Diversity of autochthonous bacterial communities in the intestinal mucosa of grass carp (Ctenopharyngodon idellus) (Valenciennes) determined by culture-dependent and culture-independent techniques

2014 ◽  
Vol 46 (10) ◽  
pp. 2344-2359 ◽  
Author(s):  
Huan Li ◽  
Qiuping Zhong ◽  
Stephan Wirth ◽  
Weiwei Wang ◽  
Yaotong Hao ◽  
...  
Keyword(s):  
Intestinal Mucosa ◽  
Grass Carp ◽  
Bacterial Communities ◽  
Ctenopharyngodon Idellus ◽  
Culture Independent ◽  
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 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

Two biomass preparation methods provide insights into studying microbial communities of intestinal mucosa in grass carp (Ctenopharyngodon idellus)

2017 ◽  
Vol 48 (8) ◽  
pp. 4272-4283 ◽  
Author(s):  
Ngoc Tuan Tran ◽  
Fan Xiong ◽  
Yao-Tong Hao ◽  
Jing Zhang ◽  
Shan-Gong Wu ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Intestinal Mucosa ◽  
Grass Carp ◽  
Ctenopharyngodon Idellus ◽  
Preparation Methods

Bacterial communities in Chinese grass carp (Ctenopharyngodon idellus) farming ponds

2012 ◽  
Vol 45 (1) ◽  
pp. 138-149 ◽  
Author(s):  
Tao Zhou ◽  
Yan Wang ◽  
Jinyu Tang ◽  
Yangxin Dai
Keyword(s):  
Grass Carp ◽  
Bacterial Communities ◽  
Ctenopharyngodon Idellus

scholarly journals Connectivity of Edaphic and Endolithic Microbial Niches in Cold Mountain Desert of Eastern Pamir (Tajikistan)

Biology ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 314
Author(s):  
Nataliia Khomutovska ◽  
Asunción de los Ríos ◽  
Marcin D. Syczewski ◽  
Iwona Jasser
Keyword(s):  
Bacterial Communities ◽  
Novel Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Arid Environments ◽  
Soil Crusts ◽  
Composition And Structure ◽  
Culture Independent ◽  
Culture Dependent ◽  
Endolithic Communities

Microbial communities found in arid environments are commonly represented by biological soil crusts (BSCs) and endolithic assemblages. There is still limited knowledge concerning endoliths and BSCs occurring in the cold mountain desert of Pamir. The aim of the study was to investigate the composition and structure of endolithic bacterial communities in comparison to surrounding BSCs in three subregions of the Eastern Pamir (Tajikistan). The endolithic and BSC communities were studied using culture-independent and culture-dependent techniques. The structure of the endolithic bacterial communities can be characterized as Actinobacteria–Proteobacteria–Bacteroidetes–Chloroflexi–Cyanobacteria, while the BSCs’ can be described as Proteobacteria–Actinobacteria–Bacteroidetes–Cyanobacteria assemblages with low representation of other bacteria. The endolithic cyanobacterial communities were characterized by the high percentage of Chroococcidiopsaceae, Nodosilineaceae, Nostocaceae and Thermosynechococcaceae, while in the BSCs were dominated by Nodosilineaceae, Phormidiaceae and Nostocaceae. The analysis of 16S rRNA genes of the cyanobacterial cultures revealed the presence of possibly novel species of Chroococcidiopsis, Gloeocapsopsis and Wilmottia. Despite the niches’ specificity, which is related to the influence of microenvironment factors on the composition and structure of endolithic communities, our results illustrate the interrelation between the endoliths and the surrounding BSCs in some regions. The structure of cyanobacterial communities from BSC was the only one to demonstrate some subregional differences.

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