Metabolic Footprinting:  A New Approach to Identify Physiological Changes in Complex Microbial Communities upon Exposure to Toxic Chemicals

2007 ◽  
Vol 41 (11) ◽  
pp. 3945-3951 ◽  
Author(s):  
Inês D. S. Henriques ◽  
Diana S. Aga ◽  
Pedro Mendes ◽  
Seamus K. O'Connor ◽  
Nancy G. Love
Keyword(s):  
Microbial Communities ◽  
Toxic Chemicals ◽  
Physiological Changes ◽  
New Approach ◽  
Metabolic Footprinting

scholarly journals Role of Helicobacter pylori and Other Environmental Factors in the Development of Gastric Dysbiosis

Pathogens ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1203
Author(s):  
Uriel Gomez-Ramirez ◽  
Pedro Valencia-Mayoral ◽  
Sandra Mendoza-Elizalde ◽  
Juan Rafael Murillo-Eliosa ◽  
Fortino Solórzano Santos ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Microbial Communities ◽  
Optimal Growth ◽  
Human Stomach ◽  
Physiological Changes ◽  
Heterogeneous Habitat ◽  
The World ◽  
H Pylori ◽  
Gastric Microbiota

Microbiomes are defined as complex microbial communities, which are mainly composed of bacteria, fungi, and viruses residing in diverse regions of the human body. The human stomach consists of a unique and heterogeneous habitat of microbial communities owing to its anatomical and functional characteristics, that allow the optimal growth of characteristic bacteria in this environment. Gastric dysbiosis, which is defined as compositional and functional alterations of the gastric microbiota, can be induced by multiple environmental factors, such as age, diet, multiple antibiotic therapies, proton pump inhibitor abuse, H. pylori status, among others. Although H. pylori colonization has been reported across the world, chronic H. pylori infection may lead to serious consequences; therefore, the infection must be treated. Multiple antibiotic therapy improvements are not always successful because of the lack of adherence to the prescribed antibiotic treatment. However, the abuse of eradication treatments can generate gastric dysbiotic states. Dysbiosis of the gastric microenvironment induces microbial resilience, due to the loss of relevant commensal bacteria and simultaneous colonization by other pathobiont bacteria, which can generate metabolic and physiological changes or even initiate and develop other gastric disorders by non-H. pylori bacteria. This systematic review opens a discussion on the effects of multiple environmental factors on gastric microbial communities.

scholarly journals Microarray-Based Analysis of Microbial Community RNAs by Whole-Community RNA Amplification

2006 ◽  
Vol 73 (2) ◽  
pp. 563-571 ◽  
Author(s):  
Haichun Gao ◽  
Zamin K. Yang ◽  
Terry J. Gentry ◽  
Liyou Wu ◽  
Christopher W. Schadt ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Environmental Samples ◽  
Bacterial Species ◽  
Shewanella Oneidensis ◽  
Rna Amplification ◽  
T7 Promoter ◽  
New Approach ◽  
Functional Activities ◽  
Amplification Method ◽  
Groundwater Samples

ABSTRACT A new approach, termed whole-community RNA amplification (WCRA), was developed to provide sufficient amounts of mRNAs from environmental samples for microarray analysis. This method employs fusion primers (six to nine random nucleotides with an attached T7 promoter) for the first-strand synthesis. The shortest primer (T7N6S) gave the best results in terms of the yield and representativeness of amplification. About 1,200- to 1,800-fold amplification was obtained with amounts of the RNA templates ranging from 10 to 100 ng, and very representative detection was obtained with 50 to 100 ng total RNA. Evaluation with a Shewanella oneidensis Δfur strain revealed that the amplification method which we developed could preserve the original abundance relationships of mRNAs. In addition, to determine whether representative detection of RNAs can be achieved with mixed community samples, amplification biases were evaluated with a mixture containing equal quantities of RNAs (100 ng each) from four bacterial species, and representative amplification was also obtained. Finally, the method which we developed was applied to the active microbial populations in a denitrifying fluidized bed reactor used for denitrification of contaminated groundwater and ethanol-stimulated groundwater samples for uranium reduction. The genes expressed were consistent with the expected functions of the bioreactor and groundwater system, suggesting that this approach is useful for analyzing the functional activities of microbial communities. This is one of the first demonstrations that microarray-based technology can be used to successfully detect the activities of microbial communities from real environmental samples in a high-throughput fashion.

scholarly journals Raman spectroscopy-based measurements of single-cell phenotypic diversity in microbial communities

2020 ◽  
Author(s):  
Cristina García-Timermans ◽  
Ruben Props ◽  
Boris Zacchetti ◽  
Myrsini Sakarika ◽  
Frank Delvigne ◽  
...  
Keyword(s):  
Raman Spectroscopy ◽  
Microbial Communities ◽  
Single Cell ◽  
Raman Spectra ◽  
Phenotypic Diversity ◽  
Single Cells ◽  
Cell Permeability ◽  
Molecular Profile ◽  
Cell Physiology ◽  
Physiological Changes

AbstractMicrobial cells experience physiological changes due to environmental change, such as pH and temperature, the release of bactericidal agents, or nutrient limitation. This, has been shown to affect community assembly and other processes such as stress tolerance, virulence or cell physiology. Metabolic stress is one such physiological changes and is typically quantified by measuring community phenotypic properties such as biomass growth, reactive oxygen species or cell permeability. However, community measurements do not take into account single-cell phenotypic diversity, important for a better understanding and management of microbial populations. Raman spectroscopy is a non-destructive alternative that provides detailed information on the biochemical make-up of each individual cell.Here, we introduce a method for describing single-cell phenotypic diversity using the Hill diversity framework of Raman spectra. Using the biomolecular profile of individual cells, we obtained a metric to compare cellular states and used it to study stress-induced changes. First, in two Escherichia coli populations either treated with ethanol or non-treated. Then, in two Saccharomyces cerevisiae subpopulations with either high or low expression of a stress reporter. In both cases, we were able to quantify single-cell phenotypic diversity and to discriminate metabolically stressed cells using a clustering algorithm. We also described how the lipid, protein and nucleic acid composition changed after the exposure to the stressor using information from the Raman spectra. Our results show that Raman spectroscopy delivers the necessary resolution to quantify phenotypic diversity within individual cells and that this information can be used to study stress-driven metabolic diversity in microbial communities.ImportanceMicrobes that live in the same community respond differently to stress. This phenomemon is known as phenotypic diversity. Describing this plethora of expressions can help to better understand and manage microbial processes. However, most tools to study phenotypic diversity only average the behaviour of the community. In this work, we present a way to quantify the phenotypic diversity of single cells using Raman spectroscopy - a tool that can describe the molecular profile of microbes. We demonstrate how this tool can be used to quantify the phenotypic diversity that arises after the exposure of microbes to stress. We also show its potential as an ‘alarm’ system to detect when communities are changing into a ‘stressed’ type.

scholarly journals Analysis of Microbial Gene Transcripts in Environmental Samples†

2005 ◽  
Vol 71 (7) ◽  
pp. 4121-4126 ◽  
Author(s):  
Rachel S. Poretsky ◽  
Nasreen Bano ◽  
Alison Buchan ◽  
Gary LeCleir ◽  
Jutta Kleikemper ◽  
...  
Keyword(s):  
Gene Expression ◽  
Microbial Communities ◽  
Environmental Samples ◽  
Sulfur Oxidation ◽  
Subtractive Hybridization ◽  
Functional Genes ◽  
New Approach ◽  
Total Rna ◽  
Gene Transcripts ◽  
Taxonomic Groups

ABSTRACT We analyzed gene expression in marine and freshwater bacterioplankton communities by the direct retrieval and analysis of microbial transcripts. Environmental mRNA, obtained from total RNA by subtractive hybridization of rRNA, was reverse transcribed, amplified with random primers, and cloned. Approximately 400 clones were analyzed, of which ∼80% were unambiguously mRNA derived. mRNAs appeared to be from diverse taxonomic groups, including both Bacteria (mainly α- and γ-Proteobacteria) and Archaea (mainly Euryarchaeota). Many transcripts could be linked to environmentally important processes such as sulfur oxidation (soxA), assimilation of C1 compounds (fdh1B), and acquisition of nitrogen via polyamine degradation (aphA). Environmental transcriptomics is a means of exploring functional gene expression within natural microbial communities without bias toward known sequences, and provides a new approach for obtaining community-specific variants of key functional genes.

The O–C diagrams of minor planets − a new approach to modelling the rotation

1999 ◽  
Vol 173 ◽  
pp. 185-188
Author(s):  
Gy. Szabó ◽  
K. Sárneczky ◽  
L.L. Kiss
Keyword(s):  
Error Analysis ◽  
Time Dependence ◽  
Theoretical Work ◽  
Minor Planet ◽  
Minor Planets ◽  
New Approach ◽  
Preliminary Results ◽  
Ccd Observations

AbstractA widely used tool in studying quasi-monoperiodic processes is the O–C diagram. This paper deals with the application of this diagram in minor planet studies. The main difference between our approach and the classical O–C diagram is that we transform the epoch (=time) dependence into the geocentric longitude domain. We outline a rotation modelling using this modified O–C and illustrate the abilities with detailed error analysis. The primary assumption, that the monotonity and the shape of this diagram is (almost) independent of the geometry of the asteroids is discussed and tested. The monotonity enables an unambiguous distinction between the prograde and retrograde rotation, thus the four-fold (or in some cases the two-fold) ambiguities can be avoided. This turned out to be the main advantage of the O–C examination. As an extension to the theoretical work, we present some preliminary results on 1727 Mette based on new CCD observations.

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