TY - JOUR

T1 - A Metabolomics-Based Toolbox to Assess and Compare the Metabolic Potential of Unexplored, Difficult-to-Grow Bacteria

AU - Fiorini, Federica

AU - Bajerski, Felizitas

AU - Jeske, Olga

AU - Lepleux, Cendrella

AU - Overmann, Jörg

AU - Brönstrup, Mark

N1 - We gratefully acknowledge the support by Alicia Geppert, Anika Methner, Franziska Klann, Javier Pascual, Ulrike Beutling and Raimo Franke. Soil sample isolates were obtained by Selma Gomes Vieira. Isolate Rhodobacteraceae bacterium D100-Iso2 was isolated by Victoria Ringel (DSMZ) from a cyanobacterial culture provided by Valeria Villanova (in the framework of the EMBRIC project). Rhodobacteraceae sp. MEBiC05055, was kindly provided by Kae Kyoung Kwon. We thank Silke Pradella and Orsola Päuker (DSMZ) for the isolation and provision of strains from algal cultures (in the frame of the Transregional Collaborative Research Center [TRR51] founded by the Deutsche Forschungsgemeinschaft [DFG, German Research Foundation]). Samples were collected during different sampling campaigns in the framework of the following projects: ATKiM (SAW-2011-IOW-3), MaCuMBA (FP7-KBBE-2012-6-311975), DFG SPP 1374 Biodiversitäts-Exploratorien: ProFunD and ProFunD-2 (OV 20/21-1 and OV 20/21-2), MikrOMIK (SAW-2014-IOW-2) and H2020-INFRADEV-2014-2015: EMBRIC (H2020_INFRADEV-1-2014-1).

PY - 2022/11

Y1 - 2022/11

N2 - Novel high-throughput cultivation techniques create a demand to pre-select strains for in-depth follow-up studies. We report a workflow to identify promising producers of novel natural products by systematically characterizing their metabolomes. For this purpose, 60 strains from four phyla (Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes) comprising 16 novel species and six novel genera were cultivated from marine and terrestrial sources. Their cellular metabolomes were recorded by LC-MS/MS; data analysis comprised databases MS/MS matching, in silico compound assignment, and GNPS-based molecular networking. Overall, 1052 different molecules were identified from 6418 features, among them were unusual metabolites such as 4-methoxychalcone. Only a minor portion of the 755 features were found in all phyla, while the majority occurred in a single phylogroup or even in a single strain. Metabolomic methods enabled the recognition of highly talented strains such as AEG42_45, which had 107 unique features, among which a family of 28 potentially novel and related compounds according to MS/MS similarities. In summary, we propose that high-throughput cultivation and isolation of bacteria in combination with the presented systematic and unbiased metabolome analysis workflow is a promising approach to capture and assess the enormous metabolic potential of previously uncultured bacteria.

AB - Novel high-throughput cultivation techniques create a demand to pre-select strains for in-depth follow-up studies. We report a workflow to identify promising producers of novel natural products by systematically characterizing their metabolomes. For this purpose, 60 strains from four phyla (Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes) comprising 16 novel species and six novel genera were cultivated from marine and terrestrial sources. Their cellular metabolomes were recorded by LC-MS/MS; data analysis comprised databases MS/MS matching, in silico compound assignment, and GNPS-based molecular networking. Overall, 1052 different molecules were identified from 6418 features, among them were unusual metabolites such as 4-methoxychalcone. Only a minor portion of the 755 features were found in all phyla, while the majority occurred in a single phylogroup or even in a single strain. Metabolomic methods enabled the recognition of highly talented strains such as AEG42_45, which had 107 unique features, among which a family of 28 potentially novel and related compounds according to MS/MS similarities. In summary, we propose that high-throughput cultivation and isolation of bacteria in combination with the presented systematic and unbiased metabolome analysis workflow is a promising approach to capture and assess the enormous metabolic potential of previously uncultured bacteria.

KW - difficult-to-grow bacteria

KW - LC-MS/MS

KW - natural products

KW - novel bacterial strains

KW - untargeted metabolomics

UR - http://www.scopus.com/inward/record.url?scp=85142632083&partnerID=8YFLogxK

U2 - 10.3390/md20110713

DO - 10.3390/md20110713

M3 - Article

C2 - 36421991

AN - SCOPUS:85142632083

VL - 20

JO - Marine Drugs

JF - Marine Drugs

SN - 1660-3397

IS - 11

M1 - 713

ER -