Culture Independent Diversity of Bacterial Communities Indigenous to Lower Altitude at Laohugou Glacial Environment

2020 ◽  
Vol 38 (1) ◽  
pp. 1-13 ◽  
Author(s):  
Barkat Ali ◽  
Wasim Sajjad ◽  
Prakriti Sharma Ghimire ◽  
Suliman Khan ◽  
Ghufranud Din ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Lower Altitude ◽  
Culture Independent

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

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 Culture-Independent Characterization of Bacterial Communities Associated with the Cold-Water Coral Lophelia pertusa in the Northeastern Gulf of Mexico

2009 ◽  
Vol 75 (8) ◽  
pp. 2294-2303 ◽  
Author(s):  
Christina A. Kellogg ◽  
John T. Lisle ◽  
Julia P. Galkiewicz
Keyword(s):  
Gulf Of Mexico ◽  
Shallow Water ◽  
Bacterial Communities ◽  
Cold Water ◽  
Environmental Gradients ◽  
Rrna Gene ◽  
Lophelia Pertusa ◽  
Culture Independent ◽  
Northeastern Gulf Of Mexico ◽  
Study Sites

ABSTRACT Bacteria are recognized as an important part of the total biology of shallow-water corals. Studies of shallow-water corals suggest that associated bacteria may benefit the corals by cycling carbon, fixing nitrogen, chelating iron, and producing antibiotics that protect the coral from other microbes. Cold-water or deep-sea corals have a fundamentally different ecology due to their adaptation to cold, dark, high-pressure environments and as such have novel microbiota. The goal of this study was to characterize the microbial associates of Lophelia pertusa in the northeastern Gulf of Mexico. This is the first study to collect the coral samples in individual insulated containers and to preserve coral samples at depth in an effort to minimize thermal shock and evaluate the effects of environmental gradients on the microbial diversity of samples. Molecular analysis of bacterial diversity showed a marked difference between the two study sites, Viosca Knoll 906/862 (VK906/862) and Viosca Knoll 826 (VK826). The bacterial communities from VK826 were dominated by a variety of unknown mycoplasmal members of the Tenericutes and Bacteroidetes, whereas the libraries from VK906/862 were dominated by members of the Proteobacteria. In addition to novel sequences, the 16S rRNA gene clone libraries revealed many bacterial sequences in common between Gulf of Mexico Lophelia corals and Norwegian fjord Lophelia corals, as well as shallow-water corals. Two Lophelia-specific bacterial groups were identified: a cluster of gammaproteobacteria related to sulfide-oxidizing gill symbionts of seep clams and a group of Mycoplasma spp. The presence of these groups in both Gulf and Norwegian Lophelia corals indicates that in spite of the geographic heterogeneity observed in Lophelia-associated bacterial communities, there are Lophelia-specific microbes.

Bacterial Communities Associated with Retail Alfalfa Sprouts

2008 ◽  
Vol 71 (1) ◽  
pp. 200-204 ◽  
Author(s):  
CINDY LOUI ◽  
GRIGOR GRIGORYAN ◽  
HAOHAO HUANG ◽  
LEE W. RILEY ◽  
SANGWEI LU
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Fresh Produce ◽  
Growth Conditions ◽  
Human Pathogens ◽  
Culture Independent ◽  
Foodborne Outbreaks ◽  
Total Bacterial Community ◽  
Alfalfa Sprouts ◽  
Alfalfa Sprout

Fresh produce, including salad, is increasingly implicated in foodborne outbreaks. Although studies have been carried out to detect specific human pathogens from fresh produce, the total bacterial community associated with fresh produce is poorly understood. In this study, we characterized the bacterial community associated with alfalfa sprouts, using a culture-independent method. Four retail-purchased alfalfa sprout samples were obtained from different producers, and the bacterial community associated with each sample was determined by 16S rDNA profiling. Our results indicate that alfalfa sprouts sampled in our study shared significant similarities in their bacterial communities. Proteobacteria was the dominant phylum detected from all alfalfa sprout samples, with Enterobacteriaceae, Oxalobacteraceae, Moraxellaceae, and Sphingomonadaceae as the most frequently detected families. These results indicate that growth conditions of alfalfa sprouts should be taken into consideration to prevent the proliferation of pathogenic proteobacteria such as Escherichia coli O157 and Salmonella.

scholarly journals Dynamics ofPanax ginsengRhizospheric Soil Microbial Community and Their Metabolic Function

2014 ◽  
Vol 2014 ◽  
pp. 1-6 ◽  
Author(s):  
Yong Li ◽  
YiXin Ying ◽  
WanLong Ding
Keyword(s):  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Restriction Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Plant Growth Promoting Bacteria ◽  
Metabolic Function ◽  
Rhizosphere Soils ◽  
Soil Microbial ◽  
Culture Independent ◽  
Plant Growth Promoting

The bacterial communities of 1- to 6-year ginseng rhizosphere soils were characterized by culture-independent approaches, random amplified polymorphic DNA (RAPD), and amplified ribosomal DNA restriction analysis (ARDRA). Culture-dependent method (Biolog) was used to investigate the metabolic function variance of microbe living in rhizosphere soil. Results showed that significant genetic and metabolic function variance were detected among soils, and, with the increasing of cultivating years, genetic diversity of bacterial communities in ginseng rhizosphere soil tended to be decreased. Also we found thatVerrucomicrobia,Acidobacteria, andProteobacteriawere the dominants in rhizosphere soils, but, with the increasing of cultivating years, plant disease prevention or plant growth promoting bacteria, such asPseudomonas,Burkholderia, andBacillus, tended to be rare.

Bacterial communities on food court tables and cleaning equipment in a shopping mall

2012 ◽  
Vol 141 (8) ◽  
pp. 1647-1651 ◽  
Author(s):  
S. DINGSDAG ◽  
N. V. COLEMAN
Keyword(s):  
Bacterial Communities ◽  
Shopping Mall ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Cross Contamination ◽  
Cleaning Equipment ◽  
Public Health Threat ◽  
Culture Independent ◽  
The Subject ◽  
Pathogenic Microbes

SUMMARYThe food court at a shopping mall is a potential transfer point for pathogenic microbes, but to date, this environment has not been the subject of detailed molecular microbiological study. We used a combination of culture-based and culture-independent approaches to investigate the types and numbers of bacteria present on food court tables, and on a food court cleaning cloth. Bacteria were found at 102–105 c.f.u./m2on food court tables and 1010 c.f.u./m2on the cleaning cloth. Tag-pyrosequencing of amplified 16S rRNA genes revealed that the dominant bacterial types on the cleaning cloth were genera known to include pathogenic species (Stenotrophomonas,Aeromonas), and that these genera were also evident at lower levels on table surfaces, suggesting possible cross-contamination. The evidence suggests a public health threat is posed by bacteria in the food court, and that this may be due to cross-contamination between cleaning equipment and table surfaces.

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