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Uncovering the hidden marine sponge microbiome by applying a multi-primer approach
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| Zeitschriftentitel: | Scientific Reports |
|---|---|
| Personen und Körperschaften: | , , |
| In: | Scientific Reports, 9, 2019, 1 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Springer Science and Business Media LLC
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| Schlagwörter: |
| author_facet |
Yang, Qi Franco, Christopher M. M. Zhang, Wei Yang, Qi Franco, Christopher M. M. Zhang, Wei |
|---|---|
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Yang, Qi Franco, Christopher M. M. Zhang, Wei |
| spellingShingle |
Yang, Qi Franco, Christopher M. M. Zhang, Wei Scientific Reports Uncovering the hidden marine sponge microbiome by applying a multi-primer approach Multidisciplinary |
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yang, qi |
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Yang, Qi Franco, Christopher M. M. Zhang, Wei 2045-2322 Springer Science and Business Media LLC Multidisciplinary http://dx.doi.org/10.1038/s41598-019-42694-w <jats:title>Abstract</jats:title><jats:p>Marine sponges (phylum Porifera) are hosts to microorganisms that make up to 40–60% of the mesohyl volume. The challenge is to characterise this microbial diversity more comprehensively. To accomplish this, a new method was for the first time proposed to obtain sequence coverage of all the variable regions of the 16S rRNA gene to analyze the amplicon-based microbiomes of four representative sponge species belonging to different orders. The five primer sets targeting nine variable regions of the 16S rRNA gene revealed a significant increase in microbiome coverage of 29.5% of phylum level OTUs and 35.5% class level OTUs compared to the community revealed by the commonly used V4 region-specific primer set alone. Among the resulting OTUs, 52.6% and 61.3% were unaffiliated, including candidate OTUs, at the phylum and class levels, respectively, which demonstrated a substantially superior performance in uncovering taxonomic ‘blind spots’. Overall, a more complete sponge microbiome profile was achieved by this multi-primer approach, given the significant improvement of microbial taxonomic coverage and the enhanced capacity to uncover novel microbial taxa. This multi-primer approach represents a fundamental and practical change from the conventional single primer set amplicon-based microbiome approach, and can be broadly applicable to other microbiome studies.</jats:p> Uncovering the hidden marine sponge microbiome by applying a multi-primer approach Scientific Reports |
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Uncovering the hidden marine sponge microbiome by applying a multi-primer approach |
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Uncovering the hidden marine sponge microbiome by applying a multi-primer approach |
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Uncovering the hidden marine sponge microbiome by applying a multi-primer approach |
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Uncovering the hidden marine sponge microbiome by applying a multi-primer approach |
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Uncovering the hidden marine sponge microbiome by applying a multi-primer approach |
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uncovering the hidden marine sponge microbiome by applying a multi-primer approach |
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<jats:title>Abstract</jats:title><jats:p>Marine sponges (phylum Porifera) are hosts to microorganisms that make up to 40–60% of the mesohyl volume. The challenge is to characterise this microbial diversity more comprehensively. To accomplish this, a new method was for the first time proposed to obtain sequence coverage of all the variable regions of the 16S rRNA gene to analyze the amplicon-based microbiomes of four representative sponge species belonging to different orders. The five primer sets targeting nine variable regions of the 16S rRNA gene revealed a significant increase in microbiome coverage of 29.5% of phylum level OTUs and 35.5% class level OTUs compared to the community revealed by the commonly used V4 region-specific primer set alone. Among the resulting OTUs, 52.6% and 61.3% were unaffiliated, including candidate OTUs, at the phylum and class levels, respectively, which demonstrated a substantially superior performance in uncovering taxonomic ‘blind spots’. Overall, a more complete sponge microbiome profile was achieved by this multi-primer approach, given the significant improvement of microbial taxonomic coverage and the enhanced capacity to uncover novel microbial taxa. This multi-primer approach represents a fundamental and practical change from the conventional single primer set amplicon-based microbiome approach, and can be broadly applicable to other microbiome studies.</jats:p> |
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| description | <jats:title>Abstract</jats:title><jats:p>Marine sponges (phylum Porifera) are hosts to microorganisms that make up to 40–60% of the mesohyl volume. The challenge is to characterise this microbial diversity more comprehensively. To accomplish this, a new method was for the first time proposed to obtain sequence coverage of all the variable regions of the 16S rRNA gene to analyze the amplicon-based microbiomes of four representative sponge species belonging to different orders. The five primer sets targeting nine variable regions of the 16S rRNA gene revealed a significant increase in microbiome coverage of 29.5% of phylum level OTUs and 35.5% class level OTUs compared to the community revealed by the commonly used V4 region-specific primer set alone. Among the resulting OTUs, 52.6% and 61.3% were unaffiliated, including candidate OTUs, at the phylum and class levels, respectively, which demonstrated a substantially superior performance in uncovering taxonomic ‘blind spots’. Overall, a more complete sponge microbiome profile was achieved by this multi-primer approach, given the significant improvement of microbial taxonomic coverage and the enhanced capacity to uncover novel microbial taxa. This multi-primer approach represents a fundamental and practical change from the conventional single primer set amplicon-based microbiome approach, and can be broadly applicable to other microbiome studies.</jats:p> |
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| spelling | Yang, Qi Franco, Christopher M. M. Zhang, Wei 2045-2322 Springer Science and Business Media LLC Multidisciplinary http://dx.doi.org/10.1038/s41598-019-42694-w <jats:title>Abstract</jats:title><jats:p>Marine sponges (phylum Porifera) are hosts to microorganisms that make up to 40–60% of the mesohyl volume. The challenge is to characterise this microbial diversity more comprehensively. To accomplish this, a new method was for the first time proposed to obtain sequence coverage of all the variable regions of the 16S rRNA gene to analyze the amplicon-based microbiomes of four representative sponge species belonging to different orders. The five primer sets targeting nine variable regions of the 16S rRNA gene revealed a significant increase in microbiome coverage of 29.5% of phylum level OTUs and 35.5% class level OTUs compared to the community revealed by the commonly used V4 region-specific primer set alone. Among the resulting OTUs, 52.6% and 61.3% were unaffiliated, including candidate OTUs, at the phylum and class levels, respectively, which demonstrated a substantially superior performance in uncovering taxonomic ‘blind spots’. Overall, a more complete sponge microbiome profile was achieved by this multi-primer approach, given the significant improvement of microbial taxonomic coverage and the enhanced capacity to uncover novel microbial taxa. This multi-primer approach represents a fundamental and practical change from the conventional single primer set amplicon-based microbiome approach, and can be broadly applicable to other microbiome studies.</jats:p> Uncovering the hidden marine sponge microbiome by applying a multi-primer approach Scientific Reports |
| spellingShingle | Yang, Qi, Franco, Christopher M. M., Zhang, Wei, Scientific Reports, Uncovering the hidden marine sponge microbiome by applying a multi-primer approach, Multidisciplinary |
| title | Uncovering the hidden marine sponge microbiome by applying a multi-primer approach |
| title_full | Uncovering the hidden marine sponge microbiome by applying a multi-primer approach |
| title_fullStr | Uncovering the hidden marine sponge microbiome by applying a multi-primer approach |
| title_full_unstemmed | Uncovering the hidden marine sponge microbiome by applying a multi-primer approach |
| title_short | Uncovering the hidden marine sponge microbiome by applying a multi-primer approach |
| title_sort | uncovering the hidden marine sponge microbiome by applying a multi-primer approach |
| title_unstemmed | Uncovering the hidden marine sponge microbiome by applying a multi-primer approach |
| topic | Multidisciplinary |
| url | http://dx.doi.org/10.1038/s41598-019-42694-w |