Genomic characterization of Lactobacillus fermentum DSM 20052

Brandt, Katelyn; Nethery, Matthew A.; O’Flaherty, Sarah; Barrangou, Rodolphe

doi:10.1186/s12864-020-6740-8

“…L. acidophilus and L. gasseri both had publically available genomes [21]. The L. fermentum's genome was completed as previously described [22]. The L. jensenii genome, was sequenced at Core-Biome (St. Paul, MN).…”

Section: Strain Selectionmentioning

confidence: 99%

Adaptive response to iterative passages of five Lactobacillus species in simulated vaginal fluid

Brandt

¹

,

Barrangou

²

2020

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Background Microbiome and metagenomic studies have given rise to a new understanding of microbial colonization of various human tissues and their ability to impact our health. One human microbiome growing in notoriety, the vaginal microbiome, stands out given its importance for women’s health, and is peculiar in terms of its relative bacterial composition, including its simplicity and typical domination by a small number of Lactobacillus species. The loss of Lactobacillus dominance is associated with disorders such as bacterial vaginosis, and efforts are now underway to understand the ability of Lactobacillus species to colonize the vaginal tract and adapt to this dynamic and acidic environment. Here, we investigate how various Lactobacillus species often isolated from the vaginal and intestinal cavities genomically and transcriptionally respond to iterative growth in simulated vaginal fluid. Results We determined the genomes and transcriptomes of L. acidophilus, L. crispatus, L. fermentum, L. gasseri, and L. jensenii and compared profiles after 50, 100, 500, and 1000 generations of iterative passages in synthetic vaginal fluid. In general, we identified relatively few genetic changes consisting of single nucleotide polymorphisms, with higher counts occurring more frequently in non-vaginal isolated species. Transcriptional profiles were more impacted over time and tended to be more extensive for species that typically do not dominate the vaginal tract, reflecting a more extensive need to adapt to a less familiar environment. Conclusions This study provides insights into how vaginal and non-vaginal Lactobacillus species respond and adapt to a simulated vaginal environment. Overall, trends indicate high genomic stability for all species involved, with more variability in the transcriptome especially for non-dominant species of the vaginal tract.

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“…While the majority of Limosilactobacillus genomic studies have focused on species most relevant to industry, e.g. the probiotic market [40–43], we focused our analysis on human Limosilactobacillus , since several species were identified in different human body sites, and occasionally in high relative abundance. For instance, L.…”

Section: Discussionmentioning

confidence: 99%

“…While the majority of Limosilactobacillus genomic studies have focused on species most relevant to industry, e.g. the probiotic market [40][41][42][43], we focused our analysis on human Limosilactobacillus, since several species were identified in different human body sites, and occasionally in high relative abundance. For instance, L. vaginalis and L. urinaemulieris were found in high relative abundance in the vaginal microbiome of healthy women [44; M. Ksiezarek and others, unpublished data], L. mucosae in the vagina of Indian women and the faeces of healthy children [45], L. fermentum in breast milk and in saliva from patients with dental caries [46,47], and L. reuteri in the intestinal microbiota of obese adults [48].…”

Section: Discussionmentioning

confidence: 99%

Genomic diversity of genus Limosilactobacillus

Ksiezarek

¹

,

Grosso

²

,

Ribeiro

³

et al. 2022

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The genus Limosilactobacillus (formerly Lactobacillus ) contains multiple species considered to be adapted to vertebrates, yet their genomic diversity has not been explored. In this study, we performed comparative genomic analysis of Limosilactobacillus (22 species; 332 genomes) isolated from different niches, further focusing on human strains (11 species; 74 genomes) and their adaptation features to specific body sites. Phylogenomic analysis of Limosilactobacillus showed misidentification of some strains deposited in public databases and existence of putative novel Limosilactobacillus species. The pangenome analysis revealed a remarkable genomic diversity (only 1.3 % of gene clusters are shared), and we did not observe a strong association of the accessory genome with different niches. The pangenome of Limosilactobacillus reuteri and Limosilactobacillus fermentum was open, suggesting that acquisition of genes is still occurring. Although most Limosilactobacillus were predicted as antibiotic susceptible (83%), acquired antibiotic-resistance genes were common in L. reuteri from food-producing animals. Genes related to lactic acid isoform production (>95 %) and putative bacteriocins (70.2%) were identified in most Limosilactobacillus strains, while prophages (55.4%) and CRISPR-Cas systems (32.0%) were less prevalent. Among strains from human sources, several metabolic pathways were predicted as conserved and completed. Their accessory genome was highly variable and did not cluster according to different human body sites, with some exceptions (urogenital Limosilactobacillus vaginalis , Limosilactobacillus portuensis , Limosilactobacillus urinaemulieris and Limosilactobacillus coleohominis or gastrointestinal Limosilactobacillus mucosae ). Moreover, we identified 12 Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologues that were significantly enriched in strains from particular body sites. We concluded that evolution of the highly diverse Limosilactobacillus is complex and not always related to niche or human body site origin.

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“…The copyright holder for this preprint this version posted October 25, 2022. ; https://doi.org/10.1101/2022.10.25.513655 doi: bioRxiv preprint and DSM 20052 originated from fermented plant materials (Yoo et al, 2017;Brandt et al, 2020).…”

Section: Functional Genomic Characterizationmentioning

confidence: 99%

Evaluation of metabolic and functional properties of cholesterol-reducing and GABA-producerLimosilactobacillus fermentumstrain AGA52 isolated from lactic acid fermented Shalgam by usingin vitroandin silicoprobiogenomic approaches

Yetiman

¹

,

Horzum²,

Akbulut

³

2022

Preprint

0

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This study aimed to characterize the genomic and metabolic properties of a novel Lb. fermentum strain AGA52 which was isolated from a lactic acid fermented beverage called Shalgam. The genome size of AGA52 was 2,001,084 bp, which is predicted to carry 2,024 genes, including 50 tRNAs, 3 rRNAs, 3ncRNAs, 15 CRISPR repeats, 14 CRISPR spacers, and 1 CRISPR array. The genome has a GC content of 51.82% including 95 predicted pseudogenes, 56 complete or partial transposases and 2 intact prophages. The similarity of the clusters of orthologous groups (COG) was analysed by comparison with the other Lb. fermentum strains. The detected resistome on the genome of AGA52 was found to be intrinsic originated. Based on genome analyses many CAZYmes were identified that are responsible for carbohydrate degradation and adaptation to gastrointestinal conditions. Besides, it has been determined that AGA52 has an obligate heterofermentative carbohydrate metabolism due to the absence of the 1-phosphofructokinase (pfK) enzyme. Additionally, it is determined that the strain has a higher antioxidant capacity and is adaptable to gastrointestinal simulated environments. It was also observed that the AGA52 has antimicrobial activity against Y. Enterocolitica ATCC9610, B. cereus ATCC33019, S. enterica sv. Typhimurium, E.coli O157:h7 ATCC43897, L.monocytogenes ATCC7644, K.pneumoniae ATCC13883, and P. vulgaris ATCC8427. Cholesterol assimilation (33.9%) and GABA production capacities were also confirmed by in silico and in vitro. Overall, investigation of genomic and metabolic features of the AGA52 revealed that is a potential psychobiotic and probiotic dietary supplement candidate and can bring functional benefits to the host.

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Genomic characterization of Lactobacillus fermentum DSM 20052

Cited by 21 publications

References 49 publications

Adaptive response to iterative passages of five Lactobacillus species in simulated vaginal fluid

Adaptive response to iterative passages of five Lactobacillus species in simulated vaginal fluid

Genomic diversity of genus Limosilactobacillus

Evaluation of metabolic and functional properties of cholesterol-reducing and GABA-producerLimosilactobacillus fermentumstrain AGA52 isolated from lactic acid fermented Shalgam by usingin vitroandin silicoprobiogenomic approaches

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