Methods for the Isolation of Genes Encoding Novel PHA Metabolism Enzymes from Complex Microbial Communities

2016 ◽  
pp. 237-248
Author(s):  
Jiujun Cheng ◽  
Ricardo Nordeste ◽  
Maria A. Trainer ◽  
Trevor C. Charles
Keyword(s):  
Microbial Communities ◽  
Metabolism Enzymes ◽  
Genes Encoding

scholarly journals Genome Reduction and Secondary Metabolism of the Marine Sponge-Associated Cyanobacterium Leptothoe

Marine Drugs ◽  
2021 ◽  
Vol 19 (6) ◽  
pp. 298
Author(s):  
Despoina Konstantinou ◽  
Rafael V. Popin ◽  
David P. Fewer ◽  
Kaarina Sivonen ◽  
Spyros Gkelis
Keyword(s):  
Natural Products ◽  
Microbial Communities ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Marine Sponges ◽  
Genome Reduction ◽  
Extracellular Polysaccharides ◽  
Comparative Genomic ◽  
Symbiotic Relationships ◽  
Genes Encoding

Sponges form symbiotic relationships with diverse and abundant microbial communities. Cyanobacteria are among the most important members of the microbial communities that are associated with sponges. Here, we performed a genus-wide comparative genomic analysis of the newly described marine benthic cyanobacterial genus Leptothoe (Synechococcales). We obtained draft genomes from Le. kymatousa TAU-MAC 1615 and Le. spongobia TAU-MAC 1115, isolated from marine sponges. We identified five additional Leptothoe genomes, host-associated or free-living, using a phylogenomic approach, and the comparison of all genomes showed that the sponge-associated strains display features of a symbiotic lifestyle. Le. kymatousa and Le. spongobia have undergone genome reduction; they harbored considerably fewer genes encoding for (i) cofactors, vitamins, prosthetic groups, pigments, proteins, and amino acid biosynthesis; (ii) DNA repair; (iii) antioxidant enzymes; and (iv) biosynthesis of capsular and extracellular polysaccharides. They have also lost several genes related to chemotaxis and motility. Eukaryotic-like proteins, such as ankyrin repeats, playing important roles in sponge-symbiont interactions, were identified in sponge-associated Leptothoe genomes. The sponge-associated Leptothoe stains harbored biosynthetic gene clusters encoding novel natural products despite genome reduction. Comparisons of the biosynthetic capacities of Leptothoe with chemically rich cyanobacteria revealed that Leptothoe is another promising marine cyanobacterium for the biosynthesis of novel natural products.

scholarly journals Denaturing gradient gel electrophoresis as a fingerprinting method for the analysis of soil microbial communities

2009 ◽  
Vol 55 (No. 10) ◽  
pp. 413-423 ◽  
Author(s):  
V. Valášková ◽  
P. Baldrian
Keyword(s):  
Microbial Communities ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Soil Microbial Communities ◽  
Soil Microbial ◽  
Genes Encoding ◽  
Gradient Gel Electrophoresis ◽  
Temperature Gradient Gel Electrophoresis ◽  
Experimental Treatments ◽  
Multiple Samples

In soil microbial ecology, the effects of environmental factors and their gradients, temporal changes or the response to specific experimental treatments of microbial communities can only be effectively analyzed using methods that address the structural differences among whole communities. Fingerprinting methods are the most appropriate technique for this task when multiple samples must be analyzed. Among the methods currently used to compare microbial communities based on nucleic acid sequences, the techniques based on differences in the melting properties of double-stranded molecules, denaturing gradient gel electrophoresis (DGGE) or temperature gradient gel electrophoresis (TGGE), are the most widely used. Their main advantage is that they provide the possibility to further analyze whole sequences contained in fingerprints using molecular methods. In addition to the analysis of microbial communities based on DNA extracted from soils, DGGE/TGGE can also be used for the assessment of the active part of the community based on the analysis of RNA-derived sequences or for the analysis of sequences of functional genes encoding for proteins involved in important soil processes.

scholarly journals Functional metagenomic analysis of dust-associated microbiomes above the Red Sea

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Nojood A. Aalismail ◽  
David K. Ngugi ◽  
Rubén Díaz-Rúa ◽  
Intikhab Alam ◽  
Michael Cusack ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Dna Sequences ◽  
Biofilm Formation ◽  
Atmospheric Transport ◽  
Taxonomic Diversity ◽  
Functional Metagenomics ◽  
Genetic Traits ◽  
Gene Catalogue ◽  
Range Transport ◽  
Genes Encoding

Abstract Atmospheric transport is a major vector for the long-range transport of microbial communities, maintaining connectivity among them and delivering functionally important microbes, such as pathogens. Though the taxonomic diversity of aeolian microorganisms is well characterized, the genomic functional traits underpinning their survival during atmospheric transport are poorly characterized. Here we use functional metagenomics of dust samples collected on the Global Dust Belt to initiate a Gene Catalogue of Aeolian Microbiome (GCAM) and explore microbial genetic traits enabling a successful aeolian lifestyle in Aeolian microbial communities. The GCAM reported here, derived from ten aeolian microbial metagenomes, includes a total of 2,370,956 non-redundant coding DNA sequences, corresponding to a yield of ~31 × 106 predicted genes per Tera base-pair of DNA sequenced for the aeolian samples sequenced. Two-thirds of the cataloged genes were assigned to bacteria, followed by eukaryotes (5.4%), archaea (1.1%), and viruses (0.69%). Genes encoding proteins involved in repairing UV-induced DNA damage and aerosolization of cells were ubiquitous across samples, and appear as fundamental requirements for the aeolian lifestyle, while genes coding for other important functions supporting the aeolian lifestyle (chemotaxis, aerotaxis, germination, thermal resistance, sporulation, and biofilm formation) varied among the communities sampled.

‘Candidatus Oscillochloris kuznetsovii’ a novel mesophilic filamentous anoxygenic phototrophic Chloroflexales bacterium from Arctic coastal environments

2020 ◽  
Vol 367 (19) ◽  
Author(s):  
Vasil A Gaisin ◽  
Denis S Grouzdev ◽  
Maria S Krutkina ◽  
Aleksandr A Ashikhmin ◽  
Maria A Sinetova ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Performance ◽  
Hot Spring ◽  
Calvin Cycle ◽  
Phylogenomic Analysis ◽  
Coastal Environments ◽  
Anoxygenic Phototrophs ◽  
Thermal Environments ◽  
Genes Encoding ◽  
Kandalaksha Gulf

ABSTRACT Chloroflexales bacteria are mostly known as filamentous anoxygenic phototrophs that thrive as members of the microbial communities of hot spring cyanobacterial mats. Recently, we described many new Chloroflexales species from non-thermal environments and showed that mesophilic Chloroflexales are more diverse than previously expected. Most of these species were isolated from aquatic environments of mid-latitudes. Here, we present the comprehensive characterization of a new filamentous multicellular anoxygenic phototrophic Chloroflexales bacterium from an Arctic coastal environment (Kandalaksha Gulf, the White Sea). Phylogenomic analysis and 16S rRNA phylogeny indicated that this bacterium belongs to the Oscillochloridaceae family as a new species. We propose that this species be named ‘Candidatus Oscillochloris kuznetsovii’. The genomes of this species possessed genes encoding sulfide:quinone reductase, the nitrogenase complex and the Calvin cycle, which indicate potential for photoautotrophic metabolism. We observed only mesophilic anaerobic anoxygenic phototrophic growth of this novel bacterium. Electron microphotography showed the presence of chlorosomes, polyhydroxyalkanoate-like granules and polyphosphate-like granules in the cells. High-performance liquid chromatography also revealed the presence of bacteriochlorophylls a, c and d as well as carotenoids. In addition, we found that this bacterium is present in benthic microbial communities of various coastal environments of the Kandalaksha Gulf.

scholarly journals Evidence for Cascades of Perturbation and Adaptation in the Metabolic Genes of Higher Termite Gut Symbionts

mBio ◽  
2012 ◽  
Vol 3 (4) ◽  
Author(s):  
Xinning Zhang ◽  
Jared R. Leadbetter
Keyword(s):  
Microbial Communities ◽  
Convergent Evolution ◽  
Last Common Ancestor ◽  
Evolutionary Mechanisms ◽  
Bacterial Gene ◽  
Family Patterns ◽  
Termite Gut ◽  
Genes Encoding ◽  
Gut Symbionts ◽  
Extinction Events

ABSTRACTTermites and their gut microbes engage in fascinating dietary mutualisms. Less is known about how these complex symbioses have evolved after first emerging in an insect ancestor over 120 million years ago. Here we examined a bacterial gene, formate dehydrogenase (fdhF), that is key to the mutualism in 8 species of “higher” termite (members of theTermitidae, the youngest and most biomass-abundant and species-rich termite family). Patterns offdhFdiversity in the gut communities of higher termites contrasted strongly with patterns in less-derived (more-primitive) insect relatives (wood-feeding “lower” termites and roaches). We observed phylogenetic evidence for (i) the sweeping loss of several clades offdhFthat may reflect extinctions of symbiotic protozoa and, importantly, bacteria dependent on them in the last common ancestor of all higher termites and (ii) a radiation of genes from the (possibly) single allele that survived. Sweeping gene loss also resulted in (iii) the elimination of an entire clade of genes encoding selenium (Se)-independent enzymes from higher termite gut communities, perhaps reflecting behavioral or morphological innovations in higher termites that relaxed preexisting environmental limitations of Se, a dietary trace element. Curiously, several higher termite gut communities may have subsequently reencountered Se limitation, reinventing genes for Se-independent proteins via convergent evolution. Lastly, the presence of a novelfdhFlineage within litter-feeding and subterranean higher (but not other) termites may indicate recent gene “invasion” events. These results imply that cascades of perturbation and adaptation by distinct evolutionary mechanisms have impacted the evolution of complex microbial communities in a highly successful lineage of insects.IMPORTANCESince patterns of relatedness between termite hosts are broadly mirrored by the relatedness of their symbiotic gut microbiota, coevolution between hosts and gut symbionts is rightly considered an important force that has shaped dietary mutualism since its inception over 120 million years ago. Apart from that concerning lateral gene or symbiont transfer between termite gut communities (for which no evidence yet exists), there has been little discussion of alternative mechanisms impacting the evolution of mutualism. Here we provide strong gene-based evidence for past environmental perturbations creating significant upheavals that continue to reverberate throughout the gut communities of species comprising a single termite lineage. We suggest that symbiont extinction events, sweeping gene losses, evolutionary radiations, relaxation and reemergence of key nutritional pressures, convergent evolution of similar traits, and recent gene invasions have all shaped gene composition in the symbiotic gut microbial communities of higher termites, currently the most dominant and successful termite family on Earth.

scholarly journals Rampant prophage movement among transient competitors drives rapid adaptation during infection

2021 ◽  
Author(s):  
Christopher W. Marshall ◽  
Erin S. Gloag ◽  
Christina Lim ◽  
Daniel J. Wozniak ◽  
Vaughn S. Cooper
Keyword(s):  
Microbial Communities ◽  
Chronic Infection ◽  
Evolutionary Dynamics ◽  
Functional Genes ◽  
Rapid Adaptation ◽  
Chronic Infections ◽  
Global Regulators ◽  
New Genes ◽  
Biofilm Production ◽  
Genes Encoding

AbstractInteractions between bacteria, their close competitors, and viral parasites are common in infections but understanding of these eco-evolutionary dynamics is limited. Most examples of adaptations caused by phage lysogeny are through the acquisition of new genes. However, integrated prophages can also insert into functional genes and impart a fitness benefit by disrupting their expression, a process called active lysogeny. Here, we show that active lysogeny can fuel rapid, parallel adaptations in establishing a chronic infection. These recombination events repeatedly disrupted genes encoding global regulators, leading to increased cyclic-di-GMP levels and elevated biofilm production. The implications of prophage-mediated adaptation are broad, as even transient members of microbial communities can alter the course of evolution and generate persistent phenotypes associated with poor clinical outcomes.One Sentence SummaryBacteriophage act as genetic regulators that are key to establishing chronic infections and are rapidly shared among co-infecting strains.

Relationship between codon biased genes, microarray expression values and physiological characteristics of Streptococcus pneumoniae

Microbiology ◽  
2004 ◽  
Vol 150 (7) ◽  
pp. 2313-2325 ◽  
Author(s):  
Antonio J. Martín-Galiano ◽  
Jerry M. Wells ◽  
Adela G. de la Campa
Keyword(s):  
Streptococcus Pneumoniae ◽  
Translation Rate ◽  
Metabolism Enzymes ◽  
Component Systems ◽  
Genes Encoding ◽  
Two Component Systems ◽  
The Right ◽  
Microarray Expression ◽  
Dna Acquisition ◽  
Gene Expression Levels

A codon-profile strategy was used to predict gene expression levels in Streptococcus pneumoniae. Predicted highly expressed (PHE) genes included those encoding glycolytic and fermentative enzymes, sugar-conversion systems and carbohydrate-transporters. Additionally, some genes required for infection that are involved in oxidative metabolism and hydrogen peroxide production were PHE. Low expression values were predicted for genes encoding specific regulatory proteins like two-component systems and competence genes. Correspondence analysis localized 484 ORFs which shared a distinctive codon profile in the right horn. These genes had a mean G+C content (33·4 %) that was lower than the bulk of the genome coding sequences (39·7 %), suggesting that many of them were acquired by horizontal transfer. Half of these genes (242) were pseudogenes, ORFs shorter than 80 codons or without assigned function. The remaining genes included several virulence factors, such as capsular genes, iga, lytB, nanB, pspA, choline-binding proteins, and functions related to DNA acquisition, such as restriction-modification systems and comDE. In order to compare predicted translation rate with the relative amounts of mRNA for each gene, the codon adaptation index (CAI) values were compared with microarray fluorescence intensity values following hybridization of labelled RNA from laboratory-grown cultures. High mRNA amounts were observed in 32·5 % of PHE genes and in 64 % of the 25 genes with the highest CAI values. However, high relative amounts of RNA were also detected in 10·4 % of non-PHE genes, such as those encoding fatty acid metabolism enzymes and proteases, suggesting that their expression might also be regulated at the level of transcription or mRNA stability under the conditions tested. The effects of codon bias and mRNA amount on different gene groups in S. pneumoniae are discussed.

Docetaxel pharmacogenetics: The influence of RXRα and HNF4α genetic variations on docetaxel disposition in Asian nasopharyngeal carcinoma patients.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. 2598-2598
Author(s):  
Sin Chi Chew ◽  
Onkar Singh ◽  
Xiangai Chen ◽  
Wan-Teck Lim ◽  
Eng-Huat Tan ◽  
...  
Keyword(s):  
Nuclear Receptors ◽  
High Frequency ◽  
Direct Sequencing ◽  
Nasopharyngeal Cancer ◽  
Genetic Variations ◽  
Individual Variability ◽  
Orphan Nuclear Receptors ◽  
Linkage Pattern ◽  
Metabolism Enzymes ◽  
Genes Encoding

2598 Background: The transactivations of the metabolism enzymes (CYP3A4/5) and efflux transporters (ABCB1/ABCC2) involved in docetaxel disposition are regulated by the orphan nuclear receptors such as PXR, CAR, RXRα and HNF4α. This study aimed to explore the associations between the genetic variations present in the genes encoding the orphan nuclear receptors, RXRα and HNF4α, on docetaxel disposition. Methods: The DNAs from healthy Chinese, Malay and Indian subjects (n=56 each) were screened for RXRα and HNF4α SNPs in exons and intronic/exonic boundaries by direct sequencing. The high frequency SNPs (>1%) were profiled in a cohort of local nasopharyngeal cancer patients (n=54). Genotypic-phenotypic correlations were conducted using Mann-Whitney U-test and Kruskal-Wallis test. Results: Eighty-eight and sixty-nine SNPs were identified from the healthy screening of RXRα and HNF4α, respectively, across 3 populations. A total of 30 and 35 high frequency SNPs in RXRα and HNF4α, respectively, were profiled in the patients. Six RXRα SNPs [IVS2+33G>A (rs2234753), IVS7+70A>G (rs1536475),*846G>A (rs4240711), *+4458G>A (rs3132291), *+4768C>A (rs4842196) and *+4988A>G (rs4842198)] and 6 HNF4α SNPs [-728A>C (rs1800963), IVS2-278A>G (rs55934816), IVS6+141A>G (rs6103731), IVS7-88T>C (rs2273618), IVS9–145T>C (rs3746574) and IVS9-67C>G (rs3746575)] were significantly associated with higher clearance and lower AUC0-∞ and/or Cmax of docetaxel (P<0.05). Conversely, HNF4α SNP [IVS9+354G>T (rs3818247)] was associated with lower clearance and higher AUC0-∞ and Cmax of docetaxel (p<0.05). A high linkage pattern was observed among the abovementioned RXRα SNPs except for IVS2+33G>A (rs2234753) (D'≥0.74). Similarly, HNF4α SNPs were found to be highly linked, except for -728A>C (rs1800963) (D'≥0.62). Conclusions: The results highlight the contributions of RXRα and HNF4α pharmacogenetics in influencing the inter-individual variability in docetaxel disposition in Asian nasopharyngeal patients.

Molecular analyses of the diversity and function of the family 1 β-glucosidase-producing microbial community in compost

2021 ◽  
Author(s):  
Xinyue Zhang ◽  
Erlie Su ◽  
Shanshan Li ◽  
Xiehui Chen ◽  
Zhihua Fan ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Environmental Changes ◽  
Diversity Index ◽  
Cellulose Degradation ◽  
Principal Component ◽  
Dna And Rna ◽  
Functional Community ◽  
Genes Encoding ◽  
The Individual ◽  
And Function

The diversity and transcription efficiency of GH1 family β-glucosidase genes were investigated in natural and inoculated composts using a DNA clone library and real-time qPCR. Compositional differences were observed in the functional community between both composting processes. Proteobacteria, Actinobacteria, Firmicutes, and Chloroflexi were the dominant phyla. Twenty representative β-glucosidase genes were quantitatively analyzed from DNA and RNA pools. Principal component analysis and Pearson’s correlation analysis showed that cellulose degradation is correlated with the composition and succession of functional microbial communities, and this correlation was mainly observed in Proteobacteria and Actinobacteria. Compared with inoculated compost, the functional microbial communities in natural compost with a low diversity index exhibited weak buffering capacity for function in response to environmental changes. This may explain the consistency and dysfunction of cellulose degradation and transcriptional regulation by dominant β-glucosidase genes. Except for the β-glucosidase genes encoding constitutive enzymes, individual β-glucosidase genes responded to environmental changes more drastically than the group β-glucosidase genes. Correlation results suggested that β-glucosidase genes belonging to Micrococcales played an important role in the regulation of intracellular β-glucosidase. These results indicated that the responses of functional microorganisms were different during both composting processes, and were reflected at both the individual and group levels.

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