Chinese leek（Allium tuberosum Rottler ex Sprengel） is a common vegetable in China. In our previous study, Chinese leek in rotation was found to have significant antifungal and nematicidal activity. This study＇s aim...Chinese leek（Allium tuberosum Rottler ex Sprengel） is a common vegetable in China. In our previous study, Chinese leek in rotation was found to have significant antifungal and nematicidal activity. This study＇s aim was to investigate the potential antifungal and nematicidal activity associated with rhizosphere or endophytic microbes of Chinese leek. Thus, a total of 79 261 high-quality sequences were obtained from Chinese leek rhizosphere soil, leaf and root samples. In the rhizosphere soil, the bacterial community comprised five dominant phyla： Proteobacteria（37.85%）, Acidobacteria（10.99%）, Bacteroidetes（8.24%）, Cyanobacteria（7.79%） and Planctomycetes（7.1%）. The leaf and root bacterial communities comprised two dominant phyla： Cyanobacteria（83.42% in leaf and 75.44% in root） and Proteobacteria（14.75% in leaf and 21.04% in root）. Microbial diversity, richness and evenness in the rhizosphere soil bacterial community were higher than that in the endophytic bacterial communities. The rhizosphere bacterial community was significantly different from the endophytic bacterial communities. The endophytic bacterial communities from the leaf and the root were slightly, but not significantly different from each other. This study＇s findings would contribute to the isolation and identification of nematicidal and antifungal bacterial communities in Chinese leek.展开更多
The microbiome has a profound impact on host fitness. pH, oxygen, nutrients, or other factors such as food or pharmaceuticals, subject the microbiome to variations in the gastrointestinal tract. This variation is a ca...The microbiome has a profound impact on host fitness. pH, oxygen, nutrients, or other factors such as food or pharmaceuticals, subject the microbiome to variations in the gastrointestinal tract. This variation is a cause for concern given dysbiosis of the microbiome is correlated with various disease states. Currently, much research relies on model organisms to study microbial communities since intact microbiomes are challenging to utilize. The objective of this study is to culture an explanted colon microbiome of 4 Balb/c mice to develop an in vitro tool for future microbiome studies. We cultured homogenates of the distal colons of 4 mice in trans-well culture dishes. These dishes were incubated for 24 hours in two different oxygen concentration levels and the pH was compared before and after incubation of the cultures. To analyze the integrity of the microbiome, we utilized massively paralleled DNA sequencing with 16S metagenomics to characterize fecal and colon samples to speculate whether future studies may utilize feces in constructing an in vitro microbial community to spare animal lives. We found that pH and familial relationships had a profound impact on community structure while oxygen did not have a significant influence. The feces and the colon were similar in community profiles, which lends credence to utilizing feces in future studies. The gut microbiome is of great interest and great importance for studies in a variety of different diseases. Many laboratories do not have access to germ-free mice, which is one optimal way to study mammalian microbiomes, but this technique allowed for the in vitro culturing of a majority of the prokaryotes isolated from the colons of mice. This may allow an alternative to study the interactions of this very diverse population of microorganisms without the need for germ-free conditions.展开更多
基金supported by the National Natural Science Foundation of China (31471864 and 31272151)the Qingdao Agricultural University High-level Personnel Startup Fund, China (6631115024)
文摘Chinese leek（Allium tuberosum Rottler ex Sprengel） is a common vegetable in China. In our previous study, Chinese leek in rotation was found to have significant antifungal and nematicidal activity. This study＇s aim was to investigate the potential antifungal and nematicidal activity associated with rhizosphere or endophytic microbes of Chinese leek. Thus, a total of 79 261 high-quality sequences were obtained from Chinese leek rhizosphere soil, leaf and root samples. In the rhizosphere soil, the bacterial community comprised five dominant phyla： Proteobacteria（37.85%）, Acidobacteria（10.99%）, Bacteroidetes（8.24%）, Cyanobacteria（7.79%） and Planctomycetes（7.1%）. The leaf and root bacterial communities comprised two dominant phyla： Cyanobacteria（83.42% in leaf and 75.44% in root） and Proteobacteria（14.75% in leaf and 21.04% in root）. Microbial diversity, richness and evenness in the rhizosphere soil bacterial community were higher than that in the endophytic bacterial communities. The rhizosphere bacterial community was significantly different from the endophytic bacterial communities. The endophytic bacterial communities from the leaf and the root were slightly, but not significantly different from each other. This study＇s findings would contribute to the isolation and identification of nematicidal and antifungal bacterial communities in Chinese leek.
文摘The microbiome has a profound impact on host fitness. pH, oxygen, nutrients, or other factors such as food or pharmaceuticals, subject the microbiome to variations in the gastrointestinal tract. This variation is a cause for concern given dysbiosis of the microbiome is correlated with various disease states. Currently, much research relies on model organisms to study microbial communities since intact microbiomes are challenging to utilize. The objective of this study is to culture an explanted colon microbiome of 4 Balb/c mice to develop an in vitro tool for future microbiome studies. We cultured homogenates of the distal colons of 4 mice in trans-well culture dishes. These dishes were incubated for 24 hours in two different oxygen concentration levels and the pH was compared before and after incubation of the cultures. To analyze the integrity of the microbiome, we utilized massively paralleled DNA sequencing with 16S metagenomics to characterize fecal and colon samples to speculate whether future studies may utilize feces in constructing an in vitro microbial community to spare animal lives. We found that pH and familial relationships had a profound impact on community structure while oxygen did not have a significant influence. The feces and the colon were similar in community profiles, which lends credence to utilizing feces in future studies. The gut microbiome is of great interest and great importance for studies in a variety of different diseases. Many laboratories do not have access to germ-free mice, which is one optimal way to study mammalian microbiomes, but this technique allowed for the in vitro culturing of a majority of the prokaryotes isolated from the colons of mice. This may allow an alternative to study the interactions of this very diverse population of microorganisms without the need for germ-free conditions.
