Full-Length SSU rRNA Gene Sequencing Allows Species-Level Detection of Bacteria, Archaea, and Yeasts Present in Milk
Full-length SSU rRNA gene sequencing allows species-level identification of the microorganisms present in milk samples. Here, we used bulk-tank raw milk samples of two German dairies and detected, using this method, a great diversity of bacteria, archaea, and yeasts within the samples. Moreover, the...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-06-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/9/6/1251 |
| _version_ | 1797530791371079680 |
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| author | Isabel Abellan-Schneyder Annemarie Siebert Katharina Hofmann Mareike Wenning Klaus Neuhaus |
| author_facet | Isabel Abellan-Schneyder Annemarie Siebert Katharina Hofmann Mareike Wenning Klaus Neuhaus |
| author_sort | Isabel Abellan-Schneyder |
| collection | DOAJ |
| description | Full-length SSU rRNA gene sequencing allows species-level identification of the microorganisms present in milk samples. Here, we used bulk-tank raw milk samples of two German dairies and detected, using this method, a great diversity of bacteria, archaea, and yeasts within the samples. Moreover, the species-level classification was improved in comparison to short amplicon sequencing. Therefore, we anticipate that this approach might be useful for the detection of possible mastitis-causing species, as well as for the control of spoilage-associated microorganisms. In a proof of concept, we showed that we were able to identify several putative mastitis-causing or mastitis-associated species such as <i>Streptococcus</i><i>uberis</i>, <i>Streptococcus</i><i>agalactiae</i>, <i>Streptococcus</i><i>dysgalactiae</i>, <i>Escherichia</i><i>coli</i> and <i>Staphylococcus</i><i>aureus</i>, as well as several <i>Candida</i> species. Overall, the presented full-length approach for the sequencing of SSU rRNA is easy to conduct, able to be standardized, and allows the screening of microorganisms in labs with Illumina sequencing machines. |
| first_indexed | 2024-03-10T10:35:01Z |
| format | Article |
| id | doaj.art-41e27a6d3f8248e982ba986013dad2b7 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T10:35:01Z |
| publishDate | 2021-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-41e27a6d3f8248e982ba986013dad2b72023-11-21T23:21:32ZengMDPI AGMicroorganisms2076-26072021-06-0196125110.3390/microorganisms9061251Full-Length SSU rRNA Gene Sequencing Allows Species-Level Detection of Bacteria, Archaea, and Yeasts Present in MilkIsabel Abellan-Schneyder0Annemarie Siebert1Katharina Hofmann2Mareike Wenning3Klaus Neuhaus4Core Facility Microbiome, ZIEL—Institute for Food & Health, Technische Universität München, 85354 Freising, GermanyChair of Microbial Ecology, ZIEL—Institute for Food & Health, Technische Universität München, 85354 Freising, GermanyChair of Microbial Ecology, ZIEL—Institute for Food & Health, Technische Universität München, 85354 Freising, GermanyChair of Microbial Ecology, ZIEL—Institute for Food & Health, Technische Universität München, 85354 Freising, GermanyCore Facility Microbiome, ZIEL—Institute for Food & Health, Technische Universität München, 85354 Freising, GermanyFull-length SSU rRNA gene sequencing allows species-level identification of the microorganisms present in milk samples. Here, we used bulk-tank raw milk samples of two German dairies and detected, using this method, a great diversity of bacteria, archaea, and yeasts within the samples. Moreover, the species-level classification was improved in comparison to short amplicon sequencing. Therefore, we anticipate that this approach might be useful for the detection of possible mastitis-causing species, as well as for the control of spoilage-associated microorganisms. In a proof of concept, we showed that we were able to identify several putative mastitis-causing or mastitis-associated species such as <i>Streptococcus</i><i>uberis</i>, <i>Streptococcus</i><i>agalactiae</i>, <i>Streptococcus</i><i>dysgalactiae</i>, <i>Escherichia</i><i>coli</i> and <i>Staphylococcus</i><i>aureus</i>, as well as several <i>Candida</i> species. Overall, the presented full-length approach for the sequencing of SSU rRNA is easy to conduct, able to be standardized, and allows the screening of microorganisms in labs with Illumina sequencing machines.https://www.mdpi.com/2076-2607/9/6/1251full-length sequencingSSU rRNA gene sequencingmilk microbiotaLoopSeq |
| spellingShingle | Isabel Abellan-Schneyder Annemarie Siebert Katharina Hofmann Mareike Wenning Klaus Neuhaus Full-Length SSU rRNA Gene Sequencing Allows Species-Level Detection of Bacteria, Archaea, and Yeasts Present in Milk Microorganisms full-length sequencing SSU rRNA gene sequencing milk microbiota LoopSeq |
| title | Full-Length SSU rRNA Gene Sequencing Allows Species-Level Detection of Bacteria, Archaea, and Yeasts Present in Milk |
| title_full | Full-Length SSU rRNA Gene Sequencing Allows Species-Level Detection of Bacteria, Archaea, and Yeasts Present in Milk |
| title_fullStr | Full-Length SSU rRNA Gene Sequencing Allows Species-Level Detection of Bacteria, Archaea, and Yeasts Present in Milk |
| title_full_unstemmed | Full-Length SSU rRNA Gene Sequencing Allows Species-Level Detection of Bacteria, Archaea, and Yeasts Present in Milk |
| title_short | Full-Length SSU rRNA Gene Sequencing Allows Species-Level Detection of Bacteria, Archaea, and Yeasts Present in Milk |
| title_sort | full length ssu rrna gene sequencing allows species level detection of bacteria archaea and yeasts present in milk |
| topic | full-length sequencing SSU rRNA gene sequencing milk microbiota LoopSeq |
| url | https://www.mdpi.com/2076-2607/9/6/1251 |
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