Taxonomic database and cut-off value for processing mcrA gene 454 pyrosequencing data by MOTHUR

2014 ◽  
Vol 103 ◽  
pp. 3-5 ◽  
Author(s):  
Sizhong Yang ◽  
Susanne Liebner ◽  
Mashal Alawi ◽  
Oliver Ebenhöh ◽  
Dirk Wagner
Keyword(s):  
454 Pyrosequencing ◽  
Mcra Gene

scholarly journals Impact of Nosema Disease and American Foulbrood on Gut Bacterial Communities of Honeybees Apis mellifera

Insects ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 525
Author(s):  
Poonnawat Panjad ◽  
Rujipas Yongsawas ◽  
Chainarong Sinpoo ◽  
Chonthicha Pakwan ◽  
Phakamas Subta ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Bacterial Communities ◽  
454 Pyrosequencing ◽  
Gut Bacteria ◽  
Nosema Ceranae ◽  
Paenibacillus Larvae ◽  
American Foulbrood ◽  
Nosema Disease ◽  
The Impact ◽  
Pathogenic Infection

Honeybees, Apis mellifera, are important pollinators of many economically important crops. However, one of the reasons for their decline is pathogenic infection. Nosema disease and American foulbrood (AFB) disease are the most common bee pathogens that propagate in the gut of honeybees. This study investigated the impact of gut-propagating pathogens, including Nosema ceranae and Paenibacillus larvae, on bacterial communities in the gut of A. mellifera using 454-pyrosequencing. Pyrosequencing results showed that N. ceranae was implicated in the elimination of Serratia and the dramatic increase in Snodgrassella and Bartonella in adult bees’ guts, while bacterial communities of P. larvae-infected larvae were not affected by the infection. The results indicated that only N. ceranae had an impact on some core bacteria in the gut of A. mellifera through increasing core gut bacteria, therefore leading to the induction of dysbiosis in the bees’ gut.

scholarly journals Viral quasispecies inference from 454 pyrosequencing

2013 ◽  
Vol 14 (1) ◽  
pp. 355 ◽  
Author(s):  
Wan-Ting Poh ◽  
Eryu Xia ◽  
Kwanrutai Chin-inmanu ◽  
Lai-Ping Wong ◽  
Anthony Cheng ◽  
...  
Keyword(s):  
454 Pyrosequencing ◽  
Viral Quasispecies

scholarly journals Impact of seasonal changes on fungal diversity of a semi-arid ecosystem revealed by 454 pyrosequencing

2015 ◽  
Vol 91 (5) ◽  
Author(s):  
Lluvia Vargas-Gastélum ◽  
Adriana L. Romero-Olivares ◽  
Ana E. Escalante ◽  
Axayácatl Rocha-Olivares ◽  
Carlos Brizuela ◽  
...  
Keyword(s):  
Seasonal Changes ◽  
Fungal Diversity ◽  
454 Pyrosequencing ◽  
Arid Ecosystem ◽  
Semi Arid

scholarly journals Plasmid Localization and Organization of Melamine Degradation Genes in Rhodococcus sp. Strain Mel

2011 ◽  
Vol 78 (5) ◽  
pp. 1397-1403 ◽  
Author(s):  
Anthony G. Dodge ◽  
Lawrence P. Wackett ◽  
Michael J. Sadowsky
Keyword(s):  
454 Pyrosequencing ◽  
Minimal Medium ◽  
Doubling Time ◽  
Cyanuric Acid ◽  
Acid Hydrolase ◽  
Content Type ◽  
N Source ◽  
Genes Encoding ◽  
Rhodococcus Sp ◽  
Roche 454

ABSTRACTRhodococcussp. strain Mel was isolated from soil by enrichment and grew in minimal medium with melamine as the sole N source with a doubling time of 3.5 h. Stoichiometry studies showed that all six nitrogen atoms of melamine were assimilated. The genome was sequenced by Roche 454 pyrosequencing to 13× coverage, and a 22.3-kb DNA region was found to contain a homolog to the melamine deaminase genetrzA. Mutagenesis studies showed that the cyanuric acid hydrolase and biuret hydrolase genes were clustered together on a different 17.9-kb contig. Curing and gene transfer studies indicated that 4 of 6 genes required for the complete degradation of melamine were located on an ∼265-kb self-transmissible linear plasmid (pMel2), but this plasmid was not required for ammeline deamination. TheRhodococcussp. strain Mel melamine metabolic pathway genes were located in at least three noncontiguous regions of the genome, and the plasmid-borne genes encoding enzymes for melamine metabolism were likely recently acquired.

scholarly journals Barcoding lichen-forming fungi using 454 pyrosequencing is challenged by artifactual and biological sequence variation

Genome ◽  
2016 ◽  
Vol 59 (9) ◽  
pp. 685-704 ◽  
Author(s):  
Kristiina Mark ◽  
Carolina Cornejo ◽  
Christine Keller ◽  
Daniela Flück ◽  
Christoph Scheidegger
Keyword(s):  
454 Pyrosequencing ◽  
Ecological Integrity ◽  
Common Species ◽  
Sequencing Error ◽  
Reference Database ◽  
Biological Sequence ◽  
Internal Transcribed Spacer Region ◽  
Epiphytic Lichen ◽  
Fungal Partner ◽  
A Genome

Although lichens (lichen-forming fungi) play an important role in the ecological integrity of many vulnerable landscapes, only a minority of lichen-forming fungi have been barcoded out of the currently accepted ∼18 000 species. Regular Sanger sequencing can be problematic when analyzing lichens since saprophytic, endophytic, and parasitic fungi live intimately admixed, resulting in low-quality sequencing reads. Here, high-throughput, long-read 454 pyrosequencing in a GS FLX+ System was tested to barcode the fungal partner of 100 epiphytic lichen species from Switzerland using fungal-specific primers when amplifying the full internal transcribed spacer region (ITS). The present study shows the potential of DNA barcoding using pyrosequencing, in that the expected lichen fungus was successfully sequenced for all samples except one. Alignment solutions such as BLAST were found to be largely adequate for the generated long reads. In addition, the NCBI nucleotide database—currently the most complete database for lichen-forming fungi—can be used as a reference database when identifying common species, since the majority of analyzed lichens were identified correctly to the species or at least to the genus level. However, several issues were encountered, including a high sequencing error rate, multiple ITS versions in a genome (incomplete concerted evolution), and in some samples the presence of mixed lichen-forming fungi (possible lichen chimeras).

scholarly journals Molecular diversity of bacteria in commercially available “Spirulina” food supplements

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1610 ◽  
Author(s):  
Elisabeth Vardaka ◽  
Konstantinos A. Kormas ◽  
Matina Katsiapi ◽  
Savvas Genitsaris ◽  
Maria Moustaka-Gouni
Keyword(s):  
Natural Product ◽  
454 Pyrosequencing ◽  
Molecular Diversity ◽  
Arthrospira Platensis ◽  
Food Supplements ◽  
Health Issues ◽  
Operational Taxonomic Units ◽  
Health Promoting ◽  
First Time ◽  
Pyrosequencing Analysis

The cyanobacteriumArthrospirais among the most well-known food supplements worldwide known as “Spirulina.” While it is a widely recognized health-promoting natural product, there are no reports on the molecular diversity of commercially available brands of “Spirulina” supplements and the occurrence of other cyanobacterial and heterotrophic bacterial microorganisms in these products. In this study, 454-pyrosequencing analysis of the total bacterial occurrence in 31 brands of “Spirulina” dietary supplements from the Greek market was applied for the first time. In all samples, operational taxonomic units (OTUs) ofArthrospira platensiswere the predominant cyanobacteria. Some products contained additional cyanobacterial OTUs including a few known potentially toxic taxa. Moreover, 469 OTUs were detected in all 31 products collectively, with most of them being related to the Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Verrucomicrobia. All samples included heterotrophic bacterial OTUs, ranging from 9–157 per product. Among the most common OTUs were ones closely related to taxa known for causing health issues (i.e.,Pseudomonas,Flavobacterium,Vibrio,Aeromonas,Clostridium,Bacillus,Fusobacterium,Enterococcus). The observed high cyanobacterial and heterotrophic bacterial OTUs richness in the final product is a point for further research on the growth and processing ofArthrospirabiomass for commercial purposes.

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