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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 In a similar study on culturable endophytic bacteria in the same A. vera plants (unpublished work), the dominance of Pseudomonas and Bacillus genera was similar, with equal proportion of four species each in root, stem and leaf tissues.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

Bacterial taxonomic composition histogram. The average composition of bacteria communities obtained from surface sterilized tissues of A. vera using culture-independent method (MiSeq Illumina platform) was analysed and compared. The nomenclatures of the phylotypes are based on the SILVA rRNA database (http://www.mothur.org/wiki/Silva_reference_files).
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f0010: Bacterial taxonomic composition histogram. The average composition of bacteria communities obtained from surface sterilized tissues of A. vera using culture-independent method (MiSeq Illumina platform) was analysed and compared. The nomenclatures of the phylotypes are based on the SILVA rRNA database (http://www.mothur.org/wiki/Silva_reference_files).

Mentions: The relative abundance of bacterial communities as obtained in the three tissues evaluated is shown in Fig. 1. Of the three tissues analysed, Proteobacteria sub-phylum is predominant followed by Firmicutes, Actinobacteria and Bacteroidetes. It was noted that the stem tissue has more of the genus—Pseudomonas and unclassified Pseudomonadaceae than the root and leaf tissues. On the contrary, leaf tissues have more of genus—Propionibacterium, Serratia and Brevibacterium than the root and stem tissues (refer Table S2, Table S3). In all, the root tissues have the highest richness of the four bacteria groupings.


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

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

Bacterial taxonomic composition histogram. The average composition of bacteria communities obtained from surface sterilized tissues of A. vera using culture-independent method (MiSeq Illumina platform) was analysed and compared. The nomenclatures of the phylotypes are based on the SILVA rRNA database (http://www.mothur.org/wiki/Silva_reference_files).
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

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

f0010: Bacterial taxonomic composition histogram. The average composition of bacteria communities obtained from surface sterilized tissues of A. vera using culture-independent method (MiSeq Illumina platform) was analysed and compared. The nomenclatures of the phylotypes are based on the SILVA rRNA database (http://www.mothur.org/wiki/Silva_reference_files).
Mentions: The relative abundance of bacterial communities as obtained in the three tissues evaluated is shown in Fig. 1. Of the three tissues analysed, Proteobacteria sub-phylum is predominant followed by Firmicutes, Actinobacteria and Bacteroidetes. It was noted that the stem tissue has more of the genus—Pseudomonas and unclassified Pseudomonadaceae than the root and leaf tissues. On the contrary, leaf tissues have more of genus—Propionibacterium, Serratia and Brevibacterium than the root and stem tissues (refer Table S2, Table S3). In all, the root tissues have the highest richness of the four bacteria groupings.

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