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

Abstract

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.

Intermittent Oxygen Supply Facilitates Codegradation of Trichloroethene and Toluene by Anaerobic Consortia

“…Bar-coded 16S rRNA gene amplicon sequences facilitated short-read sequencing on an Illumina NovaSeq 6000 sequencer (Illumina, San Diego, CA, U.S.A.). The full-length 16S rRNA genes were then reconstructed from short-read sequences by using the Loop Genomics data analysis pipeline . The amplicon sequence variant (ASV)-based pipeline was used to analyze the sequences (Section S1).…”

“…The full-length 16S rRNA genes were then reconstructed from short-read sequences by using the Loop Genomics data analysis pipeline. 30 The amplicon sequence variant (ASV)-based pipeline was used to analyze the sequences (Section S1). The full-length 16S rRNA gene sequences used in this study have been deposited in the European Sequence Read Archive: ERA 20758382.…”

Characterizing the Effect of Campylobacter jejuni Challenge on Growth Performance, Cecal Microbiota, and Cecal Short-Chain Fatty Acid Concentrations in Broilers

“…Following the DNA extraction, all nine variable regions of the 16S rRNA gene were sequenced (regions V1 to V9), as described earlier [30], at Loop Genomics (San Diego, CA, USA). The whole 16S rRNA gene was synthetically reconstructed from a series of standard Illumina PE150 reads, which were assembled to rebuild the whole 16S rRNA gene, as established previously [26].…”