A high level of variation in microflora can be observed in profiles of lactic acid bacteria (LAB) from sourdoughs. Here, we present draft genome sequences of Lactobacillus reuteri E81, L. reuteri LR5A, L. rhamnosus LR2, L. plantarum PFC-311, and the novel Lactobacillus sp.
ABSTRACT
A high level of variation in microflora can be observed in profiles of lactic acid bacteria (LAB) from sourdoughs. Here, we present draft genome sequences of Lactobacillus reuteri E81, L. reuteri LR5A, L. rhamnosus LR2, L. plantarum PFC-311, and the novel Lactobacillus sp. strain PFC-70, isolated from traditional Turkish backslopped wheat sourdoughs.
GENOME ANNOUNCEMENT
Sourdough is a mixture of flour and water that is fermented mainly with naturally occurring lactic acid bacteria (LAB), although yeasts also contribute to this fermentation process (1, 2). The addition of sourdough to bread dough can improve its technological properties, enhance nutritional and sensory properties of the bread, and increase the shelf life of the bread (3, 4). These functional roles of sourdough mainly originate from the metabolism of LAB species occurring during fermentation that include their proteolytic activity (5), their formation of volatile antibacterial and antifungal compounds (6), and their exopolysaccharide (EPS) production characteristics (7). So far, several LAB species were reported to be present in sourdoughs from different origins, with a high level of diversity depending on cultural and geographical identities (8, 9). Among LAB strains, Lactobacillus species, especially heterofermentative ones, dominate the sourdough environment (10). L. reuteri and L. plantarum strains are among the well-known sourdough LAB species (11–13).
This study reports the draft genome sequences of L. reuteri E81, L. reuteri LR5A, L. rhamnosus LR2, L. plantarum PFC-311, and the novel Lactobacillus sp. strain PFC-70, isolated from traditional Turkish backslopped wheat sourdoughs. L. reuteri E81, L. reuteri LR5A, and L. rhamnosus LR2 were isolated from traditional sourdoughs. L. plantarum PFC-311 and Lactobacillus sp. strain PFC-70 were isolated from traditional sourdoughs prepared for tarhana production. All sourdoughs were collected at their final fermentation stage. The isolation and identification of five distinct strains were performed as described previously (9) and subjected to sequencing.
DNA libraries were prepared with an Illumina Nextera XT DNA preparation kit and sequenced on the Illumina MiSeq platform with the Illumina MiSeq reagent kit v3 (2 × 300 bp, 600 cycles). CLC Genomics Workbench (v 10.0.2) was used to trim sequence files using quality scores and then de novo assemble them. After removing contigs <1,000 bp, the draft assemblies were annotated using both the Rapid Annotations using Subsystems Technology (RAST) server and the NCBI Prokaryotic Genome Annotation Pipeline. The summary statistics for the assembled genomes are presented in Table 1.
TABLE 1.
Draft genome statistics of 5 bacterial strains isolated from traditional Turkish sourdough
| Isolate | GenBank assembly no. |
No. of contigs |
Assembly size (bp) |
N50 (bp) |
G+C content (%) |
Coverage (×) |
No. of coding regions |
GenBank accession no. |
|---|---|---|---|---|---|---|---|---|
| L. reuteri E81 | GCA_003046135.1 | 55 | 1,987,461 | 39,453 | 38.6 | 463 | 1,977 | PZQO00000000 |
| L. reuteri LR5A | GCA_003046055.1 | 60 | 1,986,306 | 67,178 | 38.6 | 90 | 1,975 | PZQN00000000 |
| L. rhamnosus LR2 | GCA_003046115.1 | 39 | 2,931,997 | 121,085 | 46.7 | 38 | 2,932 | PZQM00000000 |
| Lactobacillus sp. PFC-70 | GCA_003046095.1 | 71 | 2,592,913 | 72,018 | 51.8 | 90 | 2,354 | PZQL00000000 |
| L. plantarum PFC-311 | GCA_003046075.1 | 87 | 3,323,213 | 73,995 | 44.3 | 83 | 3,188 | PZQK00000000 |
The average read length was 223 bp (±20 bp) with total read counts of 3,306,384 bp for L. reuteri E81 and average read counts of 684,706 bp (±232,675 bp) for the remaining isolates, which were sequenced in a separate analysis. The calculated genome size, GC content, and number of coding regions (based on RAST) for each of the assemblies are consistent with the expected results for the taxonomic classifications of the closest neighbors in the RAST database. Preliminary analysis of the assemblies revealed several bacteriocins identified by BAGEL4 (14). L. reuteri E81 and LR5A were both found to contain a putative enterolysin-A, L. rhamnosus LR2 had a carnocin_CP52, and L. plantarum PFC-311 had plantaricin-A, -E, -F, –J, -K, and -N. The draft genomes for these LAB are key to providing a better understanding of the complex diversity of strains associated with fermented sourdough.
Accession number(s).
The genome sequences of all 5 isolates have been deposited at DDBJ/ENA/GenBank under the accession numbers provided in Table 1.
ACKNOWLEDGMENT
This study was financially supported by TÜBİTAK with the grant numbers 116O523 and 116O525.
Footnotes
Citation Dertli E, Skory CD, Şimşek Ö. 2018. Genome sequences of five Lactobacillus sp. isolates from traditional Turkish sourdough. Genome Announc 6:e00616-18. https://doi.org/10.1128/genomeA.00616-18.
REFERENCES
- 1.De Vuyst L, Van Kerrebroeck S, Harth H, Huys G, Daniel H-M, Weckx S. 2014. Microbial ecology of sourdough fermentations: diverse or uniform? Food Microbiol 37:11–29. doi: 10.1016/j.fm.2013.06.002. [DOI] [PubMed] [Google Scholar]
- 2.Rehman S, Paterson A, Piggott JR. 2006. Flavour in sourdough breads: a review. Trends Food Sci Technol 17:557–566. doi: 10.1016/j.tifs.2006.03.006. [DOI] [Google Scholar]
- 3.Arendt EK, Ryan LAM, Dal Bello F. 2007. Impact of sourdough on the texture of bread. Food Microbiol 24:165–174. doi: 10.1016/j.fm.2006.07.011. [DOI] [PubMed] [Google Scholar]
- 4.Hammes W, Gänzle M. 1997. Sourdough breads and related products, p 199–216. In Wood BJB. (ed), Microbiology of fermented foods. Springer, Boston, MA. [Google Scholar]
- 5.Gobbetti M, Simonetti MS, Corsetti A, Santinelli F, Rossi J, Damiani P. 1995. Volatile compound and organic acid productions by mixed wheat sour dough starters: influence of fermentation parameters and dynamics during baking. Food Microbiol 12:497–507. doi: 10.1016/S0740-0020(95)80134-0. [DOI] [Google Scholar]
- 6.Corsetti A, Settanni L. 2007. Lactobacilli in sourdough fermentation. Food Res Int 40:539–558. doi: 10.1016/j.foodres.2006.11.001. [DOI] [Google Scholar]
- 7.Galle S, Schwab C, Arendt EK, Gänzle M. 2011. Structural and rheological characterisation of heteropolysaccharides produced by lactic acid bacteria in wheat and sorghum sourdough. Food Microbiol 28:547–553. doi: 10.1016/j.fm.2010.11.006. [DOI] [PubMed] [Google Scholar]
- 8.De Vuyst L, Vancanneyt M. 2007. Biodiversity and identification of sourdough lactic acid bacteria. Food Microbiol 24:120–127. doi: 10.1016/j.fm.2006.07.005. [DOI] [PubMed] [Google Scholar]
- 9.Dertli E, Mercan E, Arıcı M, Yılmaz MT, Sağdıç O. 2016. Characterisation of lactic acid bacteria from Turkish sourdough and determination of their exopolysaccharide (EPS) production characteristics. LWT Food Sci Technol 71:116–124. doi: 10.1016/j.lwt.2016.03.030. [DOI] [Google Scholar]
- 10.De Vuyst L, Neysens P. 2005. The sourdough microflora: biodiversity and metabolic interactions. Trends Food Sci Technol 16:43–56. doi: 10.1016/j.tifs.2004.02.012. [DOI] [Google Scholar]
- 11.Gänzle MG, Vogel RF. 2003. Contribution of reutericyclin production to the stable persistence of Lactobacillus reuteri in an industrial sourdough fermentation. Int J Food Microbiol 80:31–45. doi: 10.1016/S0168-1605(02)00146-0. [DOI] [PubMed] [Google Scholar]
- 12.Schwab C, Mastrangelo M, Corsetti A, Gänzle M. 2008. Formation of oligosaccharides and polysaccharides by Lactobacillus reuteri LTH5448 and Weissella cibaria 10M in sorghum sourdoughs. Cereal Chem 85:679–684. doi: 10.1094/CCHEM-85-5-0679. [DOI] [Google Scholar]
- 13.Lavermicocca P, Valerio F, Evidente A, Lazzaroni S, Corsetti A, Gobbetti M. 2000. Purification and characterization of novel antifungal compounds from the sourdough Lactobacillus plantarum strain 21B. Appl Environ Microbiol 66:4084–4090. doi: 10.1128/AEM.66.9.4084-4090.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14.Van Heel AJ, de Jong A, Montalbán-López M, Kok J, Kuipers OP. 2013. BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides. Nucleic Acids Res 41:W448–W453. doi: 10.1093/nar/gkt391. [DOI] [PMC free article] [PubMed] [Google Scholar]