opm: an R package for analysing OmniLog® phenotype microarray data

Vaas, Lea A. I.; Sikorski, Johannes; Hofner, Benjamin; Fiebig, Anne; Buddruhs, Nora; Klenk, Hans‐Peter; Göker, Markus

doi:10.1093/bioinformatics/btt291

Cited by 193 publications

(172 citation statements)

References 12 publications

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“…Assays were run in triplicate using independently obtained transformants. OmniLog Phenotype Microarray outputs were analyzed by normalizing each individual plate against well A01 (negative control) to control for any background growth as a result of the inoculation solution and then analyzed using the R package opm (98). Data were aggregated using the "opm-fast" method, analyzed using the area under curve (AUC) parameter, and tested by t test to detect significant increase in respiration rates in the pAG416 GPD vAmt strain.…”

Section: Methodsmentioning

confidence: 99%

Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton

Monier

Chambouvet

Milner

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Phytoplankton community structure is shaped by both bottomup factors, such as nutrient availability, and top-down processes, such as predation. Here we show that marine viruses can blur these distinctions, being able to amend how host cells acquire nutrients from their environment while also predating and lysing their algal hosts. Viral genomes often encode genes derived from their host. These genes may allow the virus to manipulate host metabolism to improve viral fitness. We identify in the genome of a phytoplankton virus, which infects the small green alga Ostreococcus tauri, a host-derived ammonium transporter. This gene is transcribed during infection and when expressed in yeast mutants the viral protein is located to the plasma membrane and rescues growth when cultured with ammonium as the sole nitrogen source. We also show that viral infection alters the nature of nitrogen compound uptake of host cells, by both increasing substrate affinity and allowing the host to access diverse nitrogen sources. This is important because the availability of nitrogen often limits phytoplankton growth. Collectively, these data show that a virus can acquire genes encoding nutrient transporters from a host genome and that expression of the viral gene can alter the nutrient uptake behavior of host cells. These results have implications for understanding how viruses manipulate the physiology and ecology of phytoplankton, influence marine nutrient cycles, and act as vectors for horizontal gene transfer.Phycodnaviridae | NCLDV | prasinophytes | Mamiellophyceae | lateral gene transfer

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Section: Methodsmentioning

confidence: 99%

Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton

Monier

Chambouvet

Milner

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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“…T and at 95 % T for reference strains. Data were exported and analysed using the opm package for R v.1.0.6 (Vaas et al, 2012(Vaas et al, , 2013. Reactions with different results between the two replicates were regarded as ambiguous.…”

Section: Morphological Characteristics Of Bmg 804mentioning

confidence: 99%

Blastococcus capsensis sp. nov., isolated from an archaeological Roman pool and emended description of the genus Blastococcus, B. aggregatus, B. saxobsidens, B. jejuensis and B. endophyticus

Hezbri

Louati

Nouioui

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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“…Utilization of carbon compounds and acid production were tested using GEN III microplates in an Omnilog device (Biolog) (and growth) were measured over a total running time of 5 or 10 days, depending on the strain, in Phenotype Microarray mode at 28 uC. Data were exported and analysed using the OPM package for R (Vaas et al, 2012(Vaas et al, , 2013) version 1.0.6. Each strain was studied in two independent repetitions.…”

mentioning

confidence: 99%

Geodermatophilus brasiliensis sp. nov., isolated from Brazilian soil

Bertazzo

Montero‐Calasanz

Martínez‐García

et al. 2014

International Journal of Systematic and Evolutionary Microbiology

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A Gram-reaction-positive bacterial isolate, designated Tü 6233 T , with rudimentary, coral-pink vegetative mycelium that formed neither aerial mycelium nor spores, was isolated from a Brazilian soil sample. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the genus Geodermatophilus. Cell-wall hydrolysates contained mesodiaminopimelic acid as the diagnostic diamino acid and galactose as the diagnostic sugar. The major fatty acids were iso-C 16 : 0 , iso-C 15 : 0 and C 17 : 1 v8c and the predominant menaquinone was MK-9(H 4 ). The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol, an unknown glycophospholipid and an unknown phospholipid. The DNA G+C content of the strain was 75.4 mol%. The 16S rRNA gene sequence identity with members of the genus Geodermatophilus was 94.2-98.7 %. Based on phenotypic, chemotaxonomic and phylogenetic data, strain Tü 6233 T is proposed to represent a novel species, Geodermatophilus brasiliensis sp. nov., with the type strain Tü 6233 T (5DSM 44526 T 5CECT 8402 T ).

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opm: an R package for analysing OmniLog® phenotype microarray data

Abstract: johannes.sikorski@dsmz.de.

Cited by 193 publications

References 12 publications

Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton

Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton

Blastococcus capsensis sp. nov., isolated from an archaeological Roman pool and emended description of the genus Blastococcus, B. aggregatus, B. saxobsidens, B. jejuensis and B. endophyticus

Geodermatophilus brasiliensis sp. nov., isolated from Brazilian soil

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