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Metagenomics study of endophytic bacteria in Aloe vera using next-generation technology.

Akinsanya MA, Goh JK, Lim SP, Ting AS - Genom Data (2015)

Bottom Line: The stems have more of the genus-Pseudomonas and the unclassified Pseudomonadaceae.The α-diversity analysis indicated the richness and inverse Simpson diversity index of the bacterial endophyte communities for the leaf, root and stem tissues to be 2.221, 6.603 and 1.491 respectively.It is evident that NGS technology captured effectively the metagenomics of microbiota in plant tissues and this can improve our understanding of the microbial-plant host interactions.

View Article: PubMed Central - PubMed

Affiliation: School of Science, Monash University Malaysia, 46150 Bandar Sunway, Selangor, Malaysia ; Department of Medical Biochemistry, Faculty of Basic Medical Sciences, College of Medicine, Lagos State University, P.M.B 21266 Ikeja, Lagos, Nigeria.

ABSTRACT
Next generation sequencing (NGS) enables rapid analysis of the composition and diversity of microbial communities in several habitats. We applied the high throughput techniques of NGS to the metagenomics study of endophytic bacteria in Aloe vera plant, by assessing its PCR amplicon of 16S rDNA sequences (V3-V4 regions) with the Illumina metagenomics technique used to generate a total of 5,199,102 reads from the samples. The analyses revealed Proteobacteria, Firmicutes, Actinobacteria and Bacteriodetes as the predominant genera. The roots have the largest composition with 23% not present in other tissues. The stems have more of the genus-Pseudomonas and the unclassified Pseudomonadaceae. The α-diversity analysis indicated the richness and inverse Simpson diversity index of the bacterial endophyte communities for the leaf, root and stem tissues to be 2.221, 6.603 and 1.491 respectively. In a similar study on culturable endophytic bacteria in the same A. vera plants (unpublished work), the dominance of Pseudomonas and Bacillus genera was similar, with equal proportion of four species each in root, stem and leaf tissues. It is evident that NGS technology captured effectively the metagenomics of microbiota in plant tissues and this can improve our understanding of the microbial-plant host interactions.

No MeSH data available.


Related in: MedlinePlus

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Metagenomics study of endophytic bacteria in Aloe vera using next-generation technology.

Akinsanya MA, Goh JK, Lim SP, Ting AS - Genom Data (2015)

© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664749&req=5

Bottom Line: The stems have more of the genus-Pseudomonas and the unclassified Pseudomonadaceae.The α-diversity analysis indicated the richness and inverse Simpson diversity index of the bacterial endophyte communities for the leaf, root and stem tissues to be 2.221, 6.603 and 1.491 respectively.It is evident that NGS technology captured effectively the metagenomics of microbiota in plant tissues and this can improve our understanding of the microbial-plant host interactions.

View Article: PubMed Central - PubMed

Affiliation: School of Science, Monash University Malaysia, 46150 Bandar Sunway, Selangor, Malaysia ; Department of Medical Biochemistry, Faculty of Basic Medical Sciences, College of Medicine, Lagos State University, P.M.B 21266 Ikeja, Lagos, Nigeria.

ABSTRACT
Next generation sequencing (NGS) enables rapid analysis of the composition and diversity of microbial communities in several habitats. We applied the high throughput techniques of NGS to the metagenomics study of endophytic bacteria in Aloe vera plant, by assessing its PCR amplicon of 16S rDNA sequences (V3-V4 regions) with the Illumina metagenomics technique used to generate a total of 5,199,102 reads from the samples. The analyses revealed Proteobacteria, Firmicutes, Actinobacteria and Bacteriodetes as the predominant genera. The roots have the largest composition with 23% not present in other tissues. The stems have more of the genus-Pseudomonas and the unclassified Pseudomonadaceae. The α-diversity analysis indicated the richness and inverse Simpson diversity index of the bacterial endophyte communities for the leaf, root and stem tissues to be 2.221, 6.603 and 1.491 respectively. In a similar study on culturable endophytic bacteria in the same A. vera plants (unpublished work), the dominance of Pseudomonas and Bacillus genera was similar, with equal proportion of four species each in root, stem and leaf tissues. It is evident that NGS technology captured effectively the metagenomics of microbiota in plant tissues and this can improve our understanding of the microbial-plant host interactions.

No MeSH data available.


Related in: MedlinePlus