Combining Culture-Dependent and Culture-Independent Methods: New Methodology Insight on the <i>Vibrio</i> Community of <i>Ruditapes philippinarum</i>
Vibrios represent a natural contaminant of seafood products. <i>V. alginolyticus</i>, <i>V. cholerae</i>, <i>V. parahaemolyticus</i> and <i>V. vulnificus</i> are the most hazardous species to human health. Given the worldwide consumption of mollusc pro...
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MDPI AG
2021-06-01
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| Series: | Foods |
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| Online Access: | https://www.mdpi.com/2304-8158/10/6/1271 |
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| author | Angela Zampieri Massimiliano Babbucci Lisa Carraro Massimo Milan Luca Fasolato Barbara Cardazzo |
| author_facet | Angela Zampieri Massimiliano Babbucci Lisa Carraro Massimo Milan Luca Fasolato Barbara Cardazzo |
| author_sort | Angela Zampieri |
| collection | DOAJ |
| description | Vibrios represent a natural contaminant of seafood products. <i>V. alginolyticus</i>, <i>V. cholerae</i>, <i>V. parahaemolyticus</i> and <i>V. vulnificus</i> are the most hazardous species to human health. Given the worldwide consumption of mollusc products, reliable detection of <i>Vibrio</i> species is recommended to prevent human vibriosis. In this study, culture-dependent and -independent methods were compared and integrated to implement knowledge of the Manila clam <i>Vibrio</i> community composition. Here, 16S and <i>rec</i>A<i>-pyr</i>H metabarcoding were applied to compare the microbial communities of homogenate clam samples (culture-independent method) and their culture-derived samples plated on three different media (culture-dependent method). In addition, a subset of plated clam samples was investigated using shotgun metagenomics. Homogenate metabarcoding characterized the most abundant taxa (16S) and <i>Vibrio</i> species (<i>rec</i>A<i>-pyr</i>H). Culture-dependent metabarcoding detected the cultivable taxa, including rare species. Moreover, marine agar medium was found to be a useful substrate for the recovery of several <i>Vibrio</i> species, including the main human pathogenic ones. The culture-dependent shotgun metagenomics detected all the main human pathogenic <i>Vibrio</i> species and a higher number of vibrios with respect to the <i>rec</i>A<i>-pyr</i>H metabarcoding. The study revealed that integration of culture-dependent and culture-independent methods might be a valid approach for the characterization of <i>Vibrio</i> biodiversity. |
| first_indexed | 2024-03-10T10:45:05Z |
| format | Article |
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| issn | 2304-8158 |
| language | English |
| last_indexed | 2024-03-10T10:45:05Z |
| publishDate | 2021-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Foods |
| spelling | doaj.art-9ba8e756254e4282bf4b8549b80c50332023-11-21T22:38:26ZengMDPI AGFoods2304-81582021-06-01106127110.3390/foods10061271Combining Culture-Dependent and Culture-Independent Methods: New Methodology Insight on the <i>Vibrio</i> Community of <i>Ruditapes philippinarum</i>Angela Zampieri0Massimiliano Babbucci1Lisa Carraro2Massimo Milan3Luca Fasolato4Barbara Cardazzo5Department of Comparative Biomedicine and Food Science, University of Padova, Agripolis, Viale dell’Università 16, 35020 Legnaro, ItalyDepartment of Comparative Biomedicine and Food Science, University of Padova, Agripolis, Viale dell’Università 16, 35020 Legnaro, ItalyDepartment of Comparative Biomedicine and Food Science, University of Padova, Agripolis, Viale dell’Università 16, 35020 Legnaro, ItalyDepartment of Comparative Biomedicine and Food Science, University of Padova, Agripolis, Viale dell’Università 16, 35020 Legnaro, ItalyDepartment of Comparative Biomedicine and Food Science, University of Padova, Agripolis, Viale dell’Università 16, 35020 Legnaro, ItalyDepartment of Comparative Biomedicine and Food Science, University of Padova, Agripolis, Viale dell’Università 16, 35020 Legnaro, ItalyVibrios represent a natural contaminant of seafood products. <i>V. alginolyticus</i>, <i>V. cholerae</i>, <i>V. parahaemolyticus</i> and <i>V. vulnificus</i> are the most hazardous species to human health. Given the worldwide consumption of mollusc products, reliable detection of <i>Vibrio</i> species is recommended to prevent human vibriosis. In this study, culture-dependent and -independent methods were compared and integrated to implement knowledge of the Manila clam <i>Vibrio</i> community composition. Here, 16S and <i>rec</i>A<i>-pyr</i>H metabarcoding were applied to compare the microbial communities of homogenate clam samples (culture-independent method) and their culture-derived samples plated on three different media (culture-dependent method). In addition, a subset of plated clam samples was investigated using shotgun metagenomics. Homogenate metabarcoding characterized the most abundant taxa (16S) and <i>Vibrio</i> species (<i>rec</i>A<i>-pyr</i>H). Culture-dependent metabarcoding detected the cultivable taxa, including rare species. Moreover, marine agar medium was found to be a useful substrate for the recovery of several <i>Vibrio</i> species, including the main human pathogenic ones. The culture-dependent shotgun metagenomics detected all the main human pathogenic <i>Vibrio</i> species and a higher number of vibrios with respect to the <i>rec</i>A<i>-pyr</i>H metabarcoding. The study revealed that integration of culture-dependent and culture-independent methods might be a valid approach for the characterization of <i>Vibrio</i> biodiversity.https://www.mdpi.com/2304-8158/10/6/1271culture-dependent and -independent methodsmetabarcodingshotgun metagenomics<i>Ruditapes philippinarum</i>microbiota<i>Vibrio</i> spp. |
| spellingShingle | Angela Zampieri Massimiliano Babbucci Lisa Carraro Massimo Milan Luca Fasolato Barbara Cardazzo Combining Culture-Dependent and Culture-Independent Methods: New Methodology Insight on the <i>Vibrio</i> Community of <i>Ruditapes philippinarum</i> Foods culture-dependent and -independent methods metabarcoding shotgun metagenomics <i>Ruditapes philippinarum</i> microbiota <i>Vibrio</i> spp. |
| title | Combining Culture-Dependent and Culture-Independent Methods: New Methodology Insight on the <i>Vibrio</i> Community of <i>Ruditapes philippinarum</i> |
| title_full | Combining Culture-Dependent and Culture-Independent Methods: New Methodology Insight on the <i>Vibrio</i> Community of <i>Ruditapes philippinarum</i> |
| title_fullStr | Combining Culture-Dependent and Culture-Independent Methods: New Methodology Insight on the <i>Vibrio</i> Community of <i>Ruditapes philippinarum</i> |
| title_full_unstemmed | Combining Culture-Dependent and Culture-Independent Methods: New Methodology Insight on the <i>Vibrio</i> Community of <i>Ruditapes philippinarum</i> |
| title_short | Combining Culture-Dependent and Culture-Independent Methods: New Methodology Insight on the <i>Vibrio</i> Community of <i>Ruditapes philippinarum</i> |
| title_sort | combining culture dependent and culture independent methods new methodology insight on the i vibrio i community of i ruditapes philippinarum i |
| topic | culture-dependent and -independent methods metabarcoding shotgun metagenomics <i>Ruditapes philippinarum</i> microbiota <i>Vibrio</i> spp. |
| url | https://www.mdpi.com/2304-8158/10/6/1271 |
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