Bacterial flora-typing with targeted, chip-based Pyrosequencing

Sundquist, Andreas; Bigdeli, Saharnaz; Jalili, Roxana; Druzin, Maurice L.; Waller, Sarah A.; Pullen, Kristin; El‐Sayed, Yasser Y.; Taslimi, M. Mark; Batzoglou, Serafim; Ronaghi, Mostafa

doi:10.1186/1471-2180-7-108

Cited by 210 publications

(178 citation statements)

References 33 publications

Supporting

Mentioning

172

Contrasting

Unclassified

Order By: Relevance

“…In the same manner, in the past years other researchers have been focusing on other domains for classification purposes. For instance, Sundquist et al [25] favored the domains V1,V2 and V4, Liu et al [26] the domains V2, V3 and V4, and Chakravorty et al [27] the domains V2 and V3.…”

Section: Amplified Genomic Regionsmentioning

confidence: 99%

Massive Sequencing: A New Tool for the Control of Alcoholic Fermentation in Wine?

et al. 2018

View full text Add to dashboard Cite

Abstract:In wine industry, there is a prevalent use of starter cultures to promote a controlled and efficient alcoholic fermentation preventing the growth of spoilage microbes. However, current trends in enology aim to combine the guaranteed success of monitored process and the complexity of fermentations either by inoculating autochthonous starters or by performing spontaneously to produce distinctive wines. To understand the complex roles of microorganisms on wine fermentation, we must understand their population dynamics and their relationships with wine quality and metabolome. Current metagenomics techniques based on massive sequencing are gaining relevance to study the diversity and evolution of microbial population on every stage of the wine making process. This new tool and technique increases the throughput and sensitivity to study microbial communities. This review focuses on the current knowledge about wine alcoholic fermentation, the contribution of massive sequencing techniques and the possibility of using this tool for microbial control.

show abstract

Section: Amplified Genomic Regionsmentioning

confidence: 99%

Massive Sequencing: A New Tool for the Control of Alcoholic Fermentation in Wine?

et al. 2018

View full text Add to dashboard Cite

show abstract

“…For 16S rRNA gene sequences, accurate phylogenies require from about 800 nt to full sequences and even so provide insufficient information to resolve many phylogenies, particularly for cases of heterogeneous rates and deep branches. Elaborate methods such as in 140) or extension of phylogenetic analysis to the genome scale 185) 160) suggested that reads from variable domains could allow to assign up 80% of them to a genus, but since these estimates were done using a very small subset of sequences these estimates are probably much too high. For example, using sequences from environmental clone libraries of length greater than 300 nt 73) found that nearly all of the taxonomic assignments were spurious, as the best match had a sequence similarity below 96%, and concluded that 79 to 89% of clones could not be assigned to known genera when sequences belonged to poorly defined groups with very few described species.…”

Section: Retrieving Datamentioning

confidence: 99%

“…Finally mass sequencing 30,85,187) or 16S rRNA mass cataloging 72) or even different methods 1,52,188) are appearing. Massive Parallel Sequencing (MPS) 4,56,110) that can presently produce 400,000 reads per run, with lengths averaging 200 to 300 bases per read (more than 20 million bases per 4.5-hour instrument run) now allows to sequence the entire molecule 161) or selectively variable short domains of the 16S rRNA gene 30,33,63,89,93,116,138,151,160,169) seemingly with good accuracy 70) . These short sequences will be referenced as "tags" below in this manuscript.…”

Section: Introductionmentioning

confidence: 99%

Global Sequencing: A Review of Current Molecular Data and New Methods Available to Assess Microbial Diversity

Christen

2008

Microb. Environ.

View full text Add to dashboard Cite

Roughly estimating the diversity of life has for a long time been seen as a challenge. Sequences obtained from the environment by direct amplification are now seen as the sole mean to provide information for at least 99% of the prokaryotes in natural communities. Recent massive parallel sequencing technologies now allow to sequence nearly every sequence resulting from such amplification. Are we ready to deal with such a deluge of data? Using three recent publications (16S rRNA genes amplification in soil and seawater followed by massive parallel sequencing) as case examples, this review analyses the state of the field.

show abstract

“…As with cult uring, the primary drawbacks of molecular methods include both labor and financial costs. Recently, DNA sequencing has been revolutionized by the introduction of massively parallel sequencing systems, such as 454 pyrosequencing analysis (Margulies et al, 2005;Cristea-Fernstrom et al, 2007;Huse et al, 2007;Liu et al, 2007;Roesch et al, 2007;Sundquist et al, 2007). Pyrosequencing techniques are high-throughput analytical tools that are capable of generating large numbers of DNA reads through a massively parallel sequencing-by-synthesis approach (Margulies et al, 2005).…”

Section: Introductionmentioning

confidence: 99%

Composition and structure of microbial communities associated with different domestic sewage outfalls

Wang¹,

Yang²,

Zhang³

et al. 2014

Genet. Mol. Res.

View full text Add to dashboard Cite

ABSTRACT. The diversity of microbiota in waste waters has not been thoroughly examined, despite the potential impact of microbes on effluent quality. Wastewater microbial communities harbor pathogenic bacteria, viruses, and parasites. To study microbial communities in domestic sewage outfalls, 454 pyrosequencing technology was used to investigate the composition of microbial communities associated with municipal wastewater during different seasons sampled over the course of one year. A total of 195,103 16S rRNA gene sequences were obtained from 20 samples. The R software was used to calculate the number of indices describing the alpha diversity associated with each bacterial assemblage. In this study, the a-diversity index (Hꞌ, D, J), in which higher numbers represent more diversity, was found to change with seasonal cycle. The diversity of bacterial assemblages was high Microbial communities in sewage outfalls in all samples, indicating that species diversity was also very high. The taxonomic composition of the assemblages varied considerably among samples, with some dominated by Proteobacteria, while others were dominated by Bacteroidetes or Firmicutes. In 2 samples, the relative prevalence of Proteobacteria exceeded 90%. α-Proteobacteria, b-proteobacteria, and g-proteobacteria represented 90% or more of all Proteobacteria. The present characterization of wastewater from five sewage outfalls indicated the presence of some pathogenic bacteria. The g-Proteobacteria in sewage wastefalls identified in this study included Enterobacteriaceae, Vibrionaceae, Pseudomonadaceae, Salmonella, Yersinia, Vibrio, and Pseudomonas aeruginosa.

show abstract

Bacterial flora-typing with targeted, chip-based Pyrosequencing

Cited by 210 publications

References 33 publications

Massive Sequencing: A New Tool for the Control of Alcoholic Fermentation in Wine?

Massive Sequencing: A New Tool for the Control of Alcoholic Fermentation in Wine?

Global Sequencing: A Review of Current Molecular Data and New Methods Available to Assess Microbial Diversity

Composition and structure of microbial communities associated with different domestic sewage outfalls

Contact Info

Product

Resources

About