336
16.5.4 Next-Generation Tools
With the advancement of sequencing technology that offers larger data at much
lower cost, the focus has shifted on the next-generation tools. These include Illumina
(Solexa), 454 pyrosequencing, SOLiD sequencing, and Ion Torrent: Proton/PGM
sequencing. These tools have given access to fully sequenced and annotated
genomes that enable identification of genes, genomic regions, or alleles corelated to
factors such as disease susceptibility, stress tolerance, growth rates, and metabolism. Further, access to complete genome sequences will facilitate the development
of molecular markers that differentiate selective and random population divergence.
NGS has already been applied in analyzing microbial community and their function
in coral holobiont. For instance, a study found significant different microbial community among coral compartments using a combination of DGGE with nextgeneration sequencing and electron microscopy. This study also revealed the role of
bacteria in nitrogen fixing. These bacteria were belonging to the Rhodobacteraceae
and Vibrionaceae families that form part of O. patagonica tissues of core microbiome. Furthermore, they found sequences of coral pathogens, V. mediterranei and
V. coralliilyticus, in both bleached and healthy corals (Yang et al. 2016) which suggest that these bacteria may turn pathogenic in adverse conditions. Thus, this
advance sequencing technology would also be helpful in studying pathogenic bacteria in coral holobiont.
16.5.5 Omics Tools
16.5.5.1 Metaproteomics
It is the extension of proteomics where complete expressed proteins in the complex biological system are analyzed. It uses combinations of various tools such
as for protein separation, identification, and/or assay techniques, such as liquid
chromatography- mass
spectrometry
(LC-MS),
two-dimensional
gel
electrophoresis- mass spectrometry (2DE-MS), affinity purification-mass spectrometry (AP-MS), and protein- or antibody-based microarrays. In coral microbiology, it has wide applications such as for gaining insight into the functional
diversity of microbial component in coral holobiont. Analysis of metaproteome
of healthy and diseased corals may allow tracking of new functional genes, metabolic pathways, and proteins responsible for coral health. These proteins may be
considered as functional bioindicators for the coral ecosystem. For example, a
study of metaproteomics-based approach reveals metabolic transitions between
healthy and diseased stony coral Mussismilia braziliensis. They found a set of
proteins in healthy corals that may be considered as markers of holobiont homeostasis (Garcia et al. 2016).
N.P. Patel et al.
16.5.4 Next-Generation Tools
With the advancement of sequencing technology that offers larger data at much
lower cost, the focus has shifted on the next-generation tools. These include Illumina
(Solexa), 454 pyrosequencing, SOLiD sequencing, and Ion Torrent: Proton/PGM
sequencing. These tools have given access to fully sequenced and annotated
genomes that enable identification of genes, genomic regions, or alleles corelated to
factors such as disease susceptibility, stress tolerance, growth rates, and metabolism. Further, access to complete genome sequences will facilitate the development
of molecular markers that differentiate selective and random population divergence.
NGS has already been applied in analyzing microbial community and their function
in coral holobiont. For instance, a study found significant different microbial community among coral compartments using a combination of DGGE with nextgeneration sequencing and electron microscopy. This study also revealed the role of
bacteria in nitrogen fixing. These bacteria were belonging to the Rhodobacteraceae
and Vibrionaceae families that form part of O. patagonica tissues of core microbiome. Furthermore, they found sequences of coral pathogens, V. mediterranei and
V. coralliilyticus, in both bleached and healthy corals (Yang et al. 2016) which suggest that these bacteria may turn pathogenic in adverse conditions. Thus, this
advance sequencing technology would also be helpful in studying pathogenic bacteria in coral holobiont.
16.5.5 Omics Tools
16.5.5.1 Metaproteomics
It is the extension of proteomics where complete expressed proteins in the complex biological system are analyzed. It uses combinations of various tools such
as for protein separation, identification, and/or assay techniques, such as liquid
chromatography- mass
spectrometry
(LC-MS),
two-dimensional
gel
electrophoresis- mass spectrometry (2DE-MS), affinity purification-mass spectrometry (AP-MS), and protein- or antibody-based microarrays. In coral microbiology, it has wide applications such as for gaining insight into the functional
diversity of microbial component in coral holobiont. Analysis of metaproteome
of healthy and diseased corals may allow tracking of new functional genes, metabolic pathways, and proteins responsible for coral health. These proteins may be
considered as functional bioindicators for the coral ecosystem. For example, a
study of metaproteomics-based approach reveals metabolic transitions between
healthy and diseased stony coral Mussismilia braziliensis. They found a set of
proteins in healthy corals that may be considered as markers of holobiont homeostasis (Garcia et al. 2016).
N.P. Patel et al.