Sample Preparation in Microbial Metabolomics: Advances and Challenges.

Heiter V M Boness, Hanna C de Sá, Emile K P Dos Santos, Gisele A B Canuto

Abstract read

In one paragraph

Article in Advances in experimental medicine and biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it

0cells of the map it votes in

1citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

Metabolomic insights into glutamate-induced γ-PGA biosynthesis and process optimization in Bacillus subtilis SCP017-03 for scalable production.Bioprocess and biosystems engineering · 2025
Article

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Heiter V M BonessDepartment of Analytical Chemistry, Institute of Chemistry, Federal University of Bahia, Salvador, BA, Brazil.

Hanna C de SáDepartment of Analytical Chemistry, Institute of Chemistry, Federal University of Bahia, Salvador, BA, Brazil.

Emile K P Dos SantosDepartment of Analytical Chemistry, Institute of Chemistry, Federal University of Bahia, Salvador, BA, Brazil.

Gisele A B CanutoDepartment of Analytical Chemistry, Institute of Chemistry, Federal University of Bahia, Salvador, BA, Brazil. gisele.canuto@ufba.br.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Microbial metabolomics has gained significant interest as it reflects the physiological state of microorganisms. Due to the great variability of biological organisms, in terms of physicochemical characteristics and variable range of concentration of metabolites, the choice of sample preparation methods is a crucial step in the metabolomics workflow and will reflect on the quality and reliability of the results generated. The procedures applied to the preparation of microbial samples will vary according to the type of microorganism studied, the metabolomics approach (untargeted or targeted), and the analytical platform of choice. This chapter aims to provide an overview of the sample preparation workflow for microbial metabolomics, highlighting the pre-analytical factors associated with cultivation, harvesting, metabolic quenching, and extraction. Discussions focus on obtaining intracellular and extracellular metabolites. Finally, we introduced advanced sample preparation methods based on automated systems.

Indexed as

MetabolomeMetabolomicsReproducibility of ResultsSpecimen HandlingCellular cultivationExtracellular metabolomeIntracellular metabolomeMetabolic quenchingMetabolite extractionMicrobial metabolomicsSample preparation

Identifiers

PMID37843809

DOI10.1111/1751-7915.13905

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.