A High-Resolution LC-MS-Based Secondary Metabolite Fingerprint Database of Marine Bacteria

Abstract

Marine bacteria are the most widely distributed organisms in the ocean environment and produce a wide variety of secondary metabolites. However, traditional screening for bioactive natural compounds is greatly hindered by the lack of a systematic way of cataloguing the chemical profiles of bacterial strains found in nature. Here we present a chemical fingerprint database of marine bacteria based on their secondary metabolite profiles, acquired by high-resolution LC-MS. Till now, 1,430 bacterial strains spanning 168 known species collected from different marine environments were cultured and profiled. Using this database, we demonstrated that secondary metabolite profile similarity is approximately, but not always, correlated with taxonomical similarity. We also validated the ability of this database to find species-specific metabolites, as well as to discover known bioactive compounds from previously unknown sources. An online interface to this database, as well as the accompanying software, is provided freely for the community to use.

Metabolomics‐based chemotaxonomy of root endophytic fungi for natural products discovery

“…We aimed to reduce complexity in chemical space by using an automated dereplication pipeline to match MS/MS spectra across samples, find Chemotaxonomy of root endophytic fungi 1259 patterns in their occurrence, and identify known compounds via database searches. The same strategy has been applied to screen large microbial culture collections (Lu et al, 2014;Floros et al, 2016;Cr€ usemann et al, 2017) but, to our knowledge, this is the first time they are applied to fungi.…”

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Analysis of Antimicrobial Peptide Metabolome of Bacterial Endophyte Isolated From Traditionally Used Medicinal Plant Millettia pachycarpa Benth

“…The peptides (VP_1369) were loaded with buffer A (5% acetonitrile, 0.1% formic acid) and eluted with a 0–40% gradient of buffer B (95% acetonitrile, 0.1% formic acid) at a flow rate of 300 nl/min for 90 min. Liquid chromatography coupled to tandem mass spectrometry (LC/MS/MS) was used to identify the components of extracellular protein complex ( Seidler et al, 2010 ; Lu et al, 2014 ). MS data were acquired using a data-dependent top 10 method dynamically choosing the most abundant precursor ions from the survey scan.…”

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Marine bacterial extracts as a new rich source of drugs against Alzheimer’s disease

“…The standard culture protocol was used to grow the bacterial strains (Lu et al ). Briefly, each strain was fermented in a 250 mL flask in GYPT culture medium (glucose: 10 g/L; yeast extract: 2 g/L, #LP0021, OXOID; tryptone: 2.5 g/L, #LP0042, OXOID; peptone: 2.5 g/L, #LP0037, OXOID; sea salt: 35 g/L, HAIN).…”