Full-Length SSU rRNA Gene Sequencing Allows Species-Level Detection of Bacteria, Archaea, and Yeasts Present in Milk

Microorganisms

卷:9

Annemarie Siebert¹  Katharina Hofmann¹  Mareike Wenning¹  Klaus Neuhaus²  Isabel Abellan-Schneyder² 

[1] Chair of Microbial Ecology, ZIEL—Institute for Food & Health, Technische Universität München, 85354 Freising, Germany;

[2] Core Facility Microbiome, ZIEL—Institute for Food & Health, Technische Universität München, 85354 Freising, Germany;

关键词: full-length sequencing;    SSU rRNA gene sequencing;    milk microbiota;    LoopSeq;   

DOI  :  10.3390/microorganisms9061251

来源: DOAJ

【 摘 要 】

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 Streptococcusuberis, Streptococcusagalactiae, Streptococcusdysgalactiae, Escherichiacoli and Staphylococcusaureus, as well as several Candida 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.

【 授权许可】

Unknown