The Lactic Acid Enterococci Enterococcus faecium and Enterococcus durans: Nucleotide Sequence Diversity in 16S rRNA Genes

Injera is soft fermented baked product, which is commonly prepared from teff (Eragrostis tef(Zucc.)) flour and believed to be consumed on daily basis by two-thirds of Ethiopians.As it is a product of naturally fermented dough, the course of fermentation is done by consortia of microorganisms. The study was aimed at isolating and identifying some dominant bacteria from fermentingteff (Eragrostis tef)dough. A total of 97 dough samples were collected from households, microenterprises, and hotels with different fermentation stage from Addis Ababa. The bacterial isolates obtained from the fermentingteffdough samples were selected on the basis of their acid production potentials. A total of 24 purified bacterial isolates were found to be Gram-positive (they are coccus and rod under microscope) and were good acid producers. Genomic DNA of bacterial isolates were extracted using Invisorb® Spin DNA Extraction kit. 16S rRNA of bacterial isolates were amplified using the bacteria universal primers (rD1 and fD1). The amplified product was sequenced at Genewiz, USA. Sequence analysis and comparison with the resources at the database were conducted to identify the isolated microbes into species and strain levels. The bacterial isolates were identified asLactobacillus paracasei, Lactobacillus brevis, Enterococcus durans, Enterococcus hirae, Enterococcus avium,andEnterococcus faecium. All identified lactic acid bacteria were able to produce acid at 12 h time of incubation. This study has confirmed the presence of different bacterial species in the fermentingteffdough and also supports the involvement of various groups of bacterial species in the course of the fermentation.

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Restriction fragment length polymorphism analysis of 16S rRNA genes in lactic acid bacteria isolated from red wine

Journal of Bioscience and Bioengineering ◽

10.1016/s1389-1723(00)80091-2 ◽

2000 ◽

Vol 90 (3) ◽

pp. 335-337 ◽

Cited By ~ 31

Author(s):

Hajime Sato ◽

Fujitoshi Yanagida ◽

Takashi Shinohara ◽

Koki Yokotsuka

Keyword(s):

Lactic Acid ◽

Lactic Acid Bacteria ◽

Restriction Fragment Length Polymorphism ◽

16S Rrna ◽

Red Wine ◽

Fragment Length Polymorphism ◽

16S Rrna Genes ◽

Rrna Genes ◽

Polymorphism Analysis ◽

Restriction Fragment Length

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Root Nodule Bradyrhizobium spp. Harbor tfdAα and cadA, Homologous with Genes Encoding 2,4-Dichlorophenoxyacetic Acid-Degrading Proteins

Applied and Environmental Microbiology ◽

10.1128/aem.70.4.2110-2118.2004 ◽

2004 ◽

Vol 70 (4) ◽

pp. 2110-2118 ◽

Cited By ~ 49

Author(s):

Kazuhito Itoh ◽

Yoshiko Tashiro ◽

Kazuko Uobe ◽

Yoichi Kamagata ◽

Kousuke Suyama ◽

...

Keyword(s):

Gene Transfer ◽

Nucleotide Sequence ◽

Horizontal Gene Transfer ◽

16S Rrna ◽

Root Nodule ◽

16S Rrna Genes ◽

Rrna Genes ◽

Ether Linkage ◽

Genes Encoding ◽

Sequence Identities

ABSTRACT The distribution of tfdAα and cadA, genes encoding 2,4-dichlorophenoxyacetate (2,4-D)-degrading proteins which are characteristic of the 2,4-D-degrading Bradyrhizobium sp. isolated from pristine environments, was examined by PCR and Southern hybridization in several Bradyrhizobium strains including type strains of Bradyrhizobium japonicum USDA110 and Bradyrhizobium elkanii USDA94, in phylogenetically closely related Agromonas oligotrophica and Rhodopseudomonas palustris, and in 2,4-D-degrading Sphingomonas strains. All strains showed positive signals for tfdAα, and its phylogenetic tree was congruent with that of 16S rRNA genes in α-Proteobacteria, indicating evolution of tfdAα without horizontal gene transfer. The nucleotide sequence identities between tfdAα and canonical tfdA in β- and γ-Proteobacteria were 46 to 57%, and the deduced amino acid sequence of TfdAα revealed conserved residues characteristic of the active site of α-ketoglutarate-dependent dioxygenases. On the other hand, cadA showed limited distribution in 2,4-D-degrading Bradyrhizobium sp. and Sphingomonas sp. and some strains of non-2,4-D-degrading B. elkanii. The cadA genes were phylogenetically separated between 2,4-D-degrading and nondegrading strains, and the cadA genes of 2,4-D degrading strains were further separated between Bradyrhizobium sp. and Sphingomonas sp., indicating the incongruency of cadA with 16S rRNA genes. The nucleotide sequence identities between cadA and tftA of 2,4,5-trichlorophenoxyacetate-degrading Burkholderia cepacia AC1100 were 46 to 53%. Although all root nodule Bradyrhizobium strains were unable to degrade 2,4-D, three strains carrying cadA homologs degraded 4-chlorophenoxyacetate with the accumulation of 4-chlorophenol as an intermediate, suggesting the involvement of cadA homologs in the cleavage of the aryl ether linkage. Based on codon usage patterns and GC content, it was suggested that the cadA genes of 2,4-D-degrading and nondegrading Bradyrhizobium spp. have different origins and that the genes would be obtained in the former through horizontal gene transfer.

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Differentiation Of Clarias Batrachus, C. Gariepinus And Heteropneustes Fossilis By Pcr-Sequencing Of Mitochondrial 16s Rrna Gene

Journal of the Asiatic Society of Bangladesh Science ◽

10.3329/jasbs.v41i1.46190 ◽

2015 ◽

Vol 41 (1) ◽

pp. 51-58

Author(s):

Mohammad Shamimul Alam ◽

Hawa Jahan ◽

Rowshan Ara Begum ◽

Reza M Shahjahan

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Fish Larva ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Valuable Insight ◽

Multiple Sequence ◽

Pcr Rflp ◽

Alternative Means

Heteropneustesfossilis, Clariasbatrachus and C. gariepinus are three major catfishes ofecological and economic importance. Identification of these fish species becomes aproblem when the usual external morphological features of the fish are lost or removed,such as in canned fish. Also, newly hatched fish larva is often difficult to identify. PCRsequencingprovides accurate alternative means of identification of individuals at specieslevel. So, 16S rRNA genes of three locally collected catfishes were sequenced after PCRamplification and compared with the same gene sequences available from othergeographical regions. Multiple sequence alignment of the 16S rRNA gene fragments ofthe catfish species has revealed polymorphic sites which can be used to differentiate thesethree species from one another and will provide valuable insight in choosing appropriaterestriction enzymes for PCR-RFLP based identification in future. Asiat. Soc. Bangladesh, Sci. 41(1): 51-58, June 2015

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Faculty Opinions recommendation of The influence of linkage and inbreeding on patterns of nucleotide sequence diversity at duplicate alcohol dehydrogenase loci in wild barley (Hordeum vulgare ssp. spontaneum).

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1012165.184577 ◽

2003 ◽

Author(s):

Michael Purugganan

Keyword(s):

Hordeum Vulgare ◽

Nucleotide Sequence ◽

Alcohol Dehydrogenase ◽

Wild Barley ◽

Sequence Diversity ◽

Nucleotide Sequence Diversity ◽

Hordeum Vulgare Ssp

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Effects of Supplement of Marichromatium gracile YL28 on Water Quality and Microbial Structures in Shrimp Mariculture Ecosystems

Genes ◽

10.3390/genes12010040 ◽

2020 ◽

Vol 12 (1) ◽

pp. 40

Author(s):

Liang Cui ◽

Bitong Zhu ◽

Xiaobo Zhang ◽

Zhuhua Chan ◽

Chungui Zhao ◽

...

Keyword(s):

Water Quality ◽

16S Rrna ◽

Relative Abundance ◽

Animal Health ◽

Denitrifying Bacteria ◽

Nitrite Reduction ◽

16S Rrna Genes ◽

Rrna Genes ◽

Sequencing Analysis ◽

Shrimp Culture

The elevated NH3-N and NO2-N pollution problems in mariculture have raised concerns because they pose threats to animal health and coastal and offshore environments. Supplement of Marichromatium gracile YL28 (YL28) into polluted shrimp rearing water and sediment significantly decreased ammonia and nitrite concentrations, showing that YL28 functioned as a novel safe marine probiotic in the shrimp culture industry. The diversity of aquatic bacteria in the shrimp mariculture ecosystems was studied by sequencing the V4 region of 16S rRNA genes, with respect to additions of YL28 at the low and high concentrations. It was revealed by 16S rRNA sequencing analysis that Proteobacteria, Planctomycete and Bacteroidetes dominated the community (>80% of operational taxonomic units (OTUs)). Up to 41.6% of the predominant bacterial members were placed in the classes Gammaproteobacteria (14%), Deltaproteobacteria (14%), Planctomycetacia (8%) and Alphaproteobacteria (5.6%) while 40% of OTUs belonged to unclassified ones or others, indicating that the considerable bacterial populations were novel in our shrimp mariculture. Bacterial communities were similar between YL28 supplements and control groups (without addition of YL28) revealed by the β-diversity using PCoA, demonstrating that the additions of YL28 did not disturb the microbiota in shrimp mariculture ecosystems. Instead, the addition of YL28 increased the relative abundance of ammonia-oxidizing and denitrifying bacteria. The quantitative PCR analysis further showed that key genes including nifH and amoA involved in nitrification and nitrate or nitrite reduction significantly increased with YL28 supplementation (p < 0.05). The supplement of YL28 decreased the relative abundance of potential pathogen Vibrio. Together, our studies showed that supplement of YL28 improved the water quality by increasing the relative abundance of ammonia-oxidizing and denitrifying bacteria while the microbial community structure persisted in shrimp mariculture ecosystems.

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