Virola officinalis 5 claims

species · family Myristicaceae · green plant · NCBI Taxonomy ↗

NCBI synonyms: Myristica officinalis Mart., 1828, non Myristica officinalis L.f., 1781

5 claims

Method / resourceobservedoriginal resultmeasured

Claim · model-written summary

Template, PCR protocol, chloroplast proportion, and primer bias altered bacterial amplification from plant-associated samples.

Taxon: Virola officinalisVirola officinalise0
Outcome: altered bacterial 16S rDNA amplificatione0
Comparator: direct and nested PCRe0

Verbatim

e0
“Interfering factors for the 16 s rDNA amplifications, such as the type of template, direct and nested PCR, proportion of chloroplast DNA from a tropical plant source (Virola officinalis), and biased-amplification by the primers resulted in altered bacterial 16S rDNA amplification, both on MBCs and V. officinalis leaf-extracted DNA”
✓ located verbatim in the source · abstract, characters 922–1254

Title

A 16S rDNA PCR-based theoretical to actual delta approach on culturable mock communities revealed severe losses of diversity information

Hellen Ribeiro Martins dos Santos; Caio Suzart Argolo; Ronaldo Costa Argôlo-Filho; et al. BMC Microbiology 2019. doi:10.1186/s12866-019-1446-2

Other claims from this paper (4)

Method / resource The theoretical maximum fragment counts did not differ significantly between in silico and in vitro cuts.
Method / resource Primer preferences varied with mock community composition.
Method / resource Actual digestion detected 2.3 to 8.2 times fewer OTUs than theoretical data.
Method / resource The final bacterial amplification profile was much simpler than the expected detectable fragments.

Method / resourceobservedoriginal resultnot significant (as stated)measured

Claim · model-written summary

The theoretical maximum fragment counts did not differ significantly between in silico and in vitro cuts.

Taxon: Virola officinalisVirola officinalise1
Outcome: maximum number of fragmentse0
Direction: not significantly differente0
Comparator: in vitro cutse0

Verbatim

e0
“For the theoretical data, the maximum number of fragments for in silico and in vitro cuts were not significantly different from each other”
✓ located verbatim in the source · abstract, characters 1256–1394

e1
“Virola officinalis”
✓ located verbatim in the source · abstract, characters 1089–1107

Title

A 16S rDNA PCR-based theoretical to actual delta approach on culturable mock communities revealed severe losses of diversity information

Hellen Ribeiro Martins dos Santos; Caio Suzart Argolo; Ronaldo Costa Argôlo-Filho; et al. BMC Microbiology 2019. doi:10.1186/s12866-019-1446-2

Other claims from this paper (4)

Method / resource Template, PCR protocol, chloroplast proportion, and primer bias altered bacterial amplification from plant-associated samples.
Method / resource Primer preferences varied with mock community composition.
Method / resource Actual digestion detected 2.3 to 8.2 times fewer OTUs than theoretical data.
Method / resource The final bacterial amplification profile was much simpler than the expected detectable fragments.

Method / resourceobservedoriginal resultmeasured

Claim · model-written summary

Primer preferences varied with mock community composition.

Taxon: Virola officinalisVirola officinalise1
Outcome: Primers' preferences for certain sequencese0
Comparator: MBCs' composition prior to PCRe0

Verbatim

e0
“Primers' preferences for certain sequences were detected, depending on the MBCs' composition prior to PCR”
✓ located verbatim in the source · abstract, characters 1396–1501

e1
“Virola officinalis”
✓ located verbatim in the source · abstract, characters 1089–1107

Title

A 16S rDNA PCR-based theoretical to actual delta approach on culturable mock communities revealed severe losses of diversity information

Hellen Ribeiro Martins dos Santos; Caio Suzart Argolo; Ronaldo Costa Argôlo-Filho; et al. BMC Microbiology 2019. doi:10.1186/s12866-019-1446-2

Other claims from this paper (4)

Method / resource Template, PCR protocol, chloroplast proportion, and primer bias altered bacterial amplification from plant-associated samples.
Method / resource The theoretical maximum fragment counts did not differ significantly between in silico and in vitro cuts.
Method / resource Actual digestion detected 2.3 to 8.2 times fewer OTUs than theoretical data.
Method / resource The final bacterial amplification profile was much simpler than the expected detectable fragments.

Method / resourceobservedoriginal resultnegativemeasured

Claim · model-written summary

Actual digestion detected 2.3 to 8.2 times fewer OTUs than theoretical data.

Taxon: Virola officinalisVirola officinalise1
Outcome: number of OTUs detectede0
Direction: lossese0
Value: 2.3 up to 8.2 timese0
Comparator: in silico and in vitro theoretical datae0

Verbatim

e0
“overall losses from 2.3 up to 8.2 times in the number of OTUs detected from actual AluI digestions of MBCs when compared to in silico and in vitro theoretical data”
✓ located verbatim in the source · abstract, characters 1525–1688

e1
“Virola officinalis”
✓ located verbatim in the source · abstract, characters 1089–1107

Title

A 16S rDNA PCR-based theoretical to actual delta approach on culturable mock communities revealed severe losses of diversity information

Hellen Ribeiro Martins dos Santos; Caio Suzart Argolo; Ronaldo Costa Argôlo-Filho; et al. BMC Microbiology 2019. doi:10.1186/s12866-019-1446-2

Other claims from this paper (4)

Method / resource Template, PCR protocol, chloroplast proportion, and primer bias altered bacterial amplification from plant-associated samples.
Method / resource The theoretical maximum fragment counts did not differ significantly between in silico and in vitro cuts.
Method / resource Primer preferences varied with mock community composition.
Method / resource The final bacterial amplification profile was much simpler than the expected detectable fragments.

Method / resourceobservedoriginal resultmeasured

Claim · model-written summary

The final bacterial amplification profile was much simpler than the expected detectable fragments.

Taxon: Virola officinalisVirola officinalise1
Outcome: final amplification profile of the bacterial community assemblede0
Direction: remarkably simplifiede0
Comparator: expected number of detectable fragmentse0

Verbatim

e0
“final amplification profile of the bacterial community assembled was remarkably simplified when compared to the expected number of detectable fragments known to be present in the MBC”
✓ located verbatim in the source · abstract, characters 1733–1915

e1
“Virola officinalis”
✓ located verbatim in the source · abstract, characters 1089–1107

Title

A 16S rDNA PCR-based theoretical to actual delta approach on culturable mock communities revealed severe losses of diversity information

Hellen Ribeiro Martins dos Santos; Caio Suzart Argolo; Ronaldo Costa Argôlo-Filho; et al. BMC Microbiology 2019. doi:10.1186/s12866-019-1446-2

Other claims from this paper (4)

Method / resource Template, PCR protocol, chloroplast proportion, and primer bias altered bacterial amplification from plant-associated samples.
Method / resource The theoretical maximum fragment counts did not differ significantly between in silico and in vitro cuts.
Method / resource Primer preferences varied with mock community composition.
Method / resource Actual digestion detected 2.3 to 8.2 times fewer OTUs than theoretical data.