industrial Park, Port Talbot SA12 7BZ, UK
| | - Sophie Thomas
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XW, UK
| | - Meg Rees
- Cultech Limited, Unit 2 Christchurch Road, Baglan Industrial Park, Port Talbot SA12 7BZ, UK
| | - James E. Morgan
- School of Optometry and Vision Sciences, Cardiff University, Maindy Road, Cardiff CF10 4HQ, UK
| | - Julian R. Marchesi
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Mark A. Good
- School of Psychology, Cardiff University, Cardiff CF10 3AT, UK
| | - Sue F. Plummer
- Cultech Limited, Unit 2 Christchurch Road, Baglan Industrial Park, Port Talbot SA12 7BZ, UK
| | - Duolao Wang
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Timothy R. Hughes
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XW, UK
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Webberley TS, Masetti G, Bevan RJ, Kerry-Smith J, Jack AA, Michael DR, Thomas S, Glymenaki M, Li J, McDonald JAK, John D, Morgan JE, Marchesi JR, Good MA, Plummer SF, Hughes TR. The Impact of Probiotic Supplementation on Cognitive, Pathological and Metabolic Markers in a Transgenic Mouse Model of Alzheimer's Disease. Front Neurosci 2022; 16:843105. [PMID: 35685773 PMCID: PMC9172594 DOI: 10.3389/fnins.2022.843105] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/23/2022] [Indexed: 12/12/2022] Open
Abstract
Brain degenerative disorders such as Alzheimer’s disease (AD) can be exacerbated by aberrant metabolism. Supplementation with probiotic bacteria is emerging as a promising preventative strategy for both neurodegeneration and metabolic syndrome. In this study, we assess the impact of the Lab4b probiotic consortium on (i) cognitive and pathological markers of AD progression and (ii) metabolic status in 3xTg-AD mice subjected to metabolic challenge with a high fat diet. The group receiving the probiotic performed better in the novel object recognition test and displayed higher hippocampal neuronal spine density than the control group at the end of the 12 weeks intervention period. These changes were accompanied by differences in localised (brain) and systemic anti-inflammatory responses that favoured the Probiotic group together with the prevention of diet induced weight gain and hypercholesterolaemia and the modulation of liver function. Compositional differences between the faecal microbiotas of the study groups included a lower Firmicutes:Bacteroidetes ratio and less numbers of viable yeast in the Probiotic group compared to the Control. The results illustrate the potential of the Lab4b probiotic as a neuroprotective agent and encourage further studies with human participants.
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Affiliation(s)
- Thomas S Webberley
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom.,Cultech Ltd., Port Talbot, United Kingdom
| | | | - Ryan J Bevan
- UK Dementia Research Institute, Cardiff University, Cardiff, United Kingdom.,School of Optometry and Vision Sciences, Cardiff University, Cardiff, United Kingdom
| | | | | | | | | | - Maria Glymenaki
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Jia Li
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Julie A K McDonald
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | | | - James E Morgan
- School of Optometry and Vision Sciences, Cardiff University, Cardiff, United Kingdom
| | - Julian R Marchesi
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Mark A Good
- School of Psychology, Cardiff University, Cardiff, United Kingdom
| | | | - Timothy R Hughes
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom.,UK Dementia Research Institute, Cardiff University, Cardiff, United Kingdom
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Webberley TS, Masetti G, Baker LM, Dally J, Hughes TR, Marchesi JR, Jack AA, Plummer SF, Ramanathan G, Facey PD, Michael DR. The Impact of Lab4 Probiotic Supplementation in a 90-Day Study in Wistar Rats. Front Nutr 2021; 8:778289. [PMID: 34901123 PMCID: PMC8656110 DOI: 10.3389/fnut.2021.778289] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/02/2021] [Indexed: 12/11/2022] Open
Abstract
The anti-inflammatory and cholesterol lowering capabilities of probiotic bacteria highlight them as potential prophylactics against chronic inflammatory diseases, particularly cardiovascular disease. Previous studies in silico, in vitro, and in vivo suggest that the Lab4 probiotic consortium may harbour such capabilities and in the current study, we assessed plasma levels of cytokines/chemokines, short chain fatty acids and lipids and faecal levels of bile acids in a subpopulation of healthy Wistar rats included in 90-day repeat dose oral toxicity study. In the rats receiving Lab4, circulating levels of pro-inflammatory interleukin-6, tumour necrosis factor-α and keratinocyte chemoattractant/growth regulated oncogene were significantly lower compared to the control group demonstrating a systemic anti-inflammatory effect. These changes occurred alongside significant reductions in plasma low density lipoprotein cholesterol and increases in faecal bile acid excretion implying the ability to lower circulating cholesterol via the deconjugation of intestinal bile acids. Correlative analysis identified significant associations between plasma tumour necrosis factor-α and the plasma total cholesterol:high density lipoprotein cholesterol ratio and faecal levels of bifidobacteria in the Lab4 rats. Together, these data highlight Lab4 supplementation as a holistic approach to CVD prevention and encourages further studies in humans.
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Affiliation(s)
| | | | - Laura M Baker
- Swansea University Medical School, Swansea University, Swansea, United Kingdom
| | | | - Timothy R Hughes
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Julian R Marchesi
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | | | | | - Guru Ramanathan
- Pharmacology based Clinical Trials, Pennington Biomedical Research Centre, Baton Rouge, LA, United States
| | - Paul D Facey
- Swansea University Medical School, Swansea University, Swansea, United Kingdom
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