Wekemo Bioincloud: A user‐friendly platform for meta‐omics data analyses

Gao, Yunyun; Zhang, Guoxing; Jiang, Shunyao; Liu, Yong‐Xin

doi:10.1002/imt2.175

Cited by 48 publications

(9 citation statements)

References 67 publications

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“…All figures and tables in this article are visualized by Wekemo Bioincloud (https: //www.bioincloud.tech/, accessed on 18 October 2022) [31].…”

Section: Discussionmentioning

confidence: 99%

Changes in Rhizosphere Soil Microorganisms and Metabolites during the Cultivation of Fritillaria cirrhosa

Liu,

Ying,

Liu

2024

Biology

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Fritillaria cirrhosa is an important cash crop, and its industrial development is being hampered by continuous cropping obstacles, but the composition and changes of rhizosphere soil microorganisms and metabolites in the cultivation process of Fritillaria cirrhosa have not been revealed. We used metagenomics sequencing to analyze the changes of the microbiome in rhizosphere soil during a three-year cultivation process, and combined it with LC-MS/MS to detect the changes of metabolites. Results indicate that during the cultivation of Fritillaria cirrhosa, the composition and structure of the rhizosphere soil microbial community changed significantly, especially regarding the relative abundance of some beneficial bacteria. The abundance of Bradyrhizobium decreased from 7.04% in the first year to about 5% in the second and third years; the relative abundance of Pseudomonas also decreased from 6.20% in the first year to 2.22% in the third year; and the relative abundance of Lysobacter decreased significantly from more than 4% in the first two years of cultivation to 1.01% in the third year of cultivation. However, the relative abundance of some harmful fungi has significantly increased, such as Botrytis, which increased significantly from less than 3% in the first two years to 7.93% in the third year, and Talaromyces fungi, which were almost non-existent in the first two years of cultivation, significantly increased to 3.43% in the third year of cultivation. The composition and structure of Fritillaria cirrhosa rhizosphere metabolites also changed significantly, the most important of which were carbohydrates represented by sucrose (48.00–9.36–10.07%) and some amino acid compounds related to continuous cropping obstacles. Co-occurrence analysis showed that there was a significant correlation between differential microorganisms and differential metabolites, but Procrustes analysis showed that the relationship between bacteria and metabolites was closer than that between fungi and metabolites. In general, in the process of Fritillaria cirrhosa cultivation, the beneficial bacteria in the rhizosphere decreased, the harmful bacteria increased, and the relative abundance of carbohydrate and amino acid compounds related to continuous cropping obstacles changed significantly. There is a significant correlation between microorganisms and metabolites, and the shaping of the Fritillaria cirrhosa rhizosphere’s microecology by bacteria is more relevant.

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“…All figures and tables in this article are visualized by Wekemo Bioincloud (https: //www.bioincloud.tech/, accessed on 18 October 2022) [31].…”

Section: Discussionmentioning

confidence: 99%

Changes in Rhizosphere Soil Microorganisms and Metabolites during the Cultivation of Fritillaria cirrhosa

Liu,

Ying,

Liu

2024

Biology

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“…The hierarchical tree was constructed using the unweighted paired arithmetic mean method (UPGMA) based on UniFrac distance (Wang et al 2017 ). For β-diversity, Wekemo Bioincloud (Gao et al 2024 ) was used to visualize the result of non-metric multidimensional scaling (NMDS), principal component analysis (PCA), and principal coordinate analysis (PCOA) based on Bray–Curtis distance.…”

Section: Methodsmentioning

confidence: 99%

Spatial profiles of the bacterial microbiota throughout the gastrointestinal tract of dairy goats

Hu,

Luo,

Cheng

et al. 2024

Appl Microbiol Biotechnol

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The gastrointestinal tract (GIT) is stationed by a dynamic and complex microbial community with functions in digestion, metabolism, immunomodulation, and reproduction. However, there is relatively little research on the composition and function of microorganisms in different GIT segments in dairy goats. Herein, 80 chyme samples were taken from ten GIT sites of eight Xinong Saanen dairy goats and then analyzed and identified the microbial composition via 16S rRNA V1-V9 amplicon sequencing. A total of 6669 different operational taxonomic units (OTUs) were clustered, and 187 OTUs were shared by ten GIT segments. We observed 264 species belonging to 23 different phyla scattered across ten GITs, with Firmicutes (52.42%) and Bacteroidetes (22.88%) predominating. The results revealed obvious location differences in the composition, diversity, and function of the GIT microbiota. In LEfSe analysis, unidentified_Lachnospiraceae and unidentified_Succinniclassicum were significantly enriched in the four chambers of stomach, with functions in carbohydrate fermentation to compose short-chain fatty acids. Aeriscardovia, Candidatus_Saccharimonas, and Romboutsia were significantly higher in the foregut, playing an important role in synthesizing enzymes, amino acids, and vitamins and immunomodulation. Akkermansia, Bacteroides, and Alistipes were significantly abundant in the hindgut to degrade polysaccharides and oligosaccharides, etc. From rumen to rectum, α-diversity decreased first and then increased, while β-diversity showed the opposite trend. Metabolism was the major function of the GIT microbiome predicted by PICRUSt2, but with variation in target substrates along the regions. In summary, GIT segments play a decisive role in the composition and functions of microorganisms. Key points • The jejunum and ileum were harsh for microorganisms to colonize due to the presence of bile acids, enzymes, faster chyme circulation, etc., exhibiting the lowest α-diversity and the highest β-diversity. • Variability in microbial profiles between the three foregut segments was greater than four chambers of stomach and hindgut, with a higher abundance of Firmicutes dominating than others. • Dairy goats dominated a higher abundance of Kiritimatiellaeota than cows, which was reported to be associated with fatty acid synthesis.

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“…Furthermore, we employed the Bioinformatics Cloud platform (Wekemo Bioincloud: https://www.bioincloud.tech/task-meta accessed on 4 May 2024) to perform a principal component analysis (PCA) on the functional gene sets between the two groups. To assess the variability in microbial functional communities among different group samples, we implemented a non-metric multidimensional scaling (NMDS) analysis based on the Bray-Curtis distance metric, followed by a linear discriminant analysis (LDA) [27].…”

Section: Data Visualization and Statistical Analysismentioning

confidence: 99%

The Impact of Aboveground Epichloë Endophytic Fungi on the Rhizosphere Microbial Functions of the Host Melica transsilvanica

Wang,

Shi,

Huang

et al. 2024

Microorganisms

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In nature, the symbiotic relationship between plants and microorganisms is crucial for ecosystem balance and plant growth. This study investigates the impact of Epichloë endophytic fungi, which are exclusively present aboveground, on the rhizosphere microbial functions of the host Melica transsilvanica. Using metagenomic methods, we analyzed the differences in microbial functional groups and functional genes in the rhizosphere soil between symbiotic (EI) and non-symbiotic (EF) plants. The results reveal that the presence of Epichloë altered the community structure of carbon and nitrogen cycling-related microbial populations in the host’s rhizosphere, significantly increasing the abundance of the genes (porA, porG, IDH1) involved in the rTCA cycle of the carbon fixation pathway, as well as the abundance of nxrAB genes related to nitrification in the nitrogen-cycling pathway. Furthermore, the presence of Epichloë reduces the enrichment of virulence factors in the host rhizosphere microbiome, while significantly increasing the accumulation of resistance genes against heavy metals such as Zn, Sb, and Pb. This study provides new insights into the interactions among endophytic fungi, host plants, and rhizosphere microorganisms, and offers potential applications for utilizing endophytic fungi resources to improve plant growth and soil health.

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Wekemo Bioincloud: A user‐friendly platform for meta‐omics data analyses

Cited by 48 publications

References 67 publications

Changes in Rhizosphere Soil Microorganisms and Metabolites during the Cultivation of Fritillaria cirrhosa

Changes in Rhizosphere Soil Microorganisms and Metabolites during the Cultivation of Fritillaria cirrhosa

Spatial profiles of the bacterial microbiota throughout the gastrointestinal tract of dairy goats

The Impact of Aboveground Epichloë Endophytic Fungi on the Rhizosphere Microbial Functions of the Host Melica transsilvanica

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