Recrafting the neighbor-joining method

Mailund, Thomas; Brodal, Gerth Stølting; Fagerberg, Rolf; Pedersen, Christian N. S.; Phillips, Derek

doi:10.1186/1471-2105-7-29

Cited by 48 publications

(19 citation statements)

References 9 publications

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“…All orthologous protein sequences of the 91 strains were extracted using Orthomcl-v2.0.9 software for clustering orthologous genes [28]. A phylogenetic tree was then constructed using the Neighbor-Joining (NJ) algorithm with default parameters in MEGA 7.0 software on MAFFT-aligned sequences [29], and decorated with Evolgenius (http://www.evolgenius.info/evolview/) [30].…”

Section: Phylogenetic Comparisonmentioning

confidence: 99%

Comparative Genomics Analysis of Lactobacillus ruminis from Different Niches

Wang

Yang

Ross

et al. 2020

Genes

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Lactobacillus ruminis is a commensal motile lactic acid bacterium living in the intestinal tract of humans and animals. Although a few genomes of L. ruminis were published, most of them were animal derived. To explore the genetic diversity and potential niche-specific adaptation changes of L. ruminis, in the current work, draft genomes of 81 L. ruminis strains isolated from human, bovine, piglet, and other animals were sequenced, and comparative genomic analysis was performed. The genome size and GC content of L. ruminis on average were 2.16 Mb and 43.65%, respectively. Both the origin and the sampling distance of these strains had a great influence on the phylogenetic relationship. For carbohydrate utilization, the human-derived L. ruminis strains had a higher consistency in the utilization of carbon source compared to the animal-derived strains. L. ruminis mainly increased the competitiveness of niches by producing class II bacteriocins. The type of clustered regularly interspaced short palindromic repeats /CRISPR-associated (CRISPR/Cas) system presented in L. ruminis was mainly subtype IIA. The diversity of CRISPR/Cas locus depended on the high denaturation of spacer number and sequence, although cas1 protein was relatively conservative. The genetic differences in those newly sequenced L. ruminis strains highlighted the gene gains and losses attributed to niche adaptations.

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Section: Phylogenetic Comparisonmentioning

confidence: 99%

Comparative Genomics Analysis of Lactobacillus ruminis from Different Niches

Wang

Yang

Ross

et al. 2020

Genes

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“…The screening for L-asparaginase was done using the rapid plate assay technique described at earlier publications [ 12 , 13 ]. Phenol red indicator and 0.1% asparagine was used for screening L-asparaginase production.…”

Section: Methodsmentioning

confidence: 99%

A Comprehensive Investigation of Potential Novel Marine Psychrotolerant Actinomycetes sp. Isolated from the Bay-of-Bengal

Ghosh

Gera

Singh

et al. 2020

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Background: This study was carried out to classify the diversity of the deep marine psychrotolerant actinomycetes sp. nov., in the Bay of Bengal and exploit the production of cold-active industrial and pharmaceutical biomolecules. Objective:  Characterization, optimum the growth conditions and classify the diversity of the novel isolated deep marine psychrotolerant actinomycetes sp from Bay-of -Bengal  Screening for industrially important biocatalysts and determine the antimicrobial activities against the five dreadful pathogens  The differential expression profiling of the candidate genes regulate the biosynthesis of selected enzymes. Methods: The cold-adapted actinomycetes were isolated from the deep marine water collections at 1200 mts below the surface in Bay-of-Bengal. The phenotypic and genotypic characterizations have been carried out to understand the persistent diversity of this novel marine psychrotolerant actinomycetes species. The production of cold-active enzymes such as amylase, cellulase, lipase, pectinase, and L-asparaginase were screened and the expression profiling genes determined by using qRT PCR. Indeed, the antibacterial and antifungal activities have also been investigated. Results: A total number of 37 novel actinomycetes isolated and the phenotypic and genotypic characterizations identified the genus, dominated by Streptomyces (17 distinct sub-groups) as the major group, followed by Micromonospora, Actinopolyspora, Actinosynnema, Streptoverticillium, Saccharopolyspora, Nocardiopsis, and Nocardia. The optimum growth and abundant mycelium formation are observed at 15°C to 20°C and also capability for thriving at 4°C. All the isolates are exhibited a significant role in the production of biocatalysts, and the antagonistic activities also noted against five major selected pathogens. Conclusion: The Streptomyces from the Bay-of-Bengal have high biosynthetic potential and can be served as a good resource for the exploration of bioactive natural products.

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“…Orthomcl-v2.0.9 software was used to extract all orthologous protein sequences of 68 strains and the homologous genes were clustered [44]. MEGA 7.0 software was used to construct the phylogenetic tree of the MAFFT-aligned sequence [45], and modified by Evolgenius (https://evolgenius.info//evolview) [46].…”

Section: Pan-genome and Core-genome Analysismentioning

confidence: 99%

Integrated Phenotypic-Genotypic Analysis of Latilactobacillus sakei from Different Niches

Chen

Li²,

Zhao

et al. 2021

Preprint

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Increasing attention has been paid to the potential probiotic effects of Latilactobacillus sakei. To explore the genetic diversity of L. sakei, 14 strains isolated from different niches (feces, fermented kimchi and meat products) and 54 published strains were compared and analyzed. The results showed that the average genome size and GC content of L. sakei were 1.98Mb and 41.22%, respectively. Its core genome mainly encodes translation and transcription, amino acid synthesis, glucose metabolism and defense functions. L. sakei has an open pan-genomic characteristics, and its pan-gene curve shows an upward trend. L. sakei has open pan-genome feature, and its pan-genome curve is on the rise. The genetic diversity of L. sakei is mainly reflected in carbohydrate utilization, antibiotic tolerance, and immune/competition-related factors, such as clustering regular interval short palindromic repeat sequence (CRISPR)-Cas. The CRISPR system is mainly IIA type, and a few are IIC types. This work provides a basis for the study of this species.

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Recrafting the neighbor-joining method

Cited by 48 publications

References 9 publications

Comparative Genomics Analysis of Lactobacillus ruminis from Different Niches

Comparative Genomics Analysis of Lactobacillus ruminis from Different Niches

A Comprehensive Investigation of Potential Novel Marine Psychrotolerant Actinomycetes sp. Isolated from the Bay-of-Bengal

Integrated Phenotypic-Genotypic Analysis of Latilactobacillus sakei from Different Niches

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