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A genome guided evaluation of probiotic bacteria from the Lactobacillus and Bifidobacterium genera / LAURA BAKER

Swansea University Author: LAURA BAKER

  • E-Thesis – open access under embargo until: 18th October 2024

DOI (Published version): 10.23889/SUthesis.61586

Abstract

Manipulating the microbiota has the potential to mitigate disease. Probiotics are currently a popular approach used to promote gut health. However, beneficial attributes are often strain-specific; therefore, an in-depth classification is valuable when evaluating such products. Here, the draft genome...

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Published: Swansea 2022
Institution: Swansea University
Degree level: Doctoral
Degree name: Ph.D
Supervisor: Facey, Paul D.
URI: https://cronfa.swan.ac.uk/Record/cronfa61586
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spelling 2022-10-19T10:07:26.0976602 v2 61586 2022-10-19 A genome guided evaluation of probiotic bacteria from the Lactobacillus and Bifidobacterium genera 5e24289430539563d9af4365f42da501 LAURA BAKER LAURA BAKER true false 2022-10-19 Manipulating the microbiota has the potential to mitigate disease. Probiotics are currently a popular approach used to promote gut health. However, beneficial attributes are often strain-specific; therefore, an in-depth classification is valuable when evaluating such products. Here, the draft genomes of 16 bacteria (from the Lactobacillus and Bifidobacterium genera) are presented (referred to as CUL isolates), including: L.acidophilus (CUL21, CUL60), L.gasseri (CUL09), L.helveticus (CUL76), L.salivarius (CUL61), L.plantarum (CUL66, CUL66N), L.paracasei (CUL37, CUL07, CUL08), L.casei (CUL06), L.rhamnosus (CUL63), L.fermentum (CUL40, CUL67), B.bifidum (CUL20) and B.animalis subsp. lactis (CUL34). Furthermore, multi-locus sequence analysis revealed that CUL strains are novel entries into GenBank. Genomes were mined for beneficial and deleterious features of probiotic bacteria. As such, antibiotic resistance genes and phenotypic antibiotic resistance (ABR) profiles were established. Generally, most phenotypic resistance was linked to recognized resistance profiles e.g., kanamycin and chloramphenicol (in lactobacilli) and tetracycline (in bifidobacteria). However, ampicillin resistance was common, although a genomic basis was not established. Indeed, the correlation between genotype and phenotype was often low. In addition, when challenged with a combination of antibiotics and bile, a phenotypic shift from antibiotic-resistant to sensitive typically occurred. Interestingly, L.helveticus CUL76 developed enhanced resistance against chloramphenicol and vancomycin. Beneficial traits, including adherence, bile tolerance, and host interaction properties were identified in all CUL strains. L.helveticus CUL76 putatively encoded five bacteriocins, offering scope for future antimicrobial studies. Bile Salt Hydrolase (genes with bile tolerance and cholesterol reduction capabilities) were identified in several CUL species. L.plantarum CUL66N expressed bsh genes when challenged with bile and could reduce the bile acid pool (including free cholesterol) in vitro, indicating a bsh mediated, cholesterol-lowering capability of CUL66N.Here, the first in-depth genomic analysis of CUL strains is presented, allowing future research to continue using a genome-guided approach to evaluate health-promoting attributes of CUL bacteria. E-Thesis Swansea Probiotics, Microbiology, Genomics, Bioprospecting, Lactobacillus, Bifidobacterium, Antibiotic Resistance, Bile Tolerance, Bile Salt Hydrolase 18 10 2022 2022-10-18 10.23889/SUthesis.61586 COLLEGE NANME COLLEGE CODE Swansea University Facey, Paul D. Doctoral Ph.D KESS II 2022-10-19T10:07:26.0976602 2022-10-19T09:38:16.2767935 Faculty of Medicine, Health and Life Sciences Swansea University Medical School - Medicine LAURA BAKER 1 Under embargo Under embargo 2022-10-19T09:50:46.5457030 Output 9125093 application/pdf E-Thesis – open access true 2024-10-18T00:00:00.0000000 Copyright: The author, Laura Baker, 2022. true eng
title A genome guided evaluation of probiotic bacteria from the Lactobacillus and Bifidobacterium genera
spellingShingle A genome guided evaluation of probiotic bacteria from the Lactobacillus and Bifidobacterium genera
LAURA BAKER
title_short A genome guided evaluation of probiotic bacteria from the Lactobacillus and Bifidobacterium genera
title_full A genome guided evaluation of probiotic bacteria from the Lactobacillus and Bifidobacterium genera
title_fullStr A genome guided evaluation of probiotic bacteria from the Lactobacillus and Bifidobacterium genera
title_full_unstemmed A genome guided evaluation of probiotic bacteria from the Lactobacillus and Bifidobacterium genera
title_sort A genome guided evaluation of probiotic bacteria from the Lactobacillus and Bifidobacterium genera
author_id_str_mv 5e24289430539563d9af4365f42da501
author_id_fullname_str_mv 5e24289430539563d9af4365f42da501_***_LAURA BAKER
author LAURA BAKER
author2 LAURA BAKER
format E-Thesis
publishDate 2022
institution Swansea University
doi_str_mv 10.23889/SUthesis.61586
college_str Faculty of Medicine, Health and Life Sciences
hierarchytype
hierarchy_top_id facultyofmedicinehealthandlifesciences
hierarchy_top_title Faculty of Medicine, Health and Life Sciences
hierarchy_parent_id facultyofmedicinehealthandlifesciences
hierarchy_parent_title Faculty of Medicine, Health and Life Sciences
department_str Swansea University Medical School - Medicine{{{_:::_}}}Faculty of Medicine, Health and Life Sciences{{{_:::_}}}Swansea University Medical School - Medicine
document_store_str 0
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description Manipulating the microbiota has the potential to mitigate disease. Probiotics are currently a popular approach used to promote gut health. However, beneficial attributes are often strain-specific; therefore, an in-depth classification is valuable when evaluating such products. Here, the draft genomes of 16 bacteria (from the Lactobacillus and Bifidobacterium genera) are presented (referred to as CUL isolates), including: L.acidophilus (CUL21, CUL60), L.gasseri (CUL09), L.helveticus (CUL76), L.salivarius (CUL61), L.plantarum (CUL66, CUL66N), L.paracasei (CUL37, CUL07, CUL08), L.casei (CUL06), L.rhamnosus (CUL63), L.fermentum (CUL40, CUL67), B.bifidum (CUL20) and B.animalis subsp. lactis (CUL34). Furthermore, multi-locus sequence analysis revealed that CUL strains are novel entries into GenBank. Genomes were mined for beneficial and deleterious features of probiotic bacteria. As such, antibiotic resistance genes and phenotypic antibiotic resistance (ABR) profiles were established. Generally, most phenotypic resistance was linked to recognized resistance profiles e.g., kanamycin and chloramphenicol (in lactobacilli) and tetracycline (in bifidobacteria). However, ampicillin resistance was common, although a genomic basis was not established. Indeed, the correlation between genotype and phenotype was often low. In addition, when challenged with a combination of antibiotics and bile, a phenotypic shift from antibiotic-resistant to sensitive typically occurred. Interestingly, L.helveticus CUL76 developed enhanced resistance against chloramphenicol and vancomycin. Beneficial traits, including adherence, bile tolerance, and host interaction properties were identified in all CUL strains. L.helveticus CUL76 putatively encoded five bacteriocins, offering scope for future antimicrobial studies. Bile Salt Hydrolase (genes with bile tolerance and cholesterol reduction capabilities) were identified in several CUL species. L.plantarum CUL66N expressed bsh genes when challenged with bile and could reduce the bile acid pool (including free cholesterol) in vitro, indicating a bsh mediated, cholesterol-lowering capability of CUL66N.Here, the first in-depth genomic analysis of CUL strains is presented, allowing future research to continue using a genome-guided approach to evaluate health-promoting attributes of CUL bacteria.
published_date 2022-10-18T04:20:30Z
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score 11.013148

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