Whole-Genome Sequencing and Annotation of Selected
            <i>Lactobacillales</i>
            Isolated from Commercial Cucumber Fermentation

Page, Clinton A.; Pérez‐Díaz, Ilenys M.

doi:10.1128/mra.00625-21

Cited by 7 publications

(7 citation statements)

References 14 publications

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“…Although for sauerkraut and cucumbers there is no direct evidence of beneficial effects in the prevention or treatment of obesity, they exert a beneficial effect on the microbiota [64]. They are a potential source of Lactobacillus strains with putative probiotic potential [65,66].…”

Section: Discussionmentioning

confidence: 99%

Effects of a Diet Containing Sources of Prebiotics and Probiotics and Modification of the Gut Microbiota on the Reduction of Body Fat

Jagielski

Bolesławska

Wybrańska

et al. 2023

IJERPH

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In 2022, according to the World Health Organization (WHO) report, overweight and obesity have reached epidemic proportions in the WHO European Region, affecting almost 60% of adults. Based on the assessment of BMI (Body Mass Index), a group of 56 women aged 25–45 years (31 women group A average BMI 34.9 ± 4.86 kg/m2 and 25 women group B average BMI 33.4 ± 4.02 kg/m2) were qualified for the study. In a multi-center, two-arm, parallel, non-randomized study, two types of weight-reduction diets (A and B) were used over a 3-month period. In group A, a standard low-energy diet was used with individually adjusted caloric intake of 1100–1300 kcal, with an increase in the amount and frequency of consumption of sauerkraut and groats and a daily intake of fermented milk drinks (300–400 g), fermented cucumbers (100 g), mineral water (1 L) and cod liver oil (5 mL). In group B, a standard low-energy diet with individually adjusted caloric intake of 1100–1300 kcal with daily intake of fermented milk products (150 g), highly mineralized water (0.5 L), once a week fermented cucumbers, and once a week buckwheat groats was used. The following measurements were taken: body weight, body fat mass, water content, body height, waist circumference, and hip circumference. Body weight and body composition were measured using the Tanita MC-780 MA and TANITA BC-601 analyzer using the bioelectric bioimpedance method. The stool samples were analyzed in the microbiology laboratory where quantification of Bifidobcaterium spp., Bacteroides spp., Faecalibacterium prausnitzii species, Akkermansia muciniphila and total bacterial count (TBC) was performed. Under the influence of the introduced nutritional intervention, a statistically significant reduction in body weight, body fat, waist circumference, and hip circumference was demonstrated after 3 months. Under the influence of weight reduction, as well as dietary changes, there was an increase in the number of Akkermansia muciniphila bacteria in the women studied. The low-energy diet containing sources of natural prebiotics and probiotics had a more favorable effect on the number of Faecalibacterium prausnitzii bacteria compared to the standard diet.

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Section: Discussionmentioning

confidence: 99%

Effects of a Diet Containing Sources of Prebiotics and Probiotics and Modification of the Gut Microbiota on the Reduction of Body Fat

Jagielski

Bolesławska

Wybrańska

et al. 2023

IJERPH

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“…The sequencing, assembly, and annotation, along with growth conditions, of the genomic sequences corresponding to the L. plantarum and L. pentosus cultures autochthonous to cucumber fermentation and included in this study are described by Page & Pérez-Díaz [ 39 ] and available from the National Center for Biotechnology Information (NCBI) database under BioProject Accession Number PRJNA674638. GenBank accession numbers corresponding to the genome sequences derived from the autochthonous and allochthonous lactic acid bacteria included in this study are listed in Table 1 .…”

Section: Methodsmentioning

confidence: 99%

“…A phylogenetic tree was constructed based on a computer emulated Rep-PCR using the (GTG) 5 primer [42] for the genome sequences of several lactic acid bacteria whose genome sequences are described in Table 1. The metadata for the genome sequences described in Table 1 that are autochthonous to cucumber may be found in Page & Perez-Diaz [39]. Amplicons from a computed Rep-PCR-(GTG) 5 were generated with Geneious software (v. 2021.1.1, www.geneious.com, analysed in June 2021, accessed on 1 June 2023) for each genome sequence of interest.…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Comparative Analysis of Lactiplantibacillus pentosus Isolates Autochthonous to Cucumber Fermentation Reveals Subclades of Divergent Ancestry

Page

Pérez‐Díaz

Pan

et al. 2023

Foods

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Lactiplantibacillus pentosus, commonly isolated from commercial cucumber fermentation, is a promising candidate for starter culture formulation due to its ability to achieve complete sugar utilization to an end pH of 3.3. In this study, we conducted a comparative genomic analysis encompassing 24 L. pentosus and 3 Lactiplantibacillus plantarum isolates autochthonous to commercial cucumber fermentation and 47 lactobacillales reference genomes to determine species specificity and provide insights into niche adaptation. Results showed that metrics such as average nucleotide identity score, emulated Rep-PCR-(GTG)5, computed multi-locus sequence typing (MLST), and multiple open reading frame (ORF)-based phylogenetic trees can robustly and consistently distinguish the two closely related species. Phylogenetic trees based on the alignment of 587 common ORFs separated the L. pentosus autochthonous cucumber isolates from olive fermentation isolates into clade A and B, respectively. The L. pentosus autochthonous clade partitions into subclades A.I, A.II, and A.III, suggesting substantial intraspecies diversity in the cucumber fermentation habitat. The hypervariable sequences within CRISPR arrays revealed recent evolutionary history, which aligns with the L. pentosus subclades identified in the phylogenetic trees constructed. While L. plantarum autochthonous to cucumber fermentation only encode for Type II-A CRISPR arrays, autochthonous L. pentosus clade B codes for Type I-E and L. pentosus clade A hosts both types of arrays. L. pentosus 7.8.2, for which phylogeny could not be defined using the varied methods employed, was found to uniquely encode for four distinct Type I-E CRISPR arrays and a Type II-A array. Prophage sequences in varied isolates evidence the presence of adaptive immunity in the candidate starter cultures isolated from vegetable fermentation as observed in dairy counterparts. This study provides insight into the genomic features of industrial Lactiplantibacillus species, the level of species differentiation in a vegetable fermentation habitat, and diversity profile of relevance in the selection of functional starter cultures.

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“…We document genome sequences of multiple Bacilli and Proteobacteria isolated from commercial cucumber fermentation. Nine genome sequences are higher quality versions of previous submissions ( 1 ). Three genome sequences represent the nisin producer Lactococcus lactis ( 2 ) and putative bacteriocin producing Pediococcus pentosaceus and Leuconostoc mesenteroides strains ( 3 ).…”

Section: Announcementmentioning

confidence: 99%

Annotated whole-genome sequences of fermentative and spoilage associated Bacilli and proteobacteria autochthonous to commercial cucumber fermentation

Page,

Simpson,

Pérez-Díaz

et al. 2024

Microbiol Resour Announc

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We report 36 whole-genome sequences, along with annotations, of fermentative ( n = 12) and spoilage associated ( n = 6) lactic acid bacteria, Lysinibacillus ( n = 3), Streptococcus ( n = 1), and Proteobacteria ( n = 14) isolated from commercial cucumber fermentations. Fifty-three percent of the genome sequence assemblies consist of 1–4 contigs, and the remainder have fewer than 16.

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Whole-Genome Sequencing and Annotation of Selected Lactobacillales Isolated from Commercial Cucumber Fermentation

Abstract: We report the whole-genome sequences and annotations of 42 Lactobacillales strains isolated from commercial cucumber fermentations performed in North Carolina ( n = 34) and Minnesota ( n = 9), USA. The isolates include representatives from 12 acid-producing species.

Cited by 7 publications

References 14 publications

Effects of a Diet Containing Sources of Prebiotics and Probiotics and Modification of the Gut Microbiota on the Reduction of Body Fat

Effects of a Diet Containing Sources of Prebiotics and Probiotics and Modification of the Gut Microbiota on the Reduction of Body Fat

Genome-Wide Comparative Analysis of Lactiplantibacillus pentosus Isolates Autochthonous to Cucumber Fermentation Reveals Subclades of Divergent Ancestry

Annotated whole-genome sequences of fermentative and spoilage associated Bacilli and proteobacteria autochthonous to commercial cucumber fermentation

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