<i>Escherichia coli</i>
            Gene Expression Responsive to Levels of the Response Regulator EvgA

Masuda, Nobuhisa; Church, George M.

doi:10.1128/jb.184.22.6225-6234.2002

Cited by 152 publications

(174 citation statements)

References 40 publications

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“…The purified product of the amplification of the 16S rRNA gene (200 ng) was fragmented using DNase I, biotin-labeled and then hybridized onto the PhyloChip, as described (Brodie et al, 2006). After overnight hybridization at 48 1C and 60 r.p.m., the PhyloChips were washed and stained according to standard Affymetrix protocols, as described (Masuda and Church, 2002). The PhyloChips were scanned and recorded as pixel images using Gene Array Scanning (Affimetrix Inc., Santa Clara, CA, USA), and initial data acquisition and intensity determinations were performed using the standard Affymetrix software GeneChip microarray analysis suite, version 5.1.…”

Section: The G2 Phylochipmentioning

confidence: 99%

Structure of the human gastric bacterial community in relation to Helicobacter pylori status

et al. 2010

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The human stomach is naturally colonized by Helicobacter pylori, which, when present, dominates the gastric bacterial community. In this study, we aimed to characterize the structure of the bacterial community in the stomach of patients of differing H. pylori status. We used a high-density 16S rRNA gene microarray (PhyloChip, Affymetrix, Inc.) to hybridize 16S rRNA gene amplicons from gastric biopsy DNA of 10 rural Amerindian patients from Amazonas, Venezuela, and of two immigrants to the United States (from South Asia and Africa, respectively). H. pylori status was determined by PCR amplification of H. pylori glmM from gastric biopsy samples. Of the 12 patients, 8 (6 of the 10 Amerindians and the 2 non-Amerindians) were H. pylori glmM positive. Regardless of H. pylori status, the PhyloChip detected Helicobacteriaceae DNA in all patients, although with lower relative abundance in patients who were glmM negative. The G2-chip taxonomy analysis of PhyloChip data indicated the presence of 44 bacterial phyla (of which 16 are unclassified by the Taxonomic Outline of the Bacteria and Archaea taxonomy) in a highly uneven community dominated by only four phyla: Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Positive H. pylori status was associated with increased relative abundance of non-Helicobacter bacteria from the Proteobacteria, Spirochetes and Acidobacteria, and with decreased abundance of Actinobacteria, Bacteroidetes and Firmicutes. The PhyloChip detected richness of low abundance phyla, and showed marked differences in the structure of the gastric bacterial community according to H. pylori status.

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Section: The G2 Phylochipmentioning

confidence: 99%

Structure of the human gastric bacterial community in relation to Helicobacter pylori status

et al. 2010

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“…PhyloChip washing, staining and scanning were performed as described by Masuda and Church (2002). PhyloChip data were measured at taxon/ OTU level (similar to 99% sequence homology) but were summarized to subfamily level (approximately 94% sequence homology) for further analyses to minimize OTU representation-by-subfamily biases.…”

Section: Bacterial-archaeal Community Analysismentioning

confidence: 99%

Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland

et al. 2009

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Climate change impacts on soil microbial communities could alter the structure of terrestrial ecosystems and biogeochemical cycles of the Earth. We used 16S rRNA gene microarrays to evaluate changes in the composition of grassland soil microbial communities under rainfall amendments simulating alternative climate change scenarios, and to compare these to responses of overlying plants and invertebrates. Following 5 years of rainfall manipulation, soil bacteria and archaea in plots where natural rain was supplemented differed little from ambient controls, despite profound treatment-related changes in the overlying grassland. During the sixth and seventh year, seasonal differences in bacterial and archaeal assemblages emerged among treatments, but only when watering exacerbated or alleviated periods of particularly aberrant conditions in the ambient climate. In contrast to effects on plants and invertebrates, effects on bacteria and archaea did not compound across seasons or years, indicating that soil microbial communities may be more robust than associated aboveground macroorganisms to certain alterations in climate.

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“…The arrays were subsequently washed and stained. Reagents, conditions and equipments involved are detailed elsewhere (Masuda and Church, 2002). Scanning of the arrays was performed using a GeneArray Scanner (Affymetrix) and probe intensities were treated as reported previously (Brodie et al, 2006).…”

Section: Animalsmentioning

confidence: 99%

Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows

et al. 2011

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Foregut fermentation occurs in mammalian ruminants and in one bird, the South American folivorous hoatzin. This bird has an enlarged crop with a function analogous to the rumen, where foregut microbes degrade the otherwise indigestible plant matter, providing energy to the host from foregut fermentation, in addition to the fermentation that occurs in their hindguts (cecum/colon). As foregut fermentation represents an evolutionary convergence between hoatzins and ruminants, our aim was to compare the community structure of foregut and hindgut bacterial communities in the cow and hoatzin to evaluate the influences of host phylogeny and organ function in shaping the gut microbiome. The approach used was to hybridize amplified bacterial ribosomal RNA genes onto a high-density microarray (PhyloChip). The results show that the microbial communities cluster primarily by functional environment (foreguts cluster separately from hindguts) and then by host. Bacterial community diversity was higher in the cow than in the hoatzin. Overall, compared with hindguts, foreguts have higher proportions of Bacteroidetes and Spirochaetes, and lower proportions of Firmicutes and Proteobacteria. The main host differences in gut bacterial composition include a higher representation of Spirochaetes, Synergistes and Verrucomicrobia in the cow. Despite the significant differences in host phylogeny, body size, physiology and diet, the function seems to shape the microbial communities involved in fermentation. Regardless of the independent origin of foregut fermentation in birds and mammals, organ function has led to convergence of the microbial community structure in phylogenetically distant hosts.

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Escherichia coli Gene Expression Responsive to Levels of the Response Regulator EvgA

Cited by 152 publications

References 40 publications

Structure of the human gastric bacterial community in relation to Helicobacter pylori status

Structure of the human gastric bacterial community in relation to Helicobacter pylori status

Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland

Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows

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