Specialized adaptation of a lactic acid bacterium to the milk environment: the comparative genomics of Streptococcus thermophilus LMD-9

Abstract

BackgroundStreptococcus thermophilus represents the only species among the streptococci that has “Generally Regarded As Safe” status and that plays an economically important role in the fermentation of yogurt and cheeses. We conducted comparative genome analysis of S. thermophilus LMD-9 to identify unique gene features as well as features that contribute to its adaptation to the dairy environment. In addition, we investigated the transcriptome response of LMD-9 during growth in milk in the presence of Lactobacillus delbrueckii ssp. bulgaricus, a companion culture in yogurt fermentation, and during lytic bacteriophage infection.ResultsThe S. thermophilus LMD-9 genome is comprised of a 1.8 Mbp circular chromosome (39.1% GC; 1,834 predicted open reading frames) and two small cryptic plasmids. Genome comparison with the previously sequenced LMG 18311 and CNRZ1066 strains revealed 114 kb of LMD-9 specific chromosomal region, including genes that encode for histidine biosynthetic pathway, a cell surface proteinase, various host defense mechanisms and a phage remnant. Interestingly, also unique to LMD-9 are genes encoding for a putative mucus-binding protein, a peptide transporter, and exopolysaccharide biosynthetic proteins that have close orthologs in human intestinal microorganisms. LMD-9 harbors a large number of pseudogenes (13% of ORFeome), indicating that like LMG 18311 and CNRZ1066, LMD-9 has also undergone major reductive evolution, with the loss of carbohydrate metabolic genes and virulence genes found in their streptococcal counterparts. Functional genome distribution analysis of ORFeomes among streptococci showed that all three S. thermophilus strains formed a distinct functional cluster, further establishing their specialized adaptation to the nutrient-rich milk niche. An upregulation of CRISPR1 expression in LMD-9 during lytic bacteriophage DT1 infection suggests its protective role against phage invasion. When co-cultured with L. bulgaricus, LMD-9 overexpressed genes involved in amino acid transport and metabolism as well as DNA replication.ConclusionsThe genome of S. thermophilus LMD-9 is shaped by its domestication in the dairy environment, with gene features that conferred rapid growth in milk, stress response mechanisms and host defense systems that are relevant to its industrial applications. The presence of a unique exopolysaccharide gene cluster and cell surface protein orthologs commonly associated with probiotic functionality revealed potential probiotic applications of LMD-9.

CRISPR-based screening of genomic island excision events in bacteria

“…The first island contained an operon unique to S. thermophilus LMD-9, encoding a putative ATP-dependent oligonucleotide transport system with unknown specificity (Fig. S3A) (35). The second harbors the cell-envelope proteinase PrtS, which contributes to the fast-acidification phenotype of S. thermophilus ( Fig.…”

“…3 A and B). This sequencing strategy was used for its long read length to circumvent difficulty in reliably mapping reads to the proper locus because of the high number of IS elements in the genome (35). Reads were mapped to the reference genome sequence using Geneious software and revealed the absence of a large segment (∼102 kbp) encoding the lacZ ORF (Fig.…”

“…The region contained 102 putative ORFs (STER_1278-1379), encoding ATP-binding cassette (ABC) transporters, two-component regulatory systems, bacteriocin synthesis genes, phage-related genes, lactose catabolism genes, and several cryptic genes with no annotated function (35). The effect of the deletion on growth phenotype was assessed in broth culture by measuring OD at 600 nm over time (Fig.…”

“…Genome sequencing and comparative analysis of S. thermophilus strains have revealed significant genome decay but also indicate that adaptation to nutrient-rich food environments occurred through niche-specific gene acquisition (18,35). The presence of MGEs including integrative and conjugative elements, prophages, and IS elements in S. thermophilus genomes is indicative of rapid evolution to a dairy environment (39,40).…”

Correlation of Lactobacillus rhamnosus Genotypes and Carbohydrate Utilization Signatures Determined by Phenotype Profiling

“…These properties are of significant relevance to their application in food fermentations, such as in cheese production. Genotype-phenotype correlation studies contributed to the discovery of new industrial properties for several LAB species, including Lactobacillus plantarum (4), Lactobacillus casei (5), and Streptococcus thermophilus (6). In human-associated niches, LAB can contribute to the meta-bolic capacities of the resident microbial ecosystem (7).…”