Microbial metabolomics: From novel technologies to diversified applications

Ye, Dongyang; Li, Xiaowei; Shen, Jianzhong; Xia, Xi

doi:10.1016/j.trac.2022.116540

Cited by 35 publications

(23 citation statements)

References 147 publications

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“…The MCD could also provide a useful vehicle for systematically screening large gene knockout libraries in microbial engineering projects ( Porokhin et al, 2021 ). Although the MCD was evaluated here in the context of bacterial metabolism, we anticipate it could be readily adapted to studying mammalian cell culture models ( Allen et al, 2003 ; Zukunft et al, 2018 ; Lagziel et al, 2019 ; Wright Muelas et al, 2020 ), biomarker discovery ( Tolstikov et al, 2020 ), pharmaceutical lead screening ( Tomita et al, 2018 ), environmental monitoring ( Lankadurai et al, 2013 ), microbiology ( Ye et al, 2022 ), plant biology ( Kumar et al, 2017 ), and food chemistry ( Cevallos-Cevallos et al, 2009 ).…”

Section: Discussionmentioning

confidence: 99%

Microbial containment device: A platform for comprehensive analysis of microbial metabolism without sample preparation

et al. 2022

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Metabolomics is a mainstream strategy for investigating microbial metabolism. One emerging application of metabolomics is the systematic quantification of metabolic boundary fluxes – the rates at which metabolites flow into and out of cultured cells. Metabolic boundary fluxes can capture complex metabolic phenotypes in a rapid assay, allow computational models to be built that predict the behavior of cultured organisms, and are an emerging strategy for clinical diagnostics. One advantage of quantifying metabolic boundary fluxes rather than intracellular metabolite levels is that it requires minimal sample processing. Whereas traditional intracellular analyses require a multi-step process involving extraction, centrifugation, and solvent exchange, boundary fluxes can be measured by simply analyzing the soluble components of the culture medium. To further simplify boundary flux analyses, we developed a custom 96-well sampling system—the Microbial Containment Device (MCD)—that allows water-soluble metabolites to diffuse from a microbial culture well into a bacteria-free analytical well via a semi-permeable membrane. The MCD was designed to be compatible with the autosamplers present in commercial liquid chromatography-mass spectrometry systems, allowing metabolic fluxes to be analyzed with minimal sample handling. Herein, we describe the design, evaluation, and performance testing of the MCD relative to traditional culture methods. We illustrate the utility of this platform, by quantifying the unique boundary fluxes of four bacterial species and demonstrate antibiotic-induced perturbations in their metabolic activity. We propose the use of the MCD for enabling single-step metabolomics sample preparation for microbial identification, antimicrobial susceptibility testing, and other metabolic boundary flux applications where traditional sample preparation methods are impractical.

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Section: Discussionmentioning

confidence: 99%

Microbial containment device: A platform for comprehensive analysis of microbial metabolism without sample preparation

et al. 2022

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“…However, it is worth noting that regardless of which technique is selected, a wide range of metabolites should be reliably analyzed. NMR spectroscopy is a rapid, nondestructive, highly reproducible technique, which can quantify the identified metabolites and requires minimal sample preparation (Ye et al., 2022). NMR can be considered a very robust and sensitive technique, but currently, it cannot match the metabolic coverage of MS (Ramautar et al., 2013).…”

Section: Metabolomics Studiesmentioning

confidence: 99%

“…GC‐MS and LC‐MS can be used to detect hydrophobic compounds (Hendriks et al., 2011). GC‐MS has high cost‐effectiveness, outstanding separation efficiency, ease of use, and robustness (Ye et al., 2022). Noteworthily, GC‐MS approaches usually require a derivatization step and therefore are more time‐consuming techniques than LC‐MS (Aszyk et al., 2018).…”

Section: Metabolomics Studiesmentioning

confidence: 99%

“…LC‐MS can be combined with various mass analyzers and allows for effective ionization of both polar and nonpolar compounds. However, since ionization efficiency is highly dependent on sample preparation and chromatographic separation, identifying a large number of detected ions using untargeted metabolomics is a major bottleneck in LC‐MS analysis (Aszyk et al., 2018; Ye et al., 2022).…”

Section: Metabolomics Studiesmentioning

confidence: 99%

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Integrated multi‐omics approaches to understand microbiome assembly in Jiuqu, a mixed‐culture starter

Xue

Chen

Han

2022

Comp Rev Food Sci Food Safe

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The use of Jiuqu as a saccharifying and fermenting starter in the production of fermented foods is a very old biotechnological process that can be traced back to ancient times. Jiuqu harbors a hub of microbial communities, in which prokaryotes and eukaryotes cohabit, interact, and communicate. However, the spontaneous fermentation based on empirical processing hardly guarantees the stable assembly of the microbiome and a standardized quality of Jiuqu. This review describes the state of the art, limitations, and challenges towards the application of traditional and omics-based technology to study the Jiuqu microbiome and highlights the need for integrating meta-omics data. In addition, 4076

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“…Non-targeted metabonomics is mainly used to distinguish metabolite phenotypes and compare different metabolites. By a qualitative and quantitative analysis of metabolites in the biological system, it can reflect the total metabolite information to the greatest extent, then analyze their similarity, difference, and change trends, and make reasonable explanations ( Chanana et al, 2017 ; Iqrar et al, 2021 ; Oyedeji et al, 2021 ; Ye et al, 2022 ). Barkal developed a method of microbial secondary metabonomics combined with liquid–liquid extraction separation to explore the microbial culture conditions, metabolites separation procedure, and novel metabolites discovery ( Barkal et al, 2016 ).…”

Section: Introductionmentioning

confidence: 99%

Synergistic effect of co-culture rhizosphere Streptomyces: A promising strategy to enhance antimicrobial activity and plant growth-promoting function

Zhang

et al. 2022

Front. Microbiol.

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Rhizosphere Streptomyces is one of the important types of rhizosphere microorganisms that plays an important role in promoting plant growth and controlling plant diseases to maintain agricultural ecosystem balance and green ecological agriculture development as beneficial bacteria. Microbial co-culture simulates the complex biocommunity in nature, which has more advantages than the monoculture with a synergistic effect. As the key signal mediums of microorganisms, plants, and their interactions, microbial metabolites are of great significance in revealing their functional mechanism. In this study, two potential plant growth-promoting rhizobacteria, Streptomyces albireticuli MDJK11, and Streptomyces alboflavus MDJK44, were selected to explore the effects of co-culture and monoculture on plant growth promotion and disease prevention, and the metabolic material basis was analyzed by metabonomics. Results showed that Streptomyces MDJK11, MDJK44 monoculture, and co-culture condition all showed good growth promoting and antimicrobial effects. Moreover, as compared to the monoculture, the co-culture showed the advantage of a synergistic enhancement effect. LC-MS-based metabonomics analysis showed the metabolic material bases of Streptomyces for plant growth promotion and disease prevention were mainly plant hormone and antibiotics and the co-culture condition could significantly stimulate the production of plant hormone promoters and macrolide, cyclic peptide, and aminoglycoside antibiotics. The study proved that the co-cultures of S. albireticuli MDJK11 and S. alboflavus MDJK44 have great potential in crop growth promotion and disease prevention.

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Microbial metabolomics: From novel technologies to diversified applications

Cited by 35 publications

References 147 publications

Microbial containment device: A platform for comprehensive analysis of microbial metabolism without sample preparation

Microbial containment device: A platform for comprehensive analysis of microbial metabolism without sample preparation

Integrated multi‐omics approaches to understand microbiome assembly in Jiuqu, a mixed‐culture starter

Synergistic effect of co-culture rhizosphere Streptomyces: A promising strategy to enhance antimicrobial activity and plant growth-promoting function

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