Molecular identification of different actinomycetes isolated from East Black Sea region plateau soil by 16S rDNA gene sequencing

Sodium carboxymethyl starch (CMS-Na), a kind of food additive with high degree of substitution, is also known as a prebiotic. The aim of this study was to determine the effect of CMS-Na on defecation. Constipated mouse model was prepared by loperamide. Normal rats were also used in the study. Short-chain fatty acids in rat feces were detected by gas chromatography. The bacterial communities in rat feces were identified by 16S rDNA gene sequencing. 5-hydroxytryptamine (5-HT) and tryptophan hydroxylase 1 (Tph1) were measured by ELISA. The results showed that CMS-Na increased the fecal granule counts and intestinal propulsion rate in constipated mice. The contents of water, acetic acid, propionic acid and n-butyrate in feces, Tph1 in colon and 5-HT in serum of rats were increased. In addition, CMS-Na shortened the colonic transport time in rats. The 16S rDNA gene sequencing results indicated that CMS-Na increased the relative abundance of Alloprevotella and decreased the proportion of Lactobacillus. However, the biodiversity of the normal intestinal flora was not altered. In conclusion, CMS-Na can promote defecation in constipated mice. The mechanism may be related to the regulation of Alloprevotella and Lactobacillus in colon, the increase of short-chain fatty acids, and the promotion of the synthesis of Tph1 and 5-HT.

Download Full-text

Isolation and Molecular Identification of Biosurfactant Producing Soil Bacteria

International Journal of Engineering & Technology ◽

10.14419/ijet.v7i4.14.27475 ◽

2019 ◽

Vol 7 (4.14) ◽

pp. 77

Author(s):

N A N Zamani ◽

T E Tengku Zainal Mulok ◽

R Mat Nor ◽

. .

Keyword(s):

16S Rdna ◽

Soil Bacteria ◽

Bacterial Species ◽

Gene Sequencing ◽

Bacillus Sp ◽

16S Rdna Gene ◽

Gram Positive ◽

Rdna Gene ◽

Emulsification Index ◽

16S Rdna Gene Sequencing

Biosurfactants are amphiphilic compound, having hydrophilic and hydrophobic moieties enabling them to reduce surface and interfacial tension at the surface. Their unique properties are applied in various industries such as foaming and wetting agents, emulsifiers, detergents and bioremediation. A total of 98 isolates showed biosurfactant activity using hemolytic activity, drop collapse test and oil spreading assay. All isolates were rod-shaped, Gram positive and majority of them were non-endospore former. Only the isolates showing the highest percentage of emulsification index (E24) and ability to reduce tension were used for species identification using 16S rDNA gene sequencing which were isolates A1(6) and A2(1). Both isolates were identified as Bacillus sp. cp-h50 and Bacillus sp. XT-24 respectively, rod-shaped, endospore former and Gram positive. The biosurfactant produced by both species showed high emulsification index (E24) (A1(6), 63.3% and A2(1), 46.7%) and good surfactant capacity. The size of amplified gene of 16S rDNA gene was approximately 1.5 kb. These features provide evidence that both species could be a potential biosurfactant producer with proper optimization for the production of biosurfactant. The biosurfactant produced by both bacterial species were identified as surfactin using Fourier Transform Infrared Spectroscopy (FTIR).

Download Full-text

MALDI-TOF: A useful tool for laboratory identification of uncommon glucose non-fermenting Gram-negative bacteria associated with cystic fibrosis

Journal of Medical Microbiology ◽

10.1099/jmm.0.076869-0 ◽

2014 ◽

Vol 63 (9) ◽

pp. 1148-1153 ◽

Cited By ~ 13

Author(s):

Helena Aguilar Peres Homem de Mello de Souza ◽

Libera Maria Dalla-Costa ◽

Fernando José Vicenzi ◽

Dilair Camargo de Souza ◽

Carlos Antônio Riedi ◽

...

Keyword(s):

Cystic Fibrosis ◽

16S Rdna ◽

Gene Sequencing ◽

Discriminatory Power ◽

16S Rdna Gene ◽

Gram Negative ◽

Rdna Gene ◽

Maldi Tof ◽

Micro Organisms ◽

16S Rdna Gene Sequencing

The predisposition of patients with cystic fibrosis (CF) for recurrent pulmonary infections can result in poor prognosis of the disease. Although the clinical significance in CF of micro-organisms, such as Staphylococcus aureus, Haemophilus influenzae and Pseudomonas aeruginosa, is well established, the implication of uncommon glucose non-fermenting Gram-negative bacilli (UGNF-GNB) in respiratory samples from CF patients is still unclear. Because of limitations of traditional methods used in most clinical laboratories, the accurate identification of these microbes is a challenge. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) is an alternative tool for efficient identification of bacteria. This was a retrospective study to evaluate different identification methods in a collection of UGNF-GNB isolated from children with CF during a period of three years. The performance of MALDI-TOF was compared to that of 16S rDNA gene sequencing and to a conventional and automated phenotypic identification. The discriminatory power of MALDI-TOF (75.0 % agreement) was superior to automated techniques (67.1 % agreement) and to conventional phenotypical identification (50.0 % agreement). MALDI-TOF also demonstrated high accuracy in identifying Stenotrophomonas maltophilia, Achromobacter xylosoxidans and Chryseobacterium indologenes, but had limited utility in identifying Pandoraea spp. and some species of Acinetobacter and Chryseobacterium (other than C. indologenes). Although MALDI-TOF identified only 75 % of the isolates in comparison with 16S rDNA gene sequencing, the prompt identification and high discriminatory power exhibited by MALDI-TOF make it a useful tool for the characterization of micro-organisms that are difficult to identify using routine methods.

Download Full-text

197 BACTERIAL DNA DETECTION BY REAL-TIME PCR AND 16s RDNA GENE SEQUENCING IN SPONTANEOUS BACTERIAL PERITONITIS

Journal of Hepatology ◽

10.1016/s0168-8278(10)60199-7 ◽

2010 ◽

Vol 52 ◽

pp. S85

Author(s):

G. Soriano ◽

O. Esparcia ◽

M. Montemayor ◽

C. Guarner-Argente ◽

R. Pericas ◽

...

Keyword(s):

Real Time ◽

16S Rdna ◽

Real Time Pcr ◽

Spontaneous Bacterial Peritonitis ◽

Gene Sequencing ◽

16S Rdna Gene ◽

Bacterial Dna ◽

Rdna Gene ◽

Bacterial Peritonitis ◽

16S Rdna Gene Sequencing

Download Full-text

Employment of 16S rDNA gene sequencing techniques to identify phenotypically difficult-to-identify culturable eubacteria from foods and waters

International Journal of Food Science & Technology ◽

10.1111/j.1365-2621.2004.00936.x ◽

2005 ◽

Vol 40 (2) ◽

pp. 229-233 ◽

Cited By ~ 2

Author(s):

Jiru Xu ◽

James Christopher Neville Heaney ◽

Sharon A. Marshall ◽

Beverly Cherie Millar ◽

David A. McDowell ◽

...

Keyword(s):

16S Rdna ◽

Gene Sequencing ◽

16S Rdna Gene ◽

Rdna Gene ◽

16S Rdna Gene Sequencing

Download Full-text

Screening and Isolation of Polyhydroxyalkanoates (PHA)-Producing Bacteria from Landfill by using Cocoa Pod Husks as Carbon Source

International Journal of Engineering & Technology ◽

10.14419/ijet.v7i4.14.27470 ◽

2019 ◽

Vol 7 (4.14) ◽

pp. 51

Author(s):

W R Wan Abdul Razak ◽

N J Mohamad Yusuf ◽

A Abdul-Aziz ◽

S K Navaratnam ◽

I Zubir ◽

...

Keyword(s):

Carbon Source ◽

16S Rdna ◽

Bacterial Species ◽

Gene Sequencing ◽

Morphological Identification ◽

Bacterial Isolates ◽

16S Rdna Gene ◽

Rdna Gene ◽

Cocoa Pod Husks ◽

16S Rdna Gene Sequencing

Polyhydroxyalkanoates (PHA) are bioplastics, produced by various bacteria as food and energy reservoir. PHA is an alternative for synthetic plastic because they are environmentally friendly and can be degraded naturally by microorganisms. One of the important factors for the growth of PHA producing bacteria is an excess of carbon supply. In order to reduce the overall cost of PHA production, a low cost pure substrate, which is cocoa pod husks (CPH) was used as a carbon source. The objectives of this study were to isolate and screen PHA producing bacteria from landfill samples which are leachate and soil, to identify the PHA producing bacteria by using morphological characterization and 16s rDNA gene sequencing and to determine the best percentage of CPH that can be used as a carbon source for PHA producing bacteria. PHA producing bacteria from leachate and soil from landfill in Jeram, Selangor were screened by using Nile Blue A staining method. Two potential PHA producers with the brightest fluorescence under UV light from each samples were isolated and characterized by using morphological and molecular identification. Results of morphological identification shows all bacterial isolates have a rod shape and have a capsule, three bacterial isolates (L4, S3, S5) have an endospore while the remaining does not have endospore (L1). Three out of four were Gram positive bacteria (L4, S3, S5) and the remaining was Gram negative bacteria (L1). These isolates were confirmed of their identity as K. pneumoniae (L1), B. cereus (L4 & S3) and B. toyonensis (S5) using 16s rDNA gene sequencing. Different concentration of CPH, which are 2% (w/v), 5% (w/v), 7% (w/v) and 10% (w/v) were used to study the best percentage of CPH that can be used as carbon source. PHA accumulation was the highest at 7% (w/v) for all bacterial species tested and lowest at 10% (w/v) CPH except for B. toyonensis. Therefore, K. pneumoniae, B. cereus and B. toyonensis which isolated from landfill show the ability to produce PHA and the used of 7% (w/v) cocoa pod husks as carbon source give the highest PHA accumulation.

Download Full-text