Integrated genome based evaluation of safety and probiotic characteristics of Lactiplantibacillus plantarum YW11 isolated from Tibetan kefir

Abstract

The comparative genomic analysis of Lactiplantibacillus plantarum YW11 (L. plantarum YW11) isolated from Tibetan kefir involves comparison of the complete genome sequences of the isolated strain with other closely related L. plantarum strains. This type of analysis can be used to identify the genetic diversity among strains and to explore the genetic characteristics of the YW11 strain. The genome of L. plantarum YW11 was found to be composed of a circular single chromosome of 4,597,470 bp with a G + C content of 43.2%. A total of 4,278 open reading frames (ORFs) were identified in the genome and the coding density was found to be 87.8%. A comparative genomic analysis was conducted using two other L. plantarum strains, L. plantarum C11 and L. plantarum LMG21703. Genomic comparison revealed that L. plantarum YW11 shared 72.7 and 75.2% of gene content with L. plantarum C11 and L. plantarum LMG21703, respectively. Most of the genes shared between the three L. plantarum strains were involved in carbohydrate metabolism, energy production and conversion, amino acid metabolism, and transcription. In this analysis, 10 previously sequenced entire genomes of the species were compared using an in-silico technique to discover genomic divergence in genes linked with carbohydrate intake and their potential adaptations to distinct human intestinal environments. The subspecies pan-genome was open, which correlated with its extraordinary capacity to colonize several environments. Phylogenetic analysis revealed that the novel genomes were homogenously grouped among subspecies of l Lactiplantibacillus. L. plantarum was resistant to cefoxitin, erythromycin, and metronidazole, inhibited pathogens including Listeria monocytogenes, Clostridium difficile, Vibrio cholera, and others, and had excellent aerotolerance, which is useful for industrial operations. The comparative genomic analysis of L. plantarum YW11 isolated from Tibetan kefir can provide insights into the genetic characteristics of the strain, which can be used to further understand its role in the production of kefir.

A Narrative Review on Gut Microbiome Disturbances and Microbial Preparations in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: Implications for Long COVID

“…Probiotics, as live microorganisms that are administered in adequate amounts [ 77 ] utilizing the non-digestible fibers of prebiotics, can bring health benefits to the host [ 66 ], including improved digestion and immunity, and, by modulating immune signaling pathways and enhancing gut microbiota function within the gut–lung and gut–brain axes [ 78 ], reduce common symptoms of infection [ 79 ] and increase resistance to the infectious agent. In addition, probiotic preparations can help with the management of neurodegenerative and psychiatric comorbidities related to low mood, sleep problems, depression and anxiety-like symptoms [ 80 , 81 ] and those associated with chronic GI conditions, including IBS [ 82 ].…”

Molecular docking and density functional theory (DFT) studies on the conversion of linoleic acid into fatty acid metabolites by Lactiplantibacillus plantarum 12-3

“…Molecule's chemical reactivity and kinetic stability was calculated by FMO gap. Stabilization (inhibitor-surface) was enhanced by increasing the inhibitor's HOMO energy and decreasing the surface's LUMO energy [29] .…”

“…E HOMO (the energy level of HOMO) in liquid phase is greater than gaseous zone and the components are in descending order as follow 9-trans,12-trans-octadecadienoic acid, octyldodecane, 2-amino-1,3-octadecanediol, stearic, and LA. The bigger E HOMO value than E LUMO , that imply a greater possibility of losing valance electrons and a stronger desire to donate electrons toward the surface of iron, and more inhibitory potency than gas phase [28][29] . All of the fatty acids studied had HOMOs anchored to the carboxyl group, while the LUMOs were found to be positioned on the aliphatic side.…”

Carbohydrate-active enzyme profiles of Lactiplantibacillus plantarum strain 84-3 contribute to flavor formation in fermented dairy and vegetable products

“…Lactiplantibacillus plantarum is a well-studied bacterium which can be isolated from a variety of sources, such as Tibetan kefir ( Aziz et al, 2023a , Aziz et al, 2022 , Aziz et al, 2023b ), Inner Mongolian cheese ( Zhao et al, 2023 ), and other fermented foods. Our previous findings showed that Lactiplantibacillus plantarum (Lp84-3) can affect resistant starch (RS) degradation to produce short-chain fatty acids (SCFAs) ( Liang et al, 2023 ).…”