Monitoring bacterial communities in ε-Polylysine-treated bighead carp (Aristichthys nobilis) fillets using culture-dependent and culture-independent techniques

2018 ◽  
Vol 76 ◽  
pp. 257-266 ◽  
Author(s):  
Xiaochang Liu ◽  
Dongping Li ◽  
Kaifeng Li ◽  
Yongkang Luo
Keyword(s):  
Bacterial Communities ◽  
Bighead Carp ◽  
Aristichthys Nobilis ◽  
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

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.

scholarly journals Endophytic bacterial communities in apple leaves are minimally impacted by streptomycin use for fire blight management

2021 ◽  
Author(s):  
Anna Wallis ◽  
Ganyu Gu ◽  
Padmini Ramachandran ◽  
Elizabeth Reed ◽  
Andrea R. Ottesen ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Fire Blight ◽  
High Throughput Sequencing ◽  
Organic Production ◽  
Apple Orchards ◽  
Minimal Impact ◽  
Culture Independent ◽  
Apple Production ◽  
Epiphytic Communities ◽  
Culture Dependent

In apples, the streptomycin is routinely used to manage fire blight, a devastating disease that greatly impacts commercial apple production. Applications of streptomycin may impact the endophytic bacterial communities, which are increasingly recognized for their valuable roles in plant hosts. Altering these communities may have implications for plant health and selection for streptomycin resistance in off-target bacteria. In a previous study, we found rapid selection of streptomycin resistant epiphytes following season-long streptomycin use, and now sought to investigate the season-long impact of streptomycin applications (1, 3, or 9 post-bloom applications) on endophytic bacterial communities. Studies were conducted in two orchards, and both culture-dependent and independent methods were used to assess the bacterial endophytic community. Streptomycin programs were compared to untreated trees and two programs approved for organic production. Treatments minimally impacted abundance of culturable endophytic bacteria as determined by culture-dependent methods. Similarly, there were no significant differences in relative bacterial abundance or community composition between treatments as determined by 16S rRNA high-throughput sequencing (Culture-independent). There were greater differences between orchards than between treatments suggesting a stronger influence of locality. Communities were dominated by the families Pseudomonadaceae, Enterobacteriaceae, Desulfovibrionaceae, Bacillaceae, and Burkholderiaceae, which are commonly described in other investigations of microbial communities of apple orchards. In addition, we found a high abundance of Amoebophiliaceae, a family dominated by arthropod parasites. Our results provide evidence that season-long applications of streptomycin in apple orchards have minimal impact on endophytic bacterial communities, which is in contrast to some reports on epiphytic communities.

scholarly journals Analysis of the Bacterial Diversity Associated with the Roots of Maize (Zea mays L.) through Culture-Dependent and Culture-Independent Methods

ISRN Ecology ◽  
2011 ◽  
Vol 2011 ◽  
pp. 1-10 ◽  
Author(s):  
Paola Pereira ◽  
Fernando Ibáñez ◽  
Mónica Rosenblueth ◽  
Miriam Etcheverry ◽  
Esperanza Martínez-Romero
Keyword(s):  
Bacterial Diversity ◽  
Bacterial Communities ◽  
Zea Mays L ◽  
Culture Collection ◽  
Maize Roots ◽  
Culture Independent ◽  
Internal Transcribed Spacer Sequences ◽  
Gradient Separation ◽  
Culture Dependent ◽  
Its Primers

The present study investigated bacterial diversity associated with the roots of maize through the use of culture-dependent and culture-independent methods. Bacterial 16S–23S rDNA internal transcribed spacer sequences (ITS) primers were used to amplify sequences obtained directly from the root matrix by Percoll gradient separation. This assay showed that γ-Proteobacteria within Enterobacter, Erwinia, Klebsiella, Pseudomonas, and Stenotrophomonas genera were predominant groups. The culturable component of the bacterial community was also assessed, revealing that the predominant group was Firmicutes, mainly of Bacillus genus, while Achromobacter, Lysinibacillus, and Paenibacillus genera were rarely found in association with the roots. Only two genera within γ-Proteobacteria, Enterobacter and Pseudomonas, were found in the culture collection. Differences in richness and diversity between the rhizospheric and endophytic bacterial communities were also evidenced. The spectrum of bacteria naturally associated with maize roots is wide and the magnitude of such diversity will depend on the methods chosen for analysis. The knowledge of this spectrum will facilitate the search of microorganisms capable of exerting antagonism to diverse pathogens or detecting plant growth enhancers.

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