Comparative Genome Analysis of Lactiplantibacillus paraplantarum

Ruveyda Benk; Fatih Ortakcı

Article Details

Comparative Genome Analysis of Lactiplantibacillus paraplantarum

Authors:

Ruveyda Benk | Fatih Ortakcı

Publisher:

Bitlis Eren University

Journal:

Bitlis Eren Üniversitesi Fen Bilimleri Dergisi Vol.13 Issue 2, pp.366-375

Document Type:

Article

Publication Date:

6/2024

Document Language:

English

Document ID (Org No.):

2001320318

pISSN:

2147-3129

Keywords:

Abstract:

 Lactiplantibacillus paraplantarum is a lactic acid bacteria species that is associated with food microbiomes and has been found to be either detrimental or beneficial against specific food processes. To augment our genomic understanding of L.paraplantarum and uncover metabolic differences and lifestyle adaptations between strains DSM10667, L-ZS9, AS-7 to better utilize these species in food bioprocesses. In-silico genomic approach applied using JGIs IMGMER, and PATRIC to compare DSM10667, L-ZS9 and AS-7 genomes. Bacteriocin and prophage screenings were performed using Bagel4 and PHASTER software respectively. BRIG was used to identify alignments of strains to each other for visual inspection of each genome. KEGG was used to predict putative carbohydrate, pyruvate, and amino-acid metabolisms. Genome sizes of DSM10667, L-ZS9, and AS-7 were 3.36, 3.14 and 3.01 M bp, respectively. Unique genes were found to predict evolutionary adaptation of strains against their corresponding micro-niche. For example, the gene encoding arginase was only found in sausage isolate L-ZS9 while dextran-sucrase encoding gene was unique to beer contaminant DSM10667. All three strains predicted to carry plnAEFJ operon for plantaricin biosynthesis and AS-7 genome contains leucocin K. Although DSM 10667 harbors four intact prophages, both L-ZS9 and AS-7 carried one prophage region still showing the plasticity of the genome. Genome analysis predicted isolation sources might potentially affect the metabolic capabilities of strains part of adaptation of the strains to their habitats. Our findings put forth new insights into the genomics of L.paraplantarum for future studies and uncovering potential strain manipulation elements for better use in commercial processing environment.

 Lactiplantibacillus paraplantarum is a lactic acid bacteria species that is associated with food microbiomes and has been found to be either detrimental or beneficial against specific food processes. To augment our genomic understanding of L.paraplantarum and uncover metabolic differences and lifestyle adaptations between strains DSM10667, L-ZS9, AS-7 to better utilize these species in food bioprocesses. In-silico genomic approach applied using JGIs IMGMER, and PATRIC to compare DSM10667, L-ZS9 and AS-7 genomes. Bacteriocin and prophage screenings were performed using Bagel4 and PHASTER software respectively. BRIG was used to identify alignments of strains to each other for visual inspection of each genome. KEGG was used to predict putative carbohydrate, pyruvate, and amino-acid metabolisms. Genome sizes of DSM10667, L-ZS9, and AS-7 were 3.36, 3.14 and 3.01 M bp, respectively. Unique genes were found to predict evolutionary adaptation of strains against their corresponding micro-niche. For example, the gene encoding arginase was only found in sausage isolate L-ZS9 while dextran-sucrase encoding gene was unique to beer contaminant DSM10667. All three strains predicted to carry plnAEFJ operon for plantaricin biosynthesis and AS-7 genome contains leucocin K. Although DSM 10667 harbors four intact prophages, both L-ZS9 and AS-7 carried one prophage region still showing the plasticity of the genome. Genome analysis predicted isolation sources might potentially affect the metabolic capabilities of strains part of adaptation of the strains to their habitats. Our findings put forth new insights into the genomics of L.paraplantarum for future studies and uncovering potential strain manipulation elements for better use in commercial processing environment.

 Lactiplantibacillus paraplantarum is a lactic acid bacteria species that is associated with food microbiomes and has been found to be either detrimental or beneficial against specific food processes. To augment our genomic understanding of L.paraplantarum and uncover metabolic differences and lifestyle adaptations between strains DSM10667, L-ZS9, AS-7 to better utilize these species in food bioprocesses. In-silico genomic approach applied using JGIs IMGMER, and PATRIC to compare DSM10667, L-ZS9 and AS-7 genomes. Bacteriocin and prophage screenings were performed using Bagel4 and PHASTER software respectively. BRIG was used to identify alignments of strains to each other for visual inspection of each genome. KEGG was used to predict putative carbohydrate, pyruvate, and amino-acid metabolisms. Genome sizes of DSM10667, L-ZS9, and AS-7 were 3.36, 3.14 and 3.01 M bp, respectively. Unique genes were found to predict evolutionary adaptation of strains against their corresponding micro-niche. For example, the gene encoding arginase was only found in sausage isolate L-ZS9 while dextran-sucrase encoding gene was unique to beer contaminant DSM10667. All three strains predicted to carry plnAEFJ operon for plantaricin biosynthesis and AS-7 genome contains leucocin K. Although DSM 10667 harbors four intact prophages, both L-ZS9 and AS-7 carried one prophage region still showing the plasticity of the genome. Genome analysis predicted isolation sources might potentially affect the metabolic capabilities of strains part of adaptation of the strains to their habitats. Our findings put forth new insights into the genomics of L.paraplantarum for future studies and uncovering potential strain manipulation elements for better use in commercial processing environment.

 Lactiplantibacillus paraplantarum is a lactic acid bacteria species that is associated with food microbiomes and has been found to be either detrimental or beneficial against specific food processes. To augment our genomic understanding of L.paraplantarum and uncover metabolic differences and lifestyle adaptations between strains DSM10667, L-ZS9, AS-7 to better utilize these species in food bioprocesses. In-silico genomic approach applied using JGIs IMGMER, and PATRIC to compare DSM10667, L-ZS9 and AS-7 genomes. Bacteriocin and prophage screenings were performed using Bagel4 and PHASTER software respectively. BRIG was used to identify alignments of strains to each other for visual inspection of each genome. KEGG was used to predict putative carbohydrate, pyruvate, and amino-acid metabolisms. Genome sizes of DSM10667, L-ZS9, and AS-7 were 3.36, 3.14 and 3.01 M bp, respectively. Unique genes were found to predict evolutionary adaptation of strains against their corresponding micro-niche. For example, the gene encoding arginase was only found in sausage isolate L-ZS9 while dextran-sucrase encoding gene was unique to beer contaminant DSM10667. All three strains predicted to carry plnAEFJ operon for plantaricin biosynthesis and AS-7 genome contains leucocin K. Although DSM 10667 harbors four intact prophages, both L-ZS9 and AS-7 carried one prophage region still showing the plasticity of the genome. Genome analysis predicted isolation sources might potentially affect the metabolic capabilities of strains part of adaptation of the strains to their habitats. Our findings put forth new insights into the genomics of L.paraplantarum for future studies and uncovering potential strain manipulation elements for better use in commercial processing environment.

Article Details

Comparative Genome Analysis of Lactiplantibacillus paraplantarum

Authors:

Ruveyda Benk | Fatih Ortakcı

Publisher:

Bitlis Eren University

Journal:

Bitlis Eren Üniversitesi Fen Bilimleri Dergisi Vol.13 Issue 2, pp.366-375

Document Type:

Article

Publication Date:

6/2024

Document Language:

English

Document ID (Org No.):

2001320318

pISSN:

2147-3129

Lactiplantibacillus paraplantarum

comparative genomics

bacteriocin

prophage

carbohydrate

adaptation

Issues

Article Details

Comparative Genome Analysis of Lactiplantibacillus paraplantarum

Authors: Ruveyda Benk | Fatih Ortakcı

Publisher: Bitlis Eren University

Journal: Bitlis Eren Üniversitesi Fen Bilimleri Dergisi Vol.13 Issue 2, pp.366-375

Document Type: Article

Publication Date: 6/2024

Document Language: English

Document ID (Org No.): 2001320318

pISSN: 2147-3129

Lactiplantibacillus paraplantarum

comparative genomics

bacteriocin

prophage

carbohydrate

adaptation

Issues

Authors:

Ruveyda Benk | Fatih Ortakcı

Publisher:

Bitlis Eren University

Journal:

Bitlis Eren Üniversitesi Fen Bilimleri Dergisi Vol.13 Issue 2, pp.366-375

Document Type:

Article

Publication Date:

6/2024

Document Language:

English

Document ID (Org No.):

2001320318

pISSN:

2147-3129