Genome-Scale Metabolic Modelling of the Drosophila Melanogaster Gut Microbial Community Uncovers Growth Promoting Metabolite Exchange

2021 ◽  
Author(s):  
Jürgen Wilhelm Schönborn ◽  
Fiona Anne Stewart ◽  
Kerstin Maas-Enriquez ◽  
Irfan Akhtar ◽  
Andrea Droste ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Microbial Community ◽  
Metabolic Modelling ◽  
Metabolite Exchange ◽  
Growth Promoting ◽  
Genome Scale ◽  
Gut Microbial Community

scholarly journals The impact of Rhodiola rosea on the gut microbial community of Drosophila melanogaster

Gut Pathogens ◽  
2018 ◽  
Vol 10 (1) ◽  
Author(s):  
Khachik E. Labachyan ◽  
Dara Kiani ◽  
Evgueni A. Sevrioukov ◽  
Samuel E. Schriner ◽  
Mahtab Jafari
Keyword(s):  
Drosophila Melanogaster ◽  
Microbial Community ◽  
Rhodiola Rosea ◽  
Gut Microbial Community ◽  
The Impact

The role of gut microbial community and metabolomic shifts in adaptive resistance of Atlantic killifish (Fundulus heteroclitus) to polycyclic aromatic hydrocarbons

2021 ◽  
Vol 776 ◽  
pp. 145955
Author(s):  
Lauren K. Redfern ◽  
Nishad Jayasundara ◽  
David R. Singleton ◽  
Richard T. Di Giulio ◽  
James Carlson ◽  
...  
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Microbial Community ◽  
Aromatic Hydrocarbons ◽  
Fundulus Heteroclitus ◽  
Adaptive Resistance ◽  
Polycyclic Aromatic ◽  
Gut Microbial Community ◽  
Atlantic Killifish

scholarly journals PUL-Mediated Plant Cell Wall Polysaccharide Utilization in the Gut Bacteroidetes

2021 ◽  
Vol 22 (6) ◽  
pp. 3077
Author(s):  
Zhenzhen Hao ◽  
Xiaolu Wang ◽  
Haomeng Yang ◽  
Tao Tu ◽  
Jie Zhang ◽  
...  
Keyword(s):  
Cell Wall ◽  
Microbial Community ◽  
Gut Microbiota ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Cell Wall Polysaccharide ◽  
Prominent Feature ◽  
Cell Wall Polysaccharides ◽  
Gut Microbial Community

Plant cell wall polysaccharides (PCWP) are abundantly present in the food of humans and feed of livestock. Mammalians by themselves cannot degrade PCWP but rather depend on microbes resident in the gut intestine for deconstruction. The dominant Bacteroidetes in the gut microbial community are such bacteria with PCWP-degrading ability. The polysaccharide utilization systems (PUL) responsible for PCWP degradation and utilization are a prominent feature of Bacteroidetes. In recent years, there have been tremendous efforts in elucidating how PULs assist Bacteroidetes to assimilate carbon and acquire energy from PCWP. Here, we will review the PUL-mediated plant cell wall polysaccharides utilization in the gut Bacteroidetes focusing on cellulose, xylan, mannan, and pectin utilization and discuss how the mechanisms can be exploited to modulate the gut microbiota.

scholarly journals The phyllosphere microbiome of host trees contributes more than leaf phytochemicals to variation in the Agrilus planipennis Fairmaire gut microbiome structure

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Judith Mogouong ◽  
Philippe Constant ◽  
Pierre Legendre ◽  
Claude Guertin
Keyword(s):  
Microbial Community ◽  
Gut Microbiome ◽  
Strong Predictor ◽  
Emerald Ash Borer ◽  
Agrilus Planipennis ◽  
Food Sources ◽  
Microbiome Composition ◽  
Living Organisms ◽  
Insect Gut ◽  
Gut Microbial Community

AbstractThe microbiome composition of living organisms is closely linked to essential functions determining the fitness of the host for thriving and adapting to a particular ecosystem. Although multiple factors, including the developmental stage, the diet, and host-microbe coevolution have been reported to drive compositional changes in the microbiome structures, very few attempts have been made to disentangle their various contributions in a global approach. Here, we focus on the emerald ash borer (EAB), an herbivorous pest and a real threat to North American ash tree species, to explore the responses of the adult EAB gut microbiome to ash leaf properties, and to identify potential predictors of EAB microbial variations. The relative contributions of specific host plant properties, namely bacterial and fungal communities on leaves, phytochemical composition, and the geographical coordinates of the sampling sites, to the EAB gut microbial community was examined by canonical analyses. The composition of the phyllosphere microbiome appeared to be a strong predictor of the microbial community structure in EAB guts, explaining 53 and 48% of the variation in fungi and bacteria, respectively. This study suggests a potential covariation of the microorganisms associated with food sources and the insect gut microbiome.

scholarly journals Characterization of the Gut Microbial Community of Obese Patients Following a Weight-Loss Intervention Using Whole Metagenome Shotgun Sequencing

PLoS ONE ◽  
2016 ◽  
Vol 11 (2) ◽  
pp. e0149564 ◽  
Author(s):  
Sandrine Louis ◽  
Rewati-Mukund Tappu ◽  
Antje Damms-Machado ◽  
Daniel H. Huson ◽  
Stephan C. Bischoff
Keyword(s):  
Weight Loss ◽  
Microbial Community ◽  
Shotgun Sequencing ◽  
Obese Patients ◽  
Weight Loss Intervention ◽  
Gut Microbial Community

scholarly journals An Overview of Different Techniques on the Microbial Community Structure, and Functional Diversity of Plant Growth Promoting Bacteria

2016 ◽  
Vol 49 (2) ◽  
pp. 144-156 ◽  
Author(s):  
Kiyoon Kim ◽  
Rashedul Islam ◽  
Abitha Benson ◽  
Manoharan Melvin Joe ◽  
Walitang Denver ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Plant Growth ◽  
Functional Diversity ◽  
Microbial Community Structure ◽  
Plant Growth Promoting Bacteria ◽  
Plant Growth Promoting ◽  
Growth Promoting

scholarly journals Consistency, Inconsistency and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome Scale Metabolic Modelling

2018 ◽  
Author(s):  
Nhung Pham ◽  
Ruben Van Heck ◽  
Jesse van Dam ◽  
Peter Schaap ◽  
Edoardo Saccenti ◽  
...  
Keyword(s):  
Systems Medicine ◽  
Biochemical Reactions ◽  
Metabolic Modelling ◽  
Research Areas ◽  
Limit Model ◽  
Metabolic Models ◽  
Genome Scale ◽  
Manual Verification

Genome scale metabolic models (GEMs) are manually curated repositories describing the metabolic capabilities of an organism. GEMs have been successfully used in different research areas, ranging from systems medicine to biotechnology. However, the different naming conventions (namespaces) of databases used to build GEMs limit model reusability and prevent the integration of existing models. This problem is known in the GEM community but its extent has not been analyzed in depth. In this study, we investigate the name ambiguity and the multiplicity of non-systematic identifiers and we highlight the (in)consistency in their use in eleven biochemical databases of biochemical reactions and the problems that arise when mapping between different namespaces and databases. We found that such inconsistencies can be as high as 83.1%, thus emphasizing the need for strategies to deal with these issues. Currently, manual verification of the mappings appears to be the only solution to remove inconsistencies when combining models. Finally, we discuss several possible approaches to facilitate (future) unambiguous mapping.

scholarly journals Effect of Pyroligneous Acid on the Microbial Community Composition and Plant Growth-Promoting Bacteria (PGPB) in Soils

Soil Systems ◽  
2022 ◽  
Vol 6 (1) ◽  
pp. 10
Author(s):  
Anithadevi Kenday Sivaram ◽  
Logeshwaran Panneerselvan ◽  
Kannappar Mukunthan ◽  
Mallavarapu Megharaj
Keyword(s):  
Microbial Community ◽  
Plant Growth ◽  
Microbial Diversity ◽  
Growth And Yield ◽  
Rrna Gene ◽  
Plant Growth Promoting Bacteria ◽  
Microbial Composition ◽  
Pyroligneous Acid ◽  
Plant Growth Promoting ◽  
Growth Promoting

Pyroligneous acid (PA) is often used in agriculture as a plant growth and yield enhancer. However, the influence of PA application on soil microorganisms is not often studied. Therefore, in this study, we investigated the effect of PA (0.01–5% w/w in soil) on the microbial diversity in two different soils. At the end of eight weeks of incubation, soil microbial community dynamics were determined by Illumina-MiSeq sequencing of 16S rRNA gene amplicons. The microbial composition differed between the lower (0.01% and 0.1%) and the higher (1% and 5%) concentration in both PA spiked soils. The lower concentration of PA resulted in higher microbial diversity and dehydrogenase activity (DHA) compared to the un-spiked control and the soil spiked with high PA concentrations. Interestingly, PA-induced plant growth-promoting bacterial (PGPB) genera include Bradyrhizobium, Azospirillum, Pseudomonas, Mesorhizobium, Rhizobium, Herbaspiriluum, Acetobacter, Beijerinckia, and Nitrosomonas at lower concentrations. Additionally, the PICRUSt functional analysis revealed the predominance of metabolism as the functional module’s primary component in both soils spiked with 0.01% and 0.1% PA. Overall, the results elucidated that PA application in soil at lower concentrations promoted soil DHA and microbial enrichment, particularly the PGPB genera, and thus have great implications for improving soil health.

scholarly journals Understanding the metabolism of the tetralin degrader Sphingopyxis granuli strain TFA through genome-scale metabolic modelling

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Inmaculada García-Romero ◽  
Juan Nogales ◽  
Eduardo Díaz ◽  
Eduardo Santero ◽  
Belén Floriano
Keyword(s):  
Metabolic Modelling ◽  
Genome Scale
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