scholarly journals Bacterial DNA Diversity among Clear and Cloudy Sakes, and Sake-kasu

2020 ◽  
Vol 13 (1) ◽  
pp. 74-82
Author(s):  
Momoka Terasaki ◽  
Hiromi Nishida
Keyword(s):  
Production Process ◽  
Dna Sequences ◽  
Bacterial Contamination ◽  
Yeast Cells ◽  
Bacterial Cells ◽  
Bacterial Dna ◽  
Rdna Sequences ◽  
Dna Diversity ◽  
16S Rdna Sequences ◽  
The Difference

Background: The traditional Japanese alcoholic drink, sake, is classified into two types: those that contain sediment produced during the production process (cloudy sakes) and those that do not contain such sediment (clear sakes). Leftover pressed sediment from the sake production process, sake-kasu (sake cake or sake lees), is commercially available and is highly nutritious for humans. Objective: The purpose of this study was to determine the difference among component bacterial DNA sequences of clear and cloudy sakes, and sake-kasu. Methods: We compared the 16S rDNA sequences from 44 samples of clear sake, 3 samples of cloudy sake, and 11 samples of sake-kasu. Results: The DNA sequences were divided into three major clusters; however, sequences in sake-kasu were located in just one cluster forming two lineages. The microbial diversity in sake-kasu was lower than that in clear and cloudy sakes, which may be because some of the contaminating bacterial cells do not lyse during the production process and remain intact, along with yeast cells, in sake-kasu. Conclusion: Bacterial DNA frequently detected in sake samples was from environmental bacterial contamination that occurs early in the sake production process. Contaminating bacteria are usually killed by the ethanol produced as the sake yeast grows; after which, if bacteria lyse, the bacterial DNA is released into the sake solution. However, if the bacterial cells do not lyse, they will precipitate toward the sediment. Thus, there is bacterial DNA diversity in clear and cloudy sake, but less diversity in sake-kasu.

scholarly journals Coexistence of Wolbachia with Buchnera aphidicola and a Secondary Symbiont in the Aphid Cinara cedri

2004 ◽  
Vol 186 (19) ◽  
pp. 6626-6633 ◽  
Author(s):  
Laura Gómez-Valero ◽  
Mario Soriano-Navarro ◽  
Vicente Pérez-Brocal ◽  
Abdelaziz Heddi ◽  
Andrés Moya ◽  
...  
Keyword(s):  
Bacterial Genome ◽  
Pcr Amplification ◽  
Bacterial Cells ◽  
Buchnera Aphidicola ◽  
Rdna Genes ◽  
16S Ribosomal Dna ◽  
Secondary Symbiont ◽  
Rdna Sequences ◽  
16S Rdna Sequences

ABSTRACT Intracellular symbiosis is very common in the insect world. For the aphid Cinara cedri, we have identified by electron microscopy three symbiotic bacteria that can be characterized by their different sizes, morphologies, and electrodensities. PCR amplification and sequencing of the 16S ribosomal DNA (rDNA) genes showed that, in addition to harboring Buchnera aphidicola, the primary endosymbiont of aphids, C. cedri harbors a secondary symbiont (S symbiont) that was previously found to be associated with aphids (PASS, or R type) and an α-proteobacterium that belongs to the Wolbachia genus. Using in situ hybridization with specific bacterial probes designed for symbiont 16S rDNA sequences, we have shown that Wolbachia was represented by only a few minute bacteria surrounding the S symbionts. Moreover, the observed B. aphidicola and the S symbionts had similar sizes and were housed in separate specific bacterial cells, the bacteriocytes. Interestingly, in contrast to the case for all aphids examined thus far, the S symbionts were shown to occupy a similarly sized or even larger bacteriocyte space than B. aphidicola. These findings, along with the facts that C. cedri harbors the B. aphidicola strain with the smallest bacterial genome and that the S symbionts infect all Cinara spp. analyzed so far, suggest the possibility of bacterial replacement in these species.

scholarly journals Detection and Isolation of Novel Rhizopine-Catabolizing Bacteria from the Environment

1998 ◽  
Vol 64 (12) ◽  
pp. 4944-4949 ◽  
Author(s):  
Brian B. McSpadden Gardener ◽  
Frans J. de Bruijn
Keyword(s):  
Dna Sequences ◽  
Sinorhizobium Meliloti ◽  
Southern Hybridization ◽  
Southern Hybridization Analysis ◽  
Carbon And Nitrogen ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Standard Assay ◽  
Ribosomal Dnas ◽  
Assay Conditions

ABSTRACT Microbial rhizopine-catabolizing (Moc) activity was detected in serial dilutions of soil and rhizosphere washes. The activity observed generally ranged between 106 and 107 catabolic units per g, and the numbers of nonspecific culture-forming units were found to be approximately 10 times higher. A diverse set of 37 isolates was obtained by enrichment on scyllo-inosamine-containing media. However, none of the bacteria that were isolated were found to contain DNA sequences homologous to the known mocA,mocB, and mocC genes of Sinorhizobium meliloti L5-30. Twenty-one of the isolates could utilize an SI preparation as the sole carbon and nitrogen source for growth. Partial sequencing of 16S ribosomal DNAs (rDNAs) amplified from these strains indicated that five distinct bacterial genera (Arthrobacter, Sinorhizobium,Pseudomonas, Aeromonas, andAlcaligenes) were represented in this set. Only 6 of these 21 isolates could catabolize 3-O-methyl-scyllo-inosamine under standard assay conditions. Two of these, strains D1 and R3, were found to have 16S rDNA sequences very similar to those of Sinorhizobium meliloti. However, these strains are not symbiotically effective on Medicago sativa, and DNA sequences homologous to thenodB and nodC genes were not detected in strains D1 and R3 by Southern hybridization analysis.

scholarly journals The phylogeny of the genusYersiniabased on 16S rDNA sequences

1993 ◽  
Vol 114 (2) ◽  
pp. 173-177 ◽  
Author(s):  
A. Ibrahim ◽  
B.M. Goebel ◽  
W. Liesack ◽  
M. Griffiths ◽  
E. Stackebrandt
Keyword(s):  
16S Rdna ◽  
Rdna Sequences ◽  
16S Rdna Sequences

scholarly journals Molecular analysis of the microflora in chronic venous leg ulceration

2003 ◽  
Vol 52 (4) ◽  
pp. 365-369 ◽  
Author(s):  
K.E. Hill ◽  
C.E. Davies ◽  
M.J. Wilson ◽  
P. Stephens ◽  
K.G. Harding ◽  
...  
Keyword(s):  
Individual Species ◽  
Venous Leg Ulcer ◽  
Bacterial Populations ◽  
Cultural Methods ◽  
Rdna Sequences ◽  
Oral Microflora ◽  
16S Rdna Sequences ◽  
First Time

There is growing evidence to suggest that the resident microflora of chronic venous leg ulcers impairs cellular wound-healing responses, thereby playing an important role in maintaining the non-healing phenotype of many of these wounds. The significance of individual species of bacteria will remain unclear until it is possible to characterize fully the microflora of such lesions. The limitations and biases of culture-based microbiology are being realized and the subsequent application of molecular methods is revealing greater diversity within mixed bacterial populations than that demonstrated by culture alone. To date, this approach has been limited to a small number of systems, including the oral microflora. Here, for the first time, the comprehensive characterization of the microflora present in the tissue of a chronic venous leg ulcer is described by the comparison of 16S rDNA sequences amplified directly from the wound tissue with sequences obtained from bacteria that were isolated by culture. The molecular approach demonstrated significantly greater bacterial diversity than that revealed by culture. Furthermore, sequences were retrieved that may possibly represent novel species of bacteria. It is only by the comprehensive analysis of the wound microflora by both molecular and cultural methods that it will be possible to further our understanding of the role of bacteria in this important condition.

scholarly journals Gross profit in relation to operational account analysis.

1964 ◽  
Vol 12 (3) ◽  
pp. 227-228
Author(s):  
B. Van Booen ◽  
J. Kamminga
Keyword(s):  
Production Process ◽  
Optimal Plan ◽  
Fair Comparison ◽  
The Difference

The need to define clearly the costs that are used to calculate gross profit for the purpose of operational account analysis is stressed. Gross profit should be measured by the difference between gross revenue and the costs related to one activity only, and to factors used solely in one production process. For a fair comparison of gross profits of different enterprises, each enterprise should be compared over the same unit of time. Therefore by definition only continually varying costs should be included as "variable " costs in the measurement of gross profit, and when there is a change in costs that do not vary continually there will be a new planning situation and a new optimal plan. D. A. E. (Abstract retrieved from CAB Abstracts by CABI’s permission)

scholarly journals How, when, and where relic DNA biases estimates of microbial diversity

2017 ◽  
Author(s):  
JT Lennon ◽  
ME Muscarella ◽  
SA Muscarella ◽  
BK Lehmkuhl
Keyword(s):  
Microbial Diversity ◽  
Dna Sequences ◽  
Species Abundance ◽  
Rrna Gene ◽  
Bacterial Dna ◽  
Soil Sediment ◽  
Species Abundance Distributions ◽  
Abundance And Diversity ◽  
Dna Pool ◽  
Biased Estimates

Extracellular or “relic” DNA is one of the largest pools of nucleic acids in the mbiosphere1,2. Relic DNA can influence a number of important ecological and evolutionary processes, but it may also bias estimates of microbial abundance and diversity, which has implications for understanding environmental, engineered, and host-associated ecosystems. We developed models capturing the fundamental processes that regulate the size and composition of the relic DNA pools to identify scenarios leading to biased estimates of biodiversity. Our models predict that bias increases with relic DNA pool size, but only when the species abundance distributions (SAD) of relic and intact DNA are distinct from one another. We evaluated our model predictions by quantifying relic DNA and assessing its contribution to bacterial diversity using 16S rRNA gene sequences collected from different ecosystem types, including soil, sediment, water, and the mammalian gut. On average, relic DNA made up 33 % of the total bacterial DNA pool, but exceeded 80 % in some samples. Despite its abundance, relic DNA had no effect on estimates of taxonomic and phylogenetic diversity, even in ecosystems where processes such as the physical protection of relic DNA are common and predicted by our models to generate bias. Rather, our findings are consistent with the expectation that relic DNA sequences degrade in proportion to their abundance and therefore may contribute minimally to estimates of microbial diversity.

scholarly journals Isolation and Identification of Hydrocarbon-Degrading Bacteria that Tolerant to Saponin of Sapindus Rarak Plant

2019 ◽  
Vol 4 (1) ◽  
pp. 79-88
Author(s):  
Evi Octaviany ◽  
Suharjono Suharjono ◽  
Irfan Mustafa
Keyword(s):  
Crude Oil ◽  
16S Rdna ◽  
Bacterial Isolates ◽  
High Concentration ◽  
Isolation And Identification ◽  
Rdna Sequences ◽  
Degrading Bacteria ◽  
16S Rdna Sequences ◽  
Petroleum Contaminated Soil ◽  
Cell Densities

A commercial saponin as biosurfactant can reduce the surface tension of water and increase of hydrocarbon degradation. However, this saponin can be toxic to some hydrocarbonoclastic bac-teria. This study aimed to obtain bacterial isolates that were tolerant and incapable to degrade saponin, and to identify them based on 16S rDNA sequence. Bacteria were isolated from petroleum contaminated soil in Wonocolo Village, Bojonegoro Regency, East Java, Indonesia. The soil samples were acclimated using Bushnell-Haas (BH) broth with 0.5% crude oil at room temperature for 3 weeks. The culture was spread onto BH agar incubated at 30°C for 7 days. The first screened, isolates were grown in nutrient broth with addition of sap-onin 0%, 8%, and 12% (v/v) then incubated at 30°C for three days. The bacterial cell density was measured using a spectrophotometer. Second screened, the isolates were grown on BH broth with addition of 0.5% saponin as a sole carbon source, and their cell densities were measured. The selected isolates were identified based on 16S rDNA sequences. Among 34 bacterial isolates, nine isolates were tol-erant to 12% saponin. Three bacterial isolates IHT1.3, IHT1.5, and IHT3.24 tolerant to high concentration of saponin and did not use this substance as growth nutrition. The IHT1.3, IHT1.5, and IHT3.24 isolates were identified as Ochrobactrum pseudogrignonense (99% similarity), Pseudomonas mendocina (99%), and Ochrobactrum pi-tuitosum; (97%), respectively. Those three selected isolates are good candidates as hydrocarbon-degrading bacteria to bioremediation of soil contaminated crude oil. However, the combined activity of bacteria and saponin to degrade hydrocarbon needs further study. 

scholarly journals THE DIFFERENCE OF E.COLI CONTENT IN THE CHICKEN MEAT IN THE SOUTH KEPUTRAN TRADITIONAL MARKET AND SUPERMARKET ' X ' OF SURABAYA CITY

2019 ◽  
Vol 14 (1) ◽  
pp. 24
Author(s):  
Athalla Permana ◽  
R. Bambang W
Keyword(s):  
Bacterial Contamination ◽  
Chicken Meat ◽  
Personal Hygiene ◽  
Food Handler ◽  
The South ◽  
Cross Sectional ◽  
E Coli ◽  
Traditional Market ◽  
The Difference ◽  
Meat Samples

Hygiene and sanitation practices in chicken influenced Eschericia coli bacterial contamination in food. A Study conducted by Sasmita and Juwita mentioned that there was positively E.coli content in chicken meat in supermarket. Thus, the purpose of this study was to assess the difference of E.Coli content in chicken meat and personal hygiene of food handler. It was an observational study with cross sectional approach. The population of this study included traditional market sellers and supermarkets. The sample of this study consisted of 14 samples of chicken meat in which 7 samples came from the South Keputran traditional market and other 7 samples came from Supermarket ‘X’. Moreover, 7 traditional market sellers and 2 supermarkets were involved to be examined. Variables of the study were E.coli content in chicken meat from Traditional Market of South Keputran and Supermarket ‘X’ and personal hygiene. Samples of chicken meat was done by accidental sampling. Data were collected through interview and observation, whereas the difference of E-Coli content was analyzed using statistical test. The results of this study indicated that one of chicken meat samples positively contained E.Coli bacteria, and no significant differences of the E.coli content were found on the chicken meat samples from both the Traditional Market of South Keputran and Supermarket ‘X’. The suggestion that can be given to Supermarket ‘X’ seller is to control and pay close attention to the sanitation process from suppliers to retails

Sign in / Sign up

Export Citation Format

Share Document