MPACT: An Advanced Informatics Tool for Metabolomics and Data Visualization of Specialized Metabolites from Complex Microbial Samples

Samples, Robert M.; Puckett, Sara P.; Balunas, Marcy J.

doi:10.26434/chemrxiv-2022-r0xbx

Cited by 4 publications

(3 citation statements)

References 54 publications

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“…The following electrospray ionization (ESI) settings were used in probe position D: 40 sheath gas flow, 8 auxiliary gas flow, 1 sweep gas flow, 3.5 kV spray voltage, 380°C capillary temperature, 50 radiofrequency (RF) funnel level, and 350°C auxiliary gas temperature. Data were evaluated using MS-DIAL (Tsugawa et al, 2015) and MPACT (Samples et al, 2022). See supplementary information for data processing methods.…”

Section: Lc/ms Analysesmentioning

confidence: 99%

Genomic and phenotypic characterization of a red-pigmented strain of Massilia frigida isolated from an Antarctic microbial mat

et al. 2023

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The McMurdo Dry Valleys of Antarctica experience a range of selective pressures, including extreme seasonal variation in temperature, water and nutrient availability, and UV radiation. Microbial mats in this ecosystem harbor dense concentrations of biomass in an otherwise desolate environment. Microbial inhabitants must mitigate these selective pressures via specialized enzymes, changes to the cellular envelope, and the production of secondary metabolites, such as pigments and osmoprotectants. Here, we describe the isolation and characterization of a Gram-negative, rod-shaped, motile, red-pigmented bacterium, strain DJPM01, from a microbial mat within the Don Juan Pond Basin of Wright Valley. Analysis of strain DJMP01’s genome indicates it can be classified as a member of the Massilia frigida species. The genome contains several genes associated with cold and salt tolerance, including multiple RNA helicases, protein chaperones, and cation/proton antiporters. In addition, we identified 17 putative secondary metabolite gene clusters, including a number of nonribosomal peptides and ribosomally synthesized and post-translationally modified peptides (RiPPs), among others, and the biosynthesis pathway for the antimicrobial pigment prodigiosin. When cultivated on complex agar, multiple prodiginines, including the antibiotic prodigiosin, 2-methyl-3-propyl-prodiginine, 2-methyl-3-butyl-prodiginine, 2-methyl-3-heptyl-prodiginine, and cycloprodigiosin, were detected by LC–MS. Genome analyses of sequenced members of the Massilia genus indicates prodigiosin production is unique to Antarctic strains. UV-A radiation, an ecological stressor in the Antarctic, was found to significantly decrease the abundance of prodiginines produced by strain DJPM01. Genomic and phenotypic evidence indicates strain DJPM01 can respond to the ecological conditions of the DJP microbial mat, with prodiginines produced under a range of conditions, including extreme UV radiation.

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Section: Lc/ms Analysesmentioning

confidence: 99%

Genomic and phenotypic characterization of a red-pigmented strain of Massilia frigida isolated from an Antarctic microbial mat

et al. 2023

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“…Metabolomics data processing, filtering, and statistical analyses: The peak list and fragment database were exported from Progenesis and analyzed with MPACT (78). Data were filtered using solvent blank, mispicked peak, reproducibility, and in-source fragment filters (SI Appendix, Fig.…”

Section: Metabolomics and Statistical Analyses Of Trichoderma Extract...mentioning

confidence: 99%

Trachymyrmex septentrionalisants promote fungus garden hygiene usingTrichoderma-derived metabolite cues

Kyle

Puckett

Caraballo‐Rodríguez

et al. 2022

Preprint

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Fungus-growing ants depend on a fungal mutualist that can fall prey to fungal pathogens. This mutualist is cultivated by these ants in structures called fungus gardens. Ants exhibit weeding behaviors that keep their garden healthy by physically removing compromised pieces. However, how ants detect diseases of their fungus gardens is unknown. Here, we applied the logic of Koch's postulates using environmental fungal community genomic sequencing, fungal isolation, and in vitro infection experiments to establish Trichoderma spp. as pathogens of Trachymyrmex septentrionalis fungus gardens. Our environmental data showed that Trichoderma are the most abundant non-cultivar fungi in wild T. septentrionalis fungus gardens. We further determined that metabolites produced by Trichoderma induce an ant weeding response that mirrors their response to live Trichoderma. Combining ant behavioral experiments with bioactivity-guided fractionation and statistical prioritization of metabolites in Trichoderma extracts demonstrated that T. septentrionalis ants weed in response to peptaibols, a specific class of secondary metabolites known to be produced by Trichoderma fungi. Similar assays conducted using purified peptaibols, including the two new peptaibols trichokindins VIII and IX, suggested that weeding is likely induced by peptaibols as a class rather than by a single peptaibol metabolite. In addition to their presence in laboratory experiments, we detected peptaibols in wild fungus gardens. Our combination of environmental data and in vitro experiments strongly support that peptaibols act as chemical cues of Trichoderma pathogenesis in T. septentrionalis fungus gardens.

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“…This variability in selection principles hampers automation, rendering prioritization still a mostly manual task. Currently available software solutions are typically designed with specific tasks and/or research fields in mind i.e., data quality control [22,23], statistical analysis [24,25], molecular feature annotation [26, 27], or natural product drug discovery [28, 29, 30, 31]. Further, there is a lack of tools that combine and visualize multiple (meta)data types and their relationships in one view.…”

Section: Introductionmentioning

confidence: 99%

FERMO: a Dashboard for Streamlined Rationalized Prioritization of Molecular Features from Mass Spectrometry Data

Zdouc

Bayona

Augustijn

et al. 2022

Preprint

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Small molecules can selectively modulate biological processes and thus generate phenotypic variation. Biological samples are complex matrices, and liquid chromatography tandem mass spectrometry often detects hundreds of molecules, of which only a fraction may be associated with this variation. The challenge therefore lies in the prioritization of the most relevant molecules for further investigation. Tools are needed to effectively contextualize mass spectrometric data with phenotypical and environmental (meta)data. To accelerate this task, we developed FERMO, a dashboard application combining mass spectrometry data with qualitative and quantitative biological observations. FERMO's centralized interface enables users to rapidly inspect data, formulate hypotheses, and prioritize molecules of interest. We demonstrate the applicability of FERMO in a case study on antibiotic activity of bacterial extracts, where we successfully prioritized the bioactive molecule siomycin out of 143 molecular features. We expect that besides natural product discovery, FERMO will find application in a wide range of omics-driven fields.

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MPACT: An Advanced Informatics Tool for Metabolomics and Data Visualization of Specialized Metabolites from Complex Microbial Samples

Cited by 4 publications

References 54 publications

Genomic and phenotypic characterization of a red-pigmented strain of Massilia frigida isolated from an Antarctic microbial mat

Genomic and phenotypic characterization of a red-pigmented strain of Massilia frigida isolated from an Antarctic microbial mat

Trachymyrmex septentrionalisants promote fungus garden hygiene usingTrichoderma-derived metabolite cues

FERMO: a Dashboard for Streamlined Rationalized Prioritization of Molecular Features from Mass Spectrometry Data

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