GroEL-proteotyping of bacterial communities by tandem mass spectrometry DOI Creative Commons
Simon Klaes, Shobhit Madan, Darja Deobald

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: July 3, 2023

Abstract Profiling bacterial populations in mixed communities is a common task microbiology. 16 S rRNA-based sequencing widely accepted and functional approach but relies on amplification primers cannot quantify isotope incorporation. Tandem mass spectrometry proteotyping an effective alternative for taxonomically profiling microorganisms. We suggest that targeted approaches can complement traditional population analyses. Therefore, we describe to assess community compositions at the family level using taxonomic marker protein GroEL, which ubiquitously found bacteria, except few obligate intracellular species. refer our method as GroEL-proteotyping. GroEL-proteotyping based high-resolution tandem of GroEL peptides identification GroEL-derived taxa via Galaxy workflow subsequent Python-based analysis script. Its advantage it be performed with curated extendable sample-independent database pre-separated by SDS-PAGE reduce sample complexity, improving while simultaneously decreasing instrument time. was validated employing comprehensive raw data set obtained through metaproteome from synthetic microbial well real human gut samples. Our show enables fast straightforward highly abundant reasonable resolution.

Language: Английский

Perspective Evaluation of Synthetic Biology Approaches for Effective Mitigation of Heavy Metal Pollution DOI
Sandhya Mishra, Anju Patel,

Pankaj Bhatt

et al.

Reviews of Environmental Contamination and Toxicology, Journal Year: 2024, Volume and Issue: 262(1)

Published: Oct. 11, 2024

Language: Английский

Citations

0
Bacterial synergies amplify nitrogenase activity in diverse systems DOI Creative Commons

Andrew Sher,

Robert Tournay,

Emma Gomez-Rivas

et al.

ISME Communications, Journal Year: 2024, Volume and Issue: 4(1)

Published: Jan. 1, 2024

Abstract Endophytes are microbes living within plant tissue, with some having the capacity to fix atmospheric nitrogen in both a free-living state and their host. They part of diverse microbial community whose interactions sometimes result more productive symbiosis host plant. Here, we report co-isolation diazotrophic endophytes synergistic partners sourced from two separate nutrient-limited sites. In presence these strains, nitrogen-fixing activity diazotroph is amplified. One such partnership was co-isolated extracts plants Hawaiian lava field another roots Populus trees on gravel bar Pacific Northwest. The strains were capable increasing nitrogenase different species other environments, perhaps indicating that endophytic common environments where nutrients particularly limited. Multiple overlapping mechanisms seem be involved this interaction. Though likely protecting oxygen, mechanism seems evident environments. synergies do not depend exclusively physical contact, secreted compound may involved. This work offers insights into beneficial interactions, providing potential avenues for optimizing inocula use agriculture.

Language: Английский

Citations

0
GroEL-proteotyping of bacterial communities by tandem mass spectrometry DOI Creative Commons
Simon Klaes, Shobhit Madan, Darja Deobald

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: July 3, 2023

Abstract Profiling bacterial populations in mixed communities is a common task microbiology. 16 S rRNA-based sequencing widely accepted and functional approach but relies on amplification primers cannot quantify isotope incorporation. Tandem mass spectrometry proteotyping an effective alternative for taxonomically profiling microorganisms. We suggest that targeted approaches can complement traditional population analyses. Therefore, we describe to assess community compositions at the family level using taxonomic marker protein GroEL, which ubiquitously found bacteria, except few obligate intracellular species. refer our method as GroEL-proteotyping. GroEL-proteotyping based high-resolution tandem of GroEL peptides identification GroEL-derived taxa via Galaxy workflow subsequent Python-based analysis script. Its advantage it be performed with curated extendable sample-independent database pre-separated by SDS-PAGE reduce sample complexity, improving while simultaneously decreasing instrument time. was validated employing comprehensive raw data set obtained through metaproteome from synthetic microbial well real human gut samples. Our show enables fast straightforward highly abundant reasonable resolution.

Language: Английский

Citations

1