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Genome Announcements logoLink to Genome Announcements
. 2018 Jun 28;6(26):e00621-18. doi: 10.1128/genomeA.00621-18

Fifty-Six Draft Genome Sequences of 10 Lactobacillus Species from 22 Commercial Dietary Supplements

Jayanthi Gangiredla a, Tammy J Barnaba a, Mark K Mammel a, David W Lacher a, Christopher A Elkins a, Keith A Lampel a, Chris A Whitehouse a, Carmen Tartera a,
PMCID: PMC6025929  PMID: 29954914

Here, we present the genome sequences of 56 isolates of 10 species of the genus Lactobacillus that are considered beneficial components of the gut microbiota. The isolates examined were found in commercially available dietary supplements in the U.S.

ABSTRACT

Here, we present the genome sequences of 56 isolates of 10 species of the genus Lactobacillus that are considered beneficial components of the gut microbiota. The isolates examined were found in commercially available dietary supplements in the U.S. market.

GENOME ANNOUNCEMENT

Lactobacilli are Gram-positive, facultative anaerobic or microaerophilic, non-spore-forming rods with a DNA G+C content typically below 50%. They are one of the major constituents of the lactic acid bacteria group, whose primary fermentation end product is lactic acid (1). These bacteria are part of the normal human gastrointestinal (GI) microbiota, and they may also be found in the GI tract of other mammalian species (2, 3). The genus Lactobacillus is known to be highly diverse, with more than 80 recognized species and a complex phylogenetic history (2). Some Lactobacillus species have been attributed to have probiotic properties, which upon ingestion in sufficient quantities can provide health benefits to the consumer (4). As part of our ongoing work to expand the observed genomic diversity of the Lactobacillus group, we sequenced the genomes of 56 isolates of 10 species of the genus Lactobacillus found in commercially available dietary supplement products.

Pure cultures of each isolate were grown under microaerophilic conditions in MRS broth for 48 h at 37°C. Total genomic DNA was extracted from 1.2 ml of the 48-h culture using the DNeasy blood and tissue kit (Qiagen, Hilden, Germany). DNA extractions were performed with the Qiagen QIAcube instrument using the manufacturer’s protocol for Gram-positive bacteria. Sequencing libraries were prepared with 1 ng of DNA using the Nextera XT DNA sample prep kit (Illumina, San Diego, CA, USA) and sequenced on either the Illumina MiSeq or NextSeq platform. The resulting paired-end reads were quality controlled using FastQC (Q > 30) and de novo assembled using SPAdes version 3.11.1 (5) or CLC Genomics Workbench version 8.2.1 (CLC bio, Aarhus, Denmark).

Depths of coverage for the draft genomes ranged from 21× to 229×, with the genome sizes ranging from 1,956,319 to 3,301,350 bp. The number of contigs ranged from 22 to 309, while the N50 values ranged from 30,183 to 722,638 bp. The 56 Lactobacillus isolates were identified as belonging to 1 of the following 10 species: L. acidophilus (11), L. rhamnosus (10), L. plantarum (9), L. casei (8), L. reuteri (5), L. salivarius (4), L. helveticus (4), L. fermentum (2), L. zeae (2), and L. brevis (1). The average genome size and G+C content for each of the 10 species are as follows: L. acidophilus, 2.0 Mb, 34.6%; L. brevis, 2.2 Mb, 46.1%; L. casei, 3.2 Mb, 46.1%; L. fermentum, 2.0 Mb, 51.8%; L. helveticus, 2.0 Mb, 36.6%; L. plantarum, 3.2 Mb, 44.5%; L. reuteri, 2.0 Mb, 38.7%; L. rhamnosus, 2.9 Mb, 46.7%; L. salivarius, 2.0 Mb, 32.9%; and L. zeae, 3.0 Mb, 47.3%, respectively.

Accession number(s).

The draft genome assemblies were deposited in DDBJ/ENA/GenBank under the accession numbers QAGU00000000 to QAHZ00000000 and QAZD00000000 to QBAA00000000 (BioProject number PRJNA336518). The versions described in this announcement are the first ones.

ACKNOWLEDGMENTS

The views expressed in this article are those of the authors and do not necessarily reflect the official policy of the Department of Health and Human Services, the U.S. Food and Drug Administration (FDA), or the U.S. Government. Reference to any commercial materials, equipment, or process does not in any way constitute approval, endorsement, or recommendation by the FDA.

Footnotes

Citation Gangiredla J, Barnaba TJ, Mammel MK, Lacher DW, Elkins CA, Lampel KA, Whitehouse CA, Tartera C. 2018. Fifty-six draft genome sequences of 10 Lactobacillus species from 22 commercial dietary supplements. Genome Announc 6:e00621-18. https://doi.org/10.1128/genomeA.00621-18.

REFERENCES

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