scholarly journals Comparison of specific endophytic bacterial communities in different developmental stages of Passiflora incarnata using culture‐dependent and culture‐independent analysis

2019 ◽  
Vol 8 (10) ◽  
Author(s):  
Marcela C. Goulart ◽  
Luis G. Cueva‐Yesquén ◽  
Kelly J. Hidalgo Martinez ◽  
Derlene Attili‐Angelis ◽  
Fabiana Fantinatti‐Garboggini
Keyword(s):  
Bacterial Communities ◽  
Developmental Stages ◽  
Independent Analysis ◽  
Culture Independent ◽  
Passiflora Incarnata ◽  
Culture Dependent

Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome

2020 ◽  
Vol 96 (3) ◽  
Author(s):  
Gavin J Fenske ◽  
Sudeep Ghimire ◽  
Linto Antony ◽  
Jane Christopher-Hennings ◽  
Joy Scaria
Keyword(s):  
Bacterial Communities ◽  
Bacterial Species ◽  
Shotgun Metagenomics ◽  
Culture Techniques ◽  
Microbiome Composition ◽  
Culture Independent ◽  
Health And Disease ◽  
The Media ◽  
And Function ◽  
Culture Dependent

ABSTRACT Bacterial communities resident in the hindgut of pigs, have profound impacts on health and disease. Investigations into the pig microbiome have utilized either culture-dependent, or far more commonly, culture-independent techniques using next generation sequencing. We contend that a combination of both approaches generates a more coherent view of microbiome composition. In this study, we surveyed the microbiome of Tamworth breed and feral pigs through the integration high throughput culturing and shotgun metagenomics. A single culture medium was used for culturing. Selective screens were added to the media to increase culture diversity. In total, 46 distinct bacterial species were isolated from the Tamworth and feral samples. Selective screens successfully shifted the diversity of bacteria on agar plates. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function. It allows for assemblage of defined bacterial communities for studies in bioreactors or germfree animal models.

scholarly journals Culture‐independent analysis of hydrocarbonoclastic bacterial communities in environmental samples during oil‐bioremediation

2018 ◽  
Vol 8 (2) ◽  
pp. e00630 ◽  
Author(s):  
Narjes Dashti ◽  
Nedaa Ali ◽  
Samar Salamah ◽  
Majida Khanafer ◽  
Ghada Al‐Shamy ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Environmental Samples ◽  
Independent Analysis ◽  
Culture Independent

Hydrocarbonoclastic biofilms based on sewage microorganisms and their application in hydrocarbon removal in liquid wastes

2014 ◽  
Vol 60 (7) ◽  
pp. 477-486 ◽  
Author(s):  
D.M. Al-Mailem ◽  
M.K. Kansour ◽  
S.S. Radwan
Keyword(s):  
Bacterial Flora ◽  
Culture Conditions ◽  
Sewage Effluent ◽  
Hydrocarbonoclastic Bacteria ◽  
Glass Slides ◽  
Independent Analysis ◽  
Culture Independent ◽  
Hydrocarbon Removal ◽  
Liquid Wastes ◽  
Culture Dependent

Attempts to establish hydrocarbonoclastic biofilms that could be applied in waste-hydrocarbon removal are still very rare. In this work, biofilms containing hydrocarbonoclastic bacteria were successfully established on glass slides by submerging them in oil-free and oil-containing sewage effluent for 1 month. Culture-dependent analysis of hydrocarbonoclastic bacterial communities in the biofilms revealed the occurrence of the genera Pseudomonas, Microvirga, Stenotrophomonas, Mycobacterium, Bosea, and Ancylobacter. Biofilms established in oil-containing effluent contained more hydrocarbonoclastic bacteria than those established in oil-free effluent, and both biofilms had dramatically different bacterial composition. Culture-independent analysis of the bacterial flora revealed a bacterial community structure totally different from that determined by the culture-dependent method. In microcosm experiments, these biofilms, when used as inocula, removed between 20% and 65% crude oil, n-hexadecane, and phenanthrene from the surrounding effluent in 2 weeks, depending on the biofilm type, the hydrocarbon identity, and the culture conditions. More of the hydrocarbons were removed by biofilms established in oil-containing effluent than by those established in oil-free effluent, and by cultures incubated in the light than by those incubated in the dark. Meanwhile, the bacterial numbers and diversities were enhanced in the biofilms that had been previously used in hydrocarbon bioremediation. These novel findings pave a new way for biofilm-based hydrocarbon bioremediation, both in sewage effluent and in other liquid wastes.

scholarly journals Bias problems in culture-independent analysis of environmental bacterial communities: a representative study on hydrocarbonoclastic bacteria

SpringerPlus ◽  
2013 ◽  
Vol 2 (1) ◽  
pp. 369 ◽  
Author(s):  
Husain Al-Awadhi ◽  
Narjis Dashti ◽  
Majida Khanafer ◽  
Dina Al-Mailem ◽  
Nidaa Ali ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Hydrocarbonoclastic Bacteria ◽  
Representative Study ◽  
Independent Analysis ◽  
Culture Independent

scholarly journals Culture dependent and independent analysis of bacterial communities associated with commercial salad leaf vegetables

2013 ◽  
Vol 13 (1) ◽  
pp. 274 ◽  
Author(s):  
Colin R Jackson ◽  
Kevin C Randolph ◽  
Shelly L Osborn ◽  
Heather L Tyler
Keyword(s):  
Bacterial Communities ◽  
Independent Analysis ◽  
Culture Dependent ◽  
Leaf Vegetables
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