Complete Genome Sequence of Lactobacillus fermentum CECT 5716, a Probiotic Strain Isolated from Human Milk

Abstract

Lactobacillus fermentum is a heterofermentative lactic acid bacterium and is frequently isolated from mucosal surfaces of healthy humans. Lactobacillus fermentum CECT 5716 is a well-characterized probiotic strain isolated from human milk and, at present, is used in commercial infant formulas. Here, we report the complete and annotated genome sequence of this strain.Breast milk is the best food for neonates because it provides a unique combination of nutrients and bioactive compounds, ensuring correct growth and development of the infant. In addition, it also contains probiotic bacteria (4, 5). In a previous study, we isolated Lactobacillus fermentum CECT 5716 from such biological fluid (3). Subsequent studies revealed that this strain was a good probiotic candidate since it reached high survival rates when exposed to gastrointestinal tract-like conditions, showed a strong adherence to intestinal cells, stimulated the expression of mucin-encoding genes, produced antimicrobial compounds, and displayed in vivo and in vitro immunomodulatory and antibacterial properties against pathogenic bacteria (1, 5, 7). L. fermentum CECT 5716 showed a beneficial effect in a murine model of intestinal inflammation, reducing the inflammatory response and the intestinal damage (2). In addition, consumption of this strain enhances the response to influenza vaccination in healthy volunteers and reduces the incidence of influenza-like illness (8).In order to interrogate the genome sequence of Lactobacillus fermentum CECT 5716 with regard to its probiotic properties, the complete genome sequence was determined by a whole-genome shotgun strategy using 454 pyrosequencing technology (454 Life Sciences, Banford, CT). The initial draft assembly provided by 454 Life Sciences was based on 193,362 pyrosequencing reads with an average read length of 250 nucleotides which assembled into 1,343 contigs. Sequence reads were assembled automatically with the Life Sciences GS FLX (Newbler) program. The genome sequence of Lactobacillus fermentum IFO 3956 (6) was used to order these contigs into large scaffolds. The assembling process was relatively complex due to the 83 transposase-encoding regions that were found in the CECT 5716 genome.The complete genome of Lactobacillus fermentum CECT 5716 consists of a circular chromosome of 2,100,449 bp, with a GC content of 51.49%, and has no plasmid. Its chromosome contains 1,109 predicted protein-encoding genes, 54 tRNA-encoding genes, and 20 rRNA-encoding genes. The comparison of the CECT 5716 and IFO 3956 genomes revealed that they were highly similar, with the exception of 16 protein-encoding genes that are present in CECT 5716 but not in IFO 3956. Among them, there are putative enzymes involved in the metabolism of purines (allantoinase, GMP oxidoreductase, GMP synthase), amino acids (serine-pyruvate transaminase, 3 glutamate synthases), lipids (acyltransferase), and carbohydrates (mannose-6-phosphate isomerase).Nucleotide sequence accession number. The sequence data for the L. fermentum CECT 5716 genome a...

Probiotic attributes of Lactobacillus fermentum isolated from human feces and dairy products

“…On the other hand, L. fermentum ME-3 is reported to be a pronounced probiotic strain with antimicrobial and antioxidative properties (Mikelsaar and Zilmer 2009). Being closely related to Lactobacillus reuteri, probiotic strains of L. fermentum are known to exhibit high rates of survival in the GIT environment, adhesion to mucosal surfaces, antibacterial property and also demonstrate beneficial effects on the immune system (Jiménez et al 2010;Morita et al 2008;Park et al 2005;Zoumpopoulou et al 2008). Complete genome sequence of L. fermentum is available the size of which accounts from 2-2.5 MB and approximately 52 % guaninecytosine (GC) content.…”

Interaction of Lactobacillus fermentum BGHI14 with Rat Colonic Mucosa: Implications for Colitis Induction

“…Most commonly tested potential probiotics are lactobacillus strains that possess the plethora of highly desirable properties related to host health. Lactobacillus fermentum has long been studied for its probiotic properties because of its human origin, adherence capacity in GI tract, as well as protection in animal models of bowel inflammation (26,27). Experimental data also support its role in mucosal barrier fortification (28).…”

“…Experimental data also support its role in mucosal barrier fortification (28). Also, clinical trials including L. fermentum have been undertaken with promising results (27).…”

Genome Sequence of Lactobacillus fermentum Strain NCC2970 (CNCM I-5068)

“…531). L. fermentum strains have been previously reported for their different properties, including technological (2) or probiotic functionalities (3–6). Lactobacillus fermentum NCC2970 originates from the Nestlé Culture Collection and has also been deposited at the National Collection of Microorganisms Cultures (CNCM) under CNCM I-5068.…”

“…The L. fermentum NCC2970 (CNCM I-5068) genome has a similar size and structure than other publically available L. fermentum genomes (F-6 [5], CECT 5716 [6]). It contains, however, some specific features, especially with regard to its substrate usage capacity.…”