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 In a similar study on culturable endophytic bacteria in the same A. vera plants (unpublished work), the dominance of Pseudomonas and Bacillus genera was similar, with equal proportion of four species each in root, stem and leaf tissues.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

Venn diagram describing the OTU distribution across tissue samples.
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f0015: Venn diagram describing the OTU distribution across tissue samples.

Mentions: Our study revealed for the first time the possibility of Illumina sequencing protocol to evaluate microbiota present in plant tissues–bacterial endophytes. The sequencing can be improved with good choice of primer pair to amplify a longer stretch of the 16S rRNA gene. Our empirical results highlight the utility of this platform for precise and high resolution microbiota profiling (> 90% at species level) of endophytic communities, or perhaps extended to other resources/samples. The improvement to the various analyses tools was equally important to minimise the biasness introduced by the host DNA (chloroplast) and chimaera which was removed without affecting the overall quality of the reads. Mothur pipeline relatively provides us a good opportunity to effectively process the read sequence on a single platform. This minimised the probable loss of quality of reads. The use of novel shotgun 16S rRNA gene by NGS has also revealed the overall richness and diversity of microbiota communities in plant tissues to encompass both the culturable and unculturable endophytic bacteria. 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 further elucidates the microbial colonisation of plant tissues as revealed by the Venn diagram which illustrates the distribution of the bacterial communities across the tissues and the total shared richness (Fig. 2).


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

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

Venn diagram describing the OTU distribution across tissue samples.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

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

f0015: Venn diagram describing the OTU distribution across tissue samples.
Mentions: Our study revealed for the first time the possibility of Illumina sequencing protocol to evaluate microbiota present in plant tissues–bacterial endophytes. The sequencing can be improved with good choice of primer pair to amplify a longer stretch of the 16S rRNA gene. Our empirical results highlight the utility of this platform for precise and high resolution microbiota profiling (> 90% at species level) of endophytic communities, or perhaps extended to other resources/samples. The improvement to the various analyses tools was equally important to minimise the biasness introduced by the host DNA (chloroplast) and chimaera which was removed without affecting the overall quality of the reads. Mothur pipeline relatively provides us a good opportunity to effectively process the read sequence on a single platform. This minimised the probable loss of quality of reads. The use of novel shotgun 16S rRNA gene by NGS has also revealed the overall richness and diversity of microbiota communities in plant tissues to encompass both the culturable and unculturable endophytic bacteria. 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 further elucidates the microbial colonisation of plant tissues as revealed by the Venn diagram which illustrates the distribution of the bacterial communities across the tissues and the total shared richness (Fig. 2).

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