Novel Microarray Design Strategy To Study Complex Bacterial Communities

Huyghe, Antoine; François, Patrice; Charbonnier, Yvan; Tangomo-Bento, Manuela; Bonetti, Eve-Julie; Paster, Bruce J.; Bolívar, Ignacio; Baratti-Mayer, Denise; Pittet, Didier; Schrenzel, Jacques

doi:10.1128/aem.01722-07

Cited by 55 publications

(48 citation statements)

References 50 publications

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“…Although high-throughput (or 'nextgeneration') sequencing can detect low-relative-abundance microorganisms in the environment (Andersson et al 2010;Roesch et al 2007), its high cost and complex analysis hinder its large-scale application to monitoring bacterial communities (Kircher and Kelso 2010;Seong Woon et al 2010). The large parallel nature of phylogenetic microarray hybridizations enables rapid identification of bacterial groups and reflection of their changes in the environment (Brodie et al 2006;Huyghe et al 2008). Our result showed that actinobacterial microarray can detect high-relative-abundance actinobacteria and reflect their changes in health as well as in shrimp pond conditions.…”

Section: Pyrosequencing Results Of Water Samplesmentioning

confidence: 77%

Development of a prototype 16S rRNA gene-based microarray for monitoring planktonic actinobacteria in shrimp ponds

et al. 2017

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Many reports have shown that the composition of the bacterioplankton community can serve as a biological indicator to evaluate the occurrence of shrimp diseases. However, the distribution, diversity, and function of planktonic actinobacteria in shrimp ponds are still poorly understood. In this study, a prototype of a 16S rRNA gene-based taxonomic microarray was developed and evaluated for monitoring of planktonic actinobacteria in shrimp ponds. The prototype microarray is composed of 30 probes that target ten dominant families of planktonic actinobacteria found in shrimp ponds. The specificity of the actinobacterial microarray was validated by a set of control hybridizations with 16S rRNA genes clones. The prototype microarray was subsequently tested with two seawater samples from ponds with diseased shrimp populations (PDS) and ponds with healthy shrimp populations (PHS). The actinobacteria hybridization profiles revealed a lower abundance of Microbacteriaceae and a higher abundance of Mycobacteriaceae in PDS than in PHS. The changes in planktonic actinobacterial communities were validated by pyrosequencing data. These results support the utility of the microarray for monitoring planktonic actinobacteria in shrimp ponds and aquaculture environments.

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Section: Pyrosequencing Results Of Water Samplesmentioning

confidence: 77%

Development of a prototype 16S rRNA gene-based microarray for monitoring planktonic actinobacteria in shrimp ponds

et al. 2017

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“…For example, DNA microarray chips have been designed to identify 20-100% of the 32 phyla described in the ribosomal database project (RDP). Armed with nearly 9500 probes, this is claimed to be able to identify 78.3% of the RDP sequences (Huyghe et al, 2008). Although the time spent on oral microbe identification is shortened with the use amplification-based clonal analysis, this could be shortened even further by using pyrosequencing.…”

Section: Detecting Oral Bacteria Nb Parahitiyawa Et Almentioning

confidence: 99%

“…Enables the large scale use in comparing bacterial communities in different oral conditions (Huyghe et al, 2008) Pyrosequencing to study the oral bacterial microbiome (saliva and subgingival plaque)…”

Section: Study Scope Main Findings and Remarks Referencesmentioning

confidence: 99%

Exploring the oral bacterial flora: current status and future directions

et al. 2010

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Oral Diseases (2010) 16, 136–145 Objective: The oral cavity forms an indispensable part of the human microbiome, for its unique and diverse microflora distributed within various niches. While majority of these organisms exhibit commensalism, shifts in bacterial community dynamics cause pathological changes within oral cavity and distant sites. The aim of this review was to appraise the current and emerging methods of detecting bacteria of the oral cavity paying particular attention to the cultivation independent methods. Design: Literature pertaining to cultivation based and cultivation independent methods of oral bacterial identification was reviewed. Methods: The specific advantages and disadvantages of cultivation based, microscopic, immunological and metagenomic identification methods were appraised. Results: Because of their fastidious and exacting growth requirements, cultivation based studies grossly underestimate the extent of bacterial diversity in these polymicrobial infections. Culture independent methods deemed more sensitive in identifying difficult to culture and novel bacterial species. Conclusion: Apart from characterizing potentially novel bacterial species, the nucleic acid sequence data analyzed using various bioinformatics protocols have revealed that there are in excess of 700 bacterial species inhabiting the mouth. Moreover, the latest pyrosequencing based methods have further broadened the extent of bacterial diversity in oral niches.

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“…comm.). A similarly large-scale phylochip has subsequently been published and used for oral microbial communities (Huyghe et al, 2008). …”

Section: Previous and Current Microarray Applications In Microbiamentioning

confidence: 99%

Development of a "genome-proxy" microarray for profiling marine microbial communities, and its application to a time series in Monterey Bay, California

Rich¹

2008

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Novel Microarray Design Strategy To Study Complex Bacterial Communities

Cited by 55 publications

References 50 publications

Development of a prototype 16S rRNA gene-based microarray for monitoring planktonic actinobacteria in shrimp ponds

Development of a prototype 16S rRNA gene-based microarray for monitoring planktonic actinobacteria in shrimp ponds

Exploring the oral bacterial flora: current status and future directions

Development of a "genome-proxy" microarray for profiling marine microbial communities, and its application to a time series in Monterey Bay, California

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