scholarly journals Cellulolytic Bacteria in the Foregut of the Dromedary Camel (Camelus dromedarius)

2012 ◽  
Vol 78 (24) ◽  
pp. 8836-8839 ◽  
Author(s):  
Anjas A. Samsudin ◽  
André-Denis G. Wright ◽  
Rafat Al Jassim
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Species Level ◽  
Neutral Detergent Fiber ◽  
Dromedary Camel ◽  
Rrna Gene ◽  
Cellulolytic Bacteria ◽  
16S Rrna Gene Sequences ◽  
Dromedary Camels ◽  
Operational Taxonomic Units

ABSTRACTForegut digesta from five feral dromedary camels were inoculated into three different enrichment media: cotton thread, filter paper, and neutral detergent fiber. A total of 283 16S rRNA gene sequences were assigned to 33 operational taxonomic units by using 99% species-level identity. LIBSHUFF revealed significant differences in the community composition across all three libraries.

scholarly journals Bacterial Community in the Crop of the Hoatzin, a Neotropical Folivorous Flying Bird

2008 ◽  
Vol 74 (19) ◽  
pp. 5905-5912 ◽  
Author(s):  
Filipa Godoy-Vitorino ◽  
Ruth E. Ley ◽  
Zhan Gao ◽  
Zhiheng Pei ◽  
Humberto Ortiz-Zuazaga ◽  
...  
Keyword(s):  
Species Richness ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Population ◽  
Species Level ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Digestive Efficiency ◽  
Operational Taxonomic Units

ABSTRACT The hoatzin is unique among known avian species because of the fermentative function of its enlarged crop. A small-bodied flying foregut fermenter is a paradox, and this bird provides an interesting model to examine how diet selection and the gut microbiota contribute to maximizing digestive efficiency. Therefore, we characterized the bacterial population in the crop of six adult hoatzins captured from the wild. A total of 1,235 16S rRNA gene sequences were grouped into 580 phylotypes (67% of the pooled species richness sampled, based on Good's coverage estimator, with CACE and Chao1 estimates of 1,709 and 1,795 species-level [99% identity] operational taxonomic units, respectively). Members of 9 of the ∼75 known phyla in Bacteria were identified in this gut habitat; the Firmicutes were dominant (67% of sequences, belonging to the classes Clostridia, Mollicutes, and Bacilli), followed by the Bacteroidetes (30%, mostly in the order Bacteroidales), Proteobacteria (1.8%), and Lentisphaerae, Verrucomicrobia, TM7, Spirochaetes, Actinobacteria, and Aminanaerobia (all <0.1%). The novelty in this ecosystem is great; 94% of the phylotypes were unclassified at the “species” level and thus likely include novel cellulolytic lineages.

Isolation and Identification of Thermo-Acidophilic Bacteria from Orchards in China

2010 ◽  
Vol 73 (2) ◽  
pp. 390-394 ◽  
Author(s):  
YING WANG ◽  
TIANLI YUE ◽  
YAHONG YUAN ◽  
ZHENPENG GAO
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Species Level ◽  
Shaanxi Province ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Isolation And Identification ◽  
Acidophilic Bacteria ◽  
Different Strains

Eight strains of thermo-acidophilic bacteria have been isolated from apple orchards in Shaanxi Province, China. The isolated strains were identified at the species level by comparing 16S rRNA gene sequences. It was found that all strains could be assigned to two genera. The strain YL-5 belonged to Alicyclobacillus, and other isolates belonged to Bacillus. The enzymatic patterns by the API ZYM system showed very significant differences between 12 strains of Alicyclobacillus and 8 strains of Bacillus. The ability of guaiacol production varied among different strains.

Identification of genus Campylobacter up to species level using internal features of 16S rRNA gene sequences

2016 ◽  
Vol 31 (3) ◽  
pp. 187-196
Author(s):  
ManasaSri Muralidharan ◽  
Avantika Ghosh ◽  
Nirjara Singhvi ◽  
P. S. Dhanaraj ◽  
Rup Lal ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Species Level ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences

scholarly journals OptiClust: Improved method for assigning amplicon-based sequence data to operational taxonomic units

2016 ◽  
Author(s):  
Sarah L. Westcott ◽  
Patrick D. Schloss
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Data ◽  
Significant Advance ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Operational Taxonomic Units ◽  
Computational Bottleneck

AbstractAssignment of 16S rRNA gene sequences to operational taxonomic units (OTUs) is a computational bottleneck in the process of analyzing microbial communities. Although this has been an active area of research, it has been difficult to overcome the time and memory demands while improving the quality of the OTU assignments. Here we developed a new OTU assignment algorithm that iteratively reassigns sequences to new OTUs to optimize the Matthews correlation coefficient (MCC), a measure of the quality of OTU assignments. To assess the new algorithm, OptiClust, we compared it to ten other algorithms using 16S rRNA gene sequences from two simulated and four natural communities. Using the OptiClust algorithm, the MCC values averaged 15.2 and 16.5% higher than the OTUs generated when we used the average neighbor and distance-based greedy clustering with VSEARCH, respectively. Furthermore, on average, OptiClust was 94.6-times faster than the average neighbor algorithm and just as fast as distance-based greedy clustering with VSEARCH. An empirical analysis of the efficiency of the algorithms showed that the time and memory required to perform the algorithm scaled quadratically with the number of unique sequences in the dataset. The significant improvement in the quality of the OTU assignments over previously existing methods will significantly enhance downstream analysis by limiting the splitting of similar sequences into separate OTUs and merging of dissimilar sequences into the same OTU. The development of the OptiClust algorithm represents a significant advance that is likely to have numerous other applications.

scholarly journals The Human Oral Microbiome

2010 ◽  
Vol 192 (19) ◽  
pp. 5002-5017 ◽  
Author(s):  
Floyd E. Dewhirst ◽  
Tuste Chen ◽  
Jacques Izard ◽  
Bruce J. Paster ◽  
Anne C. R. Tanner ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Species Level ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
16S Rrna Gene Sequences ◽  
Culture Independent ◽  
Health And Disease

ABSTRACT The human oral cavity contains a number of different habitats, including the teeth, gingival sulcus, tongue, cheeks, hard and soft palates, and tonsils, which are colonized by bacteria. The oral microbiome is comprised of over 600 prevalent taxa at the species level, with distinct subsets predominating at different habitats. The oral microbiome has been extensively characterized by cultivation and culture-independent molecular methods such as 16S rRNA cloning. Unfortunately, the vast majority of unnamed oral taxa are referenced by clone numbers or 16S rRNA GenBank accession numbers, often without taxonomic anchors. The first aim of this research was to collect 16S rRNA gene sequences into a curated phylogeny-based database, the Human Oral Microbiome Database (HOMD), and make it web accessible (www.homd.org ). The HOMD includes 619 taxa in 13 phyla, as follows: Actinobacteria, Bacteroidetes, Chlamydiae, Chloroflexi, Euryarchaeota, Firmicutes, Fusobacteria, Proteobacteria, Spirochaetes, SR1, Synergistetes, Tenericutes, and TM7. The second aim was to analyze 36,043 16S rRNA gene clones isolated from studies of the oral microbiota to determine the relative abundance of taxa and identify novel candidate taxa. The analysis identified 1,179 taxa, of which 24% were named, 8% were cultivated but unnamed, and 68% were uncultivated phylotypes. Upon validation, 434 novel, nonsingleton taxa will be added to the HOMD. The number of taxa needed to account for 90%, 95%, or 99% of the clones examined is 259, 413, and 875, respectively. The HOMD is the first curated description of a human-associated microbiome and provides tools for use in understanding the role of the microbiome in health and disease.

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