A New Physiological Role for the DNA Molecule as a Protector against Drying Stress in Desiccation-Tolerant Microorganisms

García-Fontana, Cristina; Narváez-Reinaldo, Juan Jesús; Castillo, Francisco; González‐López, Jesús; Luque, Irene; Manzanera, Maximino

doi:10.3389/fmicb.2016.02066

Cited by 21 publications

(18 citation statements)

References 49 publications

(58 reference statements)

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“…One aliquot was applied in the conventional microbiome analysis targeting total DNA; the other aliquot was used for the PMA microbiome method targeting viable cell DNA using PMAxx dye (Biotium Inc., Hayward, CA) (Garcia‐Fontana et al . ; Randazzo et al . , ).…”

Section: Methodsmentioning

confidence: 99%

Faecal freezing preservation period influences colonization ability for faecal microbiota transplantation

et al. 2019

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Aims There has been growing interest in faecal microbiota transplantation (FMT) as treatment. Although, frozen donor faeces preserved at −20°C has been widely used for practical advantages, freezing at −20°C can affect bacterial viability. Adequacy evaluation of fresh and frozen faeces as the transplant is necessary for the methodological improvement of FMT. Methods and Results The viable bacterial compositions of faecal specimens under fresh and freezing conditions were compared by a microbiome analysis using propidium monoazide (PMA microbiome). In addition, recovery abilities from bacterial reduction by antibiotics were compared between fresh and frozen FMT using a murine model. PMA microbiome results suggested that freezing and freeze‐thawing did not significantly affect in vitro faecal bacterial viability. However, the recovery effect from antimicrobial cleansing in frozen FMT was reduced in a freezing time‐dependent manner, especially prominent in Actinobacteria and Bacteroidetes phyla. Conclusions Short‐term freezing preservation of faeces exhibited maintenance of enteric colonization ability in frozen FMT in comparison to 1 month −20°C‐preservation. Significance and Impact of the Study Long‐term −20°C‐preservation of transplanted faeces can result in instability of the clinical outcome in FMT therapy. The standardization of practical procedures of FMT therapy according to disease types is desirable.

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Section: Methodsmentioning

confidence: 99%

Faecal freezing preservation period influences colonization ability for faecal microbiota transplantation

et al. 2019

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“…Each sample solution was divided into two separate 500-l aliquots. One aliquot was used for the culture-based method and analyses targeting total DNA such as PCR and conventional microbiome methods; the other aliquot was used for the PMA microbiome method targeting viable cell DNA using PMAxx dye (Biotium, Inc., CA) (62)(63)(64).…”

Section: Methodsmentioning

confidence: 99%

Development of a New Application for Comprehensive Viability Analysis Based on Microbiome Analysis by Next-Generation Sequencing: Insights into Staphylococcal Carriage in Human Nasal Cavities

Sasaki

Kuwahara‐Arai

et al. 2018

Appl Environ Microbiol

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The nasal carriage rate of in human is 25--30% and sporadically causes severe infections. However, mechanisms underlying staphylococcal carriage remain largely unknown. In the present study, we constructed an -based microbiome method for staphylococcal species discrimination. Based on a microbiome scheme targeting viable cell DNA using PMA dye (PMA microbiome), we also developed a new method to allow the comprehensive viability analysis of any bacterial taxon. To clarify the ecological distribution of staphylococci in the nasal microbiota, we applied these methods in 46 nasal specimens from healthy adults. PMA microbiome results showed that and were the most predominant viable taxa (average relative abundance: 0.435262 and 0.375195, respectively), and exhibited the highest viability in the nasal microbiota. detection rates from nasal specimens by-based conventional and PMA microbiome were 84.8% (39 of 46) and 69.5% (32 of 46), respectively, which substantially exceeded the values by a culture method using identical specimens (36.9%). Our results suggests that especially adapted most successfully to human nasal cavity. High detection of DNA by microbiome methods suggests that almost all healthy adults are consistently exposed to in everyday life. Furthermore, the large difference in detection rates between culture and microbiome methods suggests that cells frequently exist under the viable but non-culturable state in nasal cavities. Our method and findings will contribute to a better understanding of the mechanisms underlying carriage of indigenous bacteria. Metagenomic analyses, such as 16S rRNA microbiome, have provided new insight in various research fields. However, conventional 16S rRNA microbiome dose not permit taxonomic analysis of only viable bacteria, and has poor resolving power below the genus level. Our new schemes allowed for viabile cell specific analysis and species discrimination, nasal microbiome data using these methods provided some interesting findings regarding staphylococcal nasal carriage. According to our comprehensive viability analysis, high viability of genus, especialy in human nasal carriage suggests that this taxon has adapted most successfully to human nasal tissue. And also, higher detection of DNA by microbiome methods (84.8%) than that by a culture method (36.9%) suggests that almost all healthy adults are consistently exposed to in the medium- and long-term. Our findings will contribute to a better understanding of the mechanisms underlying carriage of indigenous bacteria.

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“…3J1 also increased the production of certain nucleotides such as thymine or uracil (by 2.56- and 4.57-fold), or their substrates such as adenosine (by 2.45-fold) that may help to increase DNA production in the plant. We have recently described the role of the DNA molecule in the protection of biomolecules from damage produced by drought (García-Fontana et al, 2016 ). Therefore, we do not discard the production of DNA by the plant in presence of the microorganism as a defensive system from the deleterious damage produced by drought.…”

Section: Resultsmentioning

confidence: 99%

Protection of Pepper Plants from Drought by Microbacterium sp. 3J1 by Modulation of the Plant's Glutamine and α-ketoglutarate Content: A Comparative Metabolomics Approach

et al. 2018

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Drought tolerance of plants such as tomato or pepper can be improved by their inoculation with rhizobacteria such as Microbacterium sp. 3J1. This interaction depends on the production of trehalose by the microorganisms that in turn modulate the phyto-hormone profile of the plant. In this work we describe the characterization of metabolic changes during the interaction of pepper plants with Microbacterium sp. 3J1 and of the microorganism alone over a period of drought. Our main findings include the observation that the plant responds to the presence of the microorganism by changing the C and N metabolism based on its glutamine and α-ketoglutarate content, these changes contribute to major changes in the concentration of molecules involved in the balance of the osmotic pressure. These include sugars and amino-acids; the concentration of antioxidant molecules, of metabolites involved in the production of phytohormones like ethylene, and of substrates used for lignin production such as ferulic and sinapic acids. Most of the altered metabolites of the plant when inoculated with Microbacterium sp. 3J1 in response to drought coincided with the profile of altered metabolites in the microorganism alone when subjected to drought, pointing to a response by which the plant relies on the microbe for the production of such metabolites. To our knowledge this is the first comparative study of the microbe colonized-plant and microbe alone metabolomes under drought stress.

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A New Physiological Role for the DNA Molecule as a Protector against Drying Stress in Desiccation-Tolerant Microorganisms

Cited by 21 publications

References 49 publications

Faecal freezing preservation period influences colonization ability for faecal microbiota transplantation

Faecal freezing preservation period influences colonization ability for faecal microbiota transplantation

Development of a New Application for Comprehensive Viability Analysis Based on Microbiome Analysis by Next-Generation Sequencing: Insights into Staphylococcal Carriage in Human Nasal Cavities

Protection of Pepper Plants from Drought by Microbacterium sp. 3J1 by Modulation of the Plant's Glutamine and α-ketoglutarate Content: A Comparative Metabolomics Approach

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