Role is in the eye of the beholder—the multiple functions of the antibacterial compound tropodithietic acid produced by marine Rhodobacteraceae DOI Creative Commons

Nathalie N. S. E. Henriksen,

L. Lindqvist, Mario Wibowo

et al.

FEMS Microbiology Reviews, Journal Year: 2022, Volume and Issue: 46(3)

Published: Jan. 27, 2022

Many microbial secondary metabolites have been studied for decades primarily because of their antimicrobial properties. However, several these also possess nonantimicrobial functions, both influencing the physiology producer and ecological neighbors. An example a versatile bacterial metabolite with multiple functions is tropone derivative tropodithietic acid (TDA). TDA broad-spectrum compound produced by members Rhodobacteraceae family, major marine lineage, within genera Phaeobacter, Tritonibacter, Pseudovibrio. The production governed mode growth influenced availability nutrient sources. antibacterial effect caused disruption proton motive force target microorganisms and, potentially, its iron-chelating acts as signaling molecule, affecting gene expression in other bacteria, altering phenotypic traits such motility, biofilm formation, antibiotic producer. In communities, TDA-producing bacteria cause reduction relative abundance closely related species some fast-growing heterotrophic bacteria. Here, we summarize current understanding chemical ecology TDA, including environmental niches molecular mechanisms governing function regulation TDA.

Language: Английский

Linking Plant Secondary Metabolites and Plant Microbiomes: A Review DOI Creative Commons
Zhiqiang Pang, Jia Chen, Tuhong Wang

et al.

Frontiers in Plant Science, Journal Year: 2021, Volume and Issue: 12

Published: March 2, 2021

Plant secondary metabolites (PSMs) play many roles including defense against pathogens, pests, and herbivores; response to environmental stresses, mediating organismal interactions. Similarly, plant microbiomes participate in of the above-mentioned processes directly or indirectly by regulating metabolism. Studies have shown that plants can influence their microbiome secreting various and, turn, may also impact metabolome host plant. However, not much is known about communications between interacting partners phenotypic changes. In this article, we review patterns potential underlying mechanisms interactions PSMs microbiomes. We describe recent developments analytical approaches methods field. The applications these new increased our understanding relationships Though current studies primarily focused on model organisms, results obtained so far should help future agriculturally important facilitate development manipulate PSMs–microbiome with predictive outcomes for sustainable crop productions.

Language: Английский

Citations

474
Small molecule metabolites: discovery of biomarkers and therapeutic targets DOI Creative Commons
Shi Qiu, Ying Cai, Hong Yao

et al.

Signal Transduction and Targeted Therapy, Journal Year: 2023, Volume and Issue: 8(1)

Published: March 20, 2023

Metabolic abnormalities lead to the dysfunction of metabolic pathways and metabolite accumulation or deficiency which is well-recognized hallmarks diseases. Metabolite signatures that have close proximity subject's phenotypic informative dimension, are useful for predicting diagnosis prognosis diseases as well monitoring treatments. The lack early biomarkers could poor serious outcomes. Therefore, noninvasive methods with high specificity selectivity desperately needed. Small molecule metabolites-based metabolomics has become a specialized tool biomarker pathway analysis, revealing possible mechanisms human various deciphering therapeutic potentials. It help identify functional related variation delineate biochemical changes indicators pathological damage prior disease development. Recently, scientists established large number profiles reveal underlying networks target exploration in biomedicine. This review summarized analysis on potential value small-molecule candidate metabolites clinical events, may better diagnosis, prognosis, drug screening treatment. We also discuss challenges need be addressed fuel next wave breakthroughs.

Language: Английский

Citations

365
Mass spectrometry-based metabolomics in microbiome investigations DOI
Anelize Bauermeister, Helena Mannochio-Russo, Letícia V. Costa‐Lotufo

et al.

Nature Reviews Microbiology, Journal Year: 2021, Volume and Issue: 20(3), P. 143 - 160

Published: Sept. 22, 2021

Language: Английский

Citations

319
New software tools, databases, and resources in metabolomics: updates from 2020 DOI Open Access
Biswapriya B. Misra

Metabolomics, Journal Year: 2021, Volume and Issue: 17(5)

Published: May 1, 2021

Language: Английский

Citations

178
Marine biofilms: diversity, interactions and biofouling DOI
Pei‐Yuan Qian, Aifang Cheng, Ruojun Wang

et al.

Nature Reviews Microbiology, Journal Year: 2022, Volume and Issue: 20(11), P. 671 - 684

Published: May 25, 2022

Language: Английский

Citations

151
The gut microbiota and its biogeography DOI
Giselle McCallum, Carolina Tropini

Nature Reviews Microbiology, Journal Year: 2023, Volume and Issue: 22(2), P. 105 - 118

Published: Sept. 22, 2023

Language: Английский

Citations

134
Advances in MALDI Mass Spectrometry Imaging Single Cell and Tissues DOI Creative Commons
Xiaoping Zhu, Tianyi Xu, Peng Chen

et al.

Frontiers in Chemistry, Journal Year: 2022, Volume and Issue: 9

Published: Feb. 3, 2022

Compared with conventional optical microscopy techniques, mass spectrometry imaging (MSI) or (IMS) is a powerful, label-free analytical technique, which can sensitively and simultaneously detect, quantify, map hundreds of biomolecules, such as peptides, proteins, lipid, other organic compounds in cells tissues. So far, although several soft ionization desorption electrospray (DESI) secondary ion (SIMS) have been used for matrix-assisted laser desorption/ionization (MALDI) still the most widespread MSI scanning method. Here, we aim to provide comprehensive review MALDI-MSI an emphasis on its advances instrumentation, methods, application, future directions single cell biological

Language: Английский

Citations

81
Machine learning for microbiologists DOI Open Access
Francesco Asnicar, Andrew Maltez Thomas, Andrea Passerini

et al.

Nature Reviews Microbiology, Journal Year: 2023, Volume and Issue: 22(4), P. 191 - 205

Published: Nov. 15, 2023

Language: Английский

Citations

81
Spatial omics technologies at multimodal and single cell/subcellular level DOI Creative Commons
Jiwoon Park, Junbum Kim,

Tyler Lewy

et al.

Genome biology, Journal Year: 2022, Volume and Issue: 23(1)

Published: Dec. 13, 2022

Abstract Spatial omics technologies enable a deeper understanding of cellular organizations and interactions within tissue interest. These assays can identify specific compartments or regions in with differential transcript protein abundance, delineate their interactions, complement other methods defining phenotypes. A variety spatial methodologies are being developed commercialized; however, these techniques differ resolution, multiplexing capability, scale/throughput, coverage. Here, we review the current prospective landscape single cell to subcellular resolution analysis tools provide comprehensive picture for both research clinical applications.

Language: Английский

Citations

76
Diverse methylotrophic methanogenic archaea cause high methane emissions from seagrass meadows DOI Creative Commons
Sina Schorn, Soeren Ahmerkamp, Emma J. Bullock

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(9)

Published: Feb. 14, 2022

Marine coastlines colonized by seagrasses are a net source of methane to the atmosphere. However, emissions from these environments still poorly constrained, and underlying processes responsible microorganisms remain largely unknown. Here, we investigated turnover in seagrass meadows

Language: Английский

Citations

71