Primer selection impacts the evaluation of microecological patterns in environmental microbiomes

He, Jintao; Zhou, Tong; Shen, Xiaoqiang; Zhang, Nan; Sun, Chao; Lu, Shipeng; Shao, Yongqi

doi:10.1002/imt2.135

Cited by 7 publications

(3 citation statements)

References 54 publications

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“…Given that all the plants belong to the same species, the low contribution of deterministic processes may also be attributed to limited sources of variable host selection. Additionally, to our knowledge, community assembly process partitioning may be influenced by primer selection ( 54 ). The finding of stochasticity could partially result from potential primer bias.…”

Section: Discussionmentioning

confidence: 99%

Assemblages of rhizospheric and root endospheric mycobiota and their ecological associations with functional traits of rice

Guo,

Ning,

et al. 2024

mBio

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The assembly processes and functions of root-associated mycobiota are among the most fascinating yet elusive topics in microbial ecology. Our results revealed that stochastic forces (dispersal limitation or ecological drift) act on fungal community assembly in both the rice rhizosphere and root endosphere at the early stage of plant growth. In addition, high covariations between the rhizosphere fungal community compositions and plant functional trait profiles were clearly demonstrated in the present study. This work provides empirical evidence of the root-associated fungal assembly principles and ecological relationships of plant functional traits with rhizospheric and root endospheric mycobiota, thereby potentially providing novel perspectives for enhancing plant performance.

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Section: Discussionmentioning

confidence: 99%

Assemblages of rhizospheric and root endospheric mycobiota and their ecological associations with functional traits of rice

Guo,

Ning,

et al. 2024

mBio

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“…Taxonomic assignment was executed utilizing a Naïve Bayes consensus taxonomy classifier within the SILVA database (version 138) 46 . ASVs identified as singletons, or those assigned to chloroplasts and mitochondria, were excluded 47 . Analyses of species richness, community diversity, and composition were conducted as described previously 48 , 49 .…”

Section: Methodsmentioning

confidence: 99%

Fitness effects of synthetic and natural diet preservatives on the edible insect Bombyx mori

Lei,

Qian,

Zhu

et al. 2024

npj Sci Food

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Silkworm pupae as widely consumed insect products are good biosources of protein and micronutrients. Silkworm rearing throughout the year can be achieved by feeding them an artificial diet instead of native plants, facilitating extensive pupa production. However, artificial diets are prone to spoilage caused by bacterial contamination. Here, we evaluated the antiseptic effect of ethylparaben (EP, chemical preservative) and medium-chain fatty acids (MCFA, natural preservative) in a silkworm artificial diet. Results showed that both preservatives effectively inhibited pathogenic bacterial growth. Furthermore, the addition of EP or MCFA did not negatively impact the production capacity of silkworms and the homeostasis of gut microbiota. However, the expression of genes involved in detoxification such as Ugt2, and immune response such as Cecropin B, were upregulated after EP consumption. Therefore, natural preservative MCFA emerges as a suitable option from a safety perspective. These findings highlight future directions for improving insect artificial diet formulation.

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“…The mentioned studies contribute to uncovering responsible transcriptional regulation or signaling pathways related to disease processes and stress factors. Furthermore, the present state of environmental pollution not only heightens the risk of diseases but also functions as a persistent stressor, impacting both our well-being and the planet [ 113 , 114 ]. In future, scRNA-seq should be extended to investigate various diseases and stress factors (environmental and others) for enhanced understanding.…”

Section: Single-cell Transcriptomics In Insects: Applicationsmentioning

confidence: 99%

Insect Insights at the Single-Cell Level: Technologies and Applications

Sun,

Shao,

Iqbal

2023

Cells

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Single-cell techniques are a promising way to unravel the complexity and heterogeneity of transcripts at the cellular level and to reveal the composition of different cell types and functions in a tissue or organ. In recent years, advances in single-cell RNA sequencing (scRNA-seq) have further changed our view of biological systems. The application of scRNA-seq in insects enables the comprehensive characterization of both common and rare cell types and cell states, the discovery of new cell types, and revealing how cell types relate to each other. The recent application of scRNA-seq techniques to insect tissues has led to a number of exciting discoveries. Here we provide an overview of scRNA-seq and its application in insect research, focusing on biological applications, current challenges, and future opportunities to make new discoveries with scRNA-seq in insects.

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Primer selection impacts the evaluation of microecological patterns in environmental microbiomes

Cited by 7 publications

References 54 publications

Assemblages of rhizospheric and root endospheric mycobiota and their ecological associations with functional traits of rice

Assemblages of rhizospheric and root endospheric mycobiota and their ecological associations with functional traits of rice

Fitness effects of synthetic and natural diet preservatives on the edible insect Bombyx mori

Insect Insights at the Single-Cell Level: Technologies and Applications

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