Pangenome Analysis Reveals the Genetic Basis for Taxonomic Classification of the Lactobacillaceae Family

Rajput, Abhishek; Chauhan, Siddharth M.; Mohite, Omkar S.; Hyun, Jason C.; Ardalani, Omid; Jahn, Leonie Johanna; Sommer, Morten Otto Alexander; Palsson, Bernhard

doi:10.2139/ssrn.4368218

Cited by 4 publications

(11 citation statements)

References 70 publications

(98 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This suggests that this phylogroup with high genetic diversity might inhabit a variety of isolation sources, which was evident in the varied isolation sources hosted by it (Figure 6A). This observation also aligns with the pan-genomic studies of L. plantarum , where this phylogroup was found to originate from a divergent set of strains, as indicated by Mash distance values, forming its distinct clade (Rajput et al, 2023; Li et al, 2022). The higher number of core variant genes in this phylogroup might indicate versatility, allowing them to strive in diverse environments.…”

Section: Discussionsupporting

confidence: 89%

“…In the pangenome study of Lactobacillaceae , specific genes were identified and assigned to COG categories (Rajput et al, 2023). These COGs were mapped with the core genes corresponding to variants of L. plantarum , allowing for the investigation of how the variants are distributed across distinct COG categories.…”

Section: Resultsmentioning

confidence: 99%

“…These strains were further mapped with phylogroups and isolation sources. The nine distinct phylogroups were revealed using Mash from pangenome analysis of 611 L. plantarum strains (Rajput et al, 2023). The phylogenetic analysis revealed that even within the same phylogroups, strains are not closely related, indicating substantial core genetic variations among these strains.…”

Section: Resultsmentioning

confidence: 99%

“…On the other hand, L. acidophilus is a natural inhabitant of the human gut, and various strains are employed as probiotics (Taverniti and Guglielmetti, 2012). Additionally, of the 26 species , L. acidophilus and L. helveticus are the species with the most closed pangenome and the most open pangenome, respectively (Rajput et al, 2023), where a closed pangenome reflects the lower possibility of the addition of new gene families, while the open pangenome indicates the inclusion of new gene families in a lineage. The trend towards diversifying selection in L. helveticus and its open pangenome nature might be due to the diverse industrial environments it encounters and its adaptive and survival abilities.…”

Section: Discussionmentioning

confidence: 99%

“…First, the COG categories from pangenome analysis (Rajput et al, 2023) were mapped with the core variant genes in the core alleleome of all 26 species, and the percentage distribution of all variant types (substitution, insertion, and deletion) across all COG categories was calculated. Their distribution was plotted using a heatmap (Figure S2).…”

Section: Methodsmentioning

confidence: 99%

See 4 more Smart Citations

Genomic insights intoLactobacillaceae: Analyzing the “Alleleome” of core pangenomes for enhanced understanding of strain diversity and revealing Phylogroup-specific unique variants

Harke,

Josephs-Spauling,

Mohite

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

The Lactobacillaceae family's significance in food and health, combined with available strain-specific genomes, enables genome assessment through pangenome analysis. The Alleleome of the core pangenomes of the Lactobacillaceae family, which identifies natural sequence variations, was reconstructed from the amino acid and nucleotide sequences of the core genes across 2,447 strains of 26 species. It comprised 3.71 million amino acid variants in 29,448 core genes across the family. The alleleome analysis of the Lactobacillaceae family revealed key findings: 1) In the core pangenome, amino acid substitutions prevailed over rare insertions and deletions, 2) Purifying negative selection primarily influenced core gene variations in the family, with diversifying selection noted in L. helveticus. L. plantarum core alleleome was investigated due to its industrial importance. In L. plantarum, the defining characteristics of its core alleleome included: 1) It is highly conserved; 2) Among 235 isolation sources, the primary categories displaying variant prevalence were fermented food, feces, and unidentified sources; 3) It is predominantly characterized by conservative and moderately conservative mutations; and 4) Phylogroup-specific core variant gene analysis identified unique variants (DltX, FabZ1, Pts23B, CspP) in phylogroups I and B which could be used as identifier or validation markers of strain or phylogroup.

show abstract

Section: Discussionsupporting

confidence: 89%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 3 more Smart Citations

Genomic insights intoLactobacillaceae: Analyzing the “Alleleome” of core pangenomes for enhanced understanding of strain diversity and revealing Phylogroup-specific unique variants

Harke,

Josephs-Spauling,

Mohite

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

Pangenome reconstruction ofLactobacillaceaemetabolism predicts species-specific metabolic traits

Ardalani,

Phaneuf,

Mohite

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traits

Ardalani,

Phaneuf,

Mohite

et al. 2024

mSystems

View full text Add to dashboard Cite

Strains across the Lactobacillaceae family form the basis for a trillion-dollar industry. Our understanding of the genomic basis for their key traits is fragmented, however, including the metabolism that is foundational to their industrial uses. Pangenome analysis of publicly available Lactobacillaceae genomes allowed us to generate genome-scale metabolic network reconstructions for 26 species of industrial importance. Their manual curation led to more than 75,000 gene-protein-reaction associations that were deployed to generate 2,446 genome-scale metabolic models. Cross-referencing genomes and known metabolic traits allowed for manual metabolic network curation and validation of the metabolic models. As a result, we provide the first pangenomic basis for metabolism in the Lactobacillaceae family and a collection of predictive computational metabolic models that enable a variety of practical uses. IMPORTANCE Lactobacillaceae , a bacterial family foundational to a trillion-dollar industry, is increasingly relevant to biosustainability initiatives. Our study, leveraging approximately 2,400 genome sequences, provides a pangenomic analysis of Lactobacillaceae metabolism, creating over 2,400 curated and validated genome-scale models (GEMs). These GEMs successfully predict (i) unique, species-specific metabolic reactions; (ii) niche-enriched reactions that increase organism fitness; (iii) essential media components, offering insights into the global amino acid essentiality of Lactobacillaceae ; and (iv) fermentation capabilities across the family, shedding light on the metabolic basis of Lactobacillaceae -based commercial products. This quantitative understanding of Lactobacillaceae metabolic properties and their genomic basis will have profound implications for the food industry and biosustainability, offering new insights and tools for strain selection and manipulation.

show abstract

Pangenome Analysis Reveals the Genetic Basis for Taxonomic Classification of the Lactobacillaceae Family

Cited by 4 publications

References 70 publications

Genomic insights intoLactobacillaceae: Analyzing the “Alleleome” of core pangenomes for enhanced understanding of strain diversity and revealing Phylogroup-specific unique variants

Genomic insights intoLactobacillaceae: Analyzing the “Alleleome” of core pangenomes for enhanced understanding of strain diversity and revealing Phylogroup-specific unique variants

Pangenome reconstruction ofLactobacillaceaemetabolism predicts species-specific metabolic traits

Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traits

Contact Info

Product

Resources

About