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Bifidobacteria Strain Typing by Fourier Transform Infrared Spectroscopy

Fourier transform infrared (FTIR) spectroscopy, a technology traditionally used in chemistry to determine the molecular composition of a wide range of sample types, has gained growing interest in microbial typing. It is based on the different vibrational modes of the covalent bonds between atoms of...

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Autores principales: Deidda, Francesca, Bozzi Cionci, Nicole, Cordovana, Miriam, Campedelli, Ilenia, Fracchetti, Fabio, Di Gioia, Diana, Ambretti, Simone, Pane, Marco
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8473902/
https://www.ncbi.nlm.nih.gov/pubmed/34589064
http://dx.doi.org/10.3389/fmicb.2021.692975
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author Deidda, Francesca
Bozzi Cionci, Nicole
Cordovana, Miriam
Campedelli, Ilenia
Fracchetti, Fabio
Di Gioia, Diana
Ambretti, Simone
Pane, Marco
author_facet Deidda, Francesca
Bozzi Cionci, Nicole
Cordovana, Miriam
Campedelli, Ilenia
Fracchetti, Fabio
Di Gioia, Diana
Ambretti, Simone
Pane, Marco
author_sort Deidda, Francesca
collection PubMed
description Fourier transform infrared (FTIR) spectroscopy, a technology traditionally used in chemistry to determine the molecular composition of a wide range of sample types, has gained growing interest in microbial typing. It is based on the different vibrational modes of the covalent bonds between atoms of a given sample, as bacterial cells, induced by the absorption of infrared radiation. This technique has been largely used for the study of pathogenic species, especially in the clinical field, and has been proposed also for the typing at different subspecies levels. The high throughput, speed, low cost, and simplicity make FTIR spectroscopy an attractive technique also for industrial applications, in particular, for probiotics. The aim of this study was to compare FTIR spectroscopy with established genotyping methods, pulsed-field gel electrophoresis (PFGE), whole-genome sequencing (WGS), and multilocus sequence typing (MLST), in order to highlight the FTIR spectroscopy potential discriminatory power at strain level. Our study focused on bifidobacteria, an important group of intestinal commensals generally recognized as probiotics. For their properties in promoting and maintaining health, bifidobacteria are largely marketed by the pharmaceutical, food, and dairy industries. Strains belonging to Bifidobacterium longum subsp. longum and Bifidobacterium animalis subsp. lactis were taken into consideration together with some additional type strains. For B. longum subsp. longum, it was possible to discriminate the strains with all the methods used. Although two isolates were shown to be strictly phylogenetically related, constituting a unique cluster, based on PFGE, WGS, and MLST, no clustering was observed with FTIR. For B. animalis subsp. lactis group, PFGE, WGS, and MLST were non-discriminatory, and only one strain was easily distinguished. On the other hand, FTIR discriminated all the isolates one by one, and no clustering was observed. According to these results, FTIR analysis is not only equivalent to PFGE, WGS, and MLST, but also for some strains, in particular, for B. animalis subsp. lactis group, more informative, being able to differentiate strains not discernible with the other two methods based on phenotypic variations likely deriving from certain genetic changes. Fourier transform infrared spectroscopy has highlighted the possibility of using the cell surface as a kind of barcode making tracing strains possible, representing an important aspect in probiotic applications. Furthermore, this work constitutes the first investigation on bifidobacterial strain typing using FTIR spectroscopy.
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spelling pubmed-84739022021-09-28 Bifidobacteria Strain Typing by Fourier Transform Infrared Spectroscopy Deidda, Francesca Bozzi Cionci, Nicole Cordovana, Miriam Campedelli, Ilenia Fracchetti, Fabio Di Gioia, Diana Ambretti, Simone Pane, Marco Front Microbiol Microbiology Fourier transform infrared (FTIR) spectroscopy, a technology traditionally used in chemistry to determine the molecular composition of a wide range of sample types, has gained growing interest in microbial typing. It is based on the different vibrational modes of the covalent bonds between atoms of a given sample, as bacterial cells, induced by the absorption of infrared radiation. This technique has been largely used for the study of pathogenic species, especially in the clinical field, and has been proposed also for the typing at different subspecies levels. The high throughput, speed, low cost, and simplicity make FTIR spectroscopy an attractive technique also for industrial applications, in particular, for probiotics. The aim of this study was to compare FTIR spectroscopy with established genotyping methods, pulsed-field gel electrophoresis (PFGE), whole-genome sequencing (WGS), and multilocus sequence typing (MLST), in order to highlight the FTIR spectroscopy potential discriminatory power at strain level. Our study focused on bifidobacteria, an important group of intestinal commensals generally recognized as probiotics. For their properties in promoting and maintaining health, bifidobacteria are largely marketed by the pharmaceutical, food, and dairy industries. Strains belonging to Bifidobacterium longum subsp. longum and Bifidobacterium animalis subsp. lactis were taken into consideration together with some additional type strains. For B. longum subsp. longum, it was possible to discriminate the strains with all the methods used. Although two isolates were shown to be strictly phylogenetically related, constituting a unique cluster, based on PFGE, WGS, and MLST, no clustering was observed with FTIR. For B. animalis subsp. lactis group, PFGE, WGS, and MLST were non-discriminatory, and only one strain was easily distinguished. On the other hand, FTIR discriminated all the isolates one by one, and no clustering was observed. According to these results, FTIR analysis is not only equivalent to PFGE, WGS, and MLST, but also for some strains, in particular, for B. animalis subsp. lactis group, more informative, being able to differentiate strains not discernible with the other two methods based on phenotypic variations likely deriving from certain genetic changes. Fourier transform infrared spectroscopy has highlighted the possibility of using the cell surface as a kind of barcode making tracing strains possible, representing an important aspect in probiotic applications. Furthermore, this work constitutes the first investigation on bifidobacterial strain typing using FTIR spectroscopy. Frontiers Media S.A. 2021-09-13 /pmc/articles/PMC8473902/ /pubmed/34589064 http://dx.doi.org/10.3389/fmicb.2021.692975 Text en Copyright © 2021 Deidda, Bozzi Cionci, Cordovana, Campedelli, Fracchetti, Di Gioia, Ambretti and Pane. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Deidda, Francesca
Bozzi Cionci, Nicole
Cordovana, Miriam
Campedelli, Ilenia
Fracchetti, Fabio
Di Gioia, Diana
Ambretti, Simone
Pane, Marco
Bifidobacteria Strain Typing by Fourier Transform Infrared Spectroscopy
title Bifidobacteria Strain Typing by Fourier Transform Infrared Spectroscopy
title_full Bifidobacteria Strain Typing by Fourier Transform Infrared Spectroscopy
title_fullStr Bifidobacteria Strain Typing by Fourier Transform Infrared Spectroscopy
title_full_unstemmed Bifidobacteria Strain Typing by Fourier Transform Infrared Spectroscopy
title_short Bifidobacteria Strain Typing by Fourier Transform Infrared Spectroscopy
title_sort bifidobacteria strain typing by fourier transform infrared spectroscopy
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8473902/
https://www.ncbi.nlm.nih.gov/pubmed/34589064
http://dx.doi.org/10.3389/fmicb.2021.692975
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