Caenorhabditis nematodes influence microbiome and metabolome characteristics of their natural apple substrates over time

Authors: J. Johnke, J. Zimmermann, T. Stegemann, D. Langel, A. Franke, L. Thingholm, H. Schulenburg

Source: mSystems, Vol 10, Iss 2 (2025)

Subject Terms: microbiome assembly, microbiome functions, Caenorhabditis elegans, apple metabolome, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2379-5077

Access URL: https://doaj.org/article/09368eea9ac644608a980eb881e02dc0

Understanding the microbiome–crop rotation nexus in karst agricultural systems: insights from Southwestern China

Authors: Bin Wang, Nianjie Shang, Xinwei Feng, Zongling Hu, Pengfei Li, Yi Chen, Binbin Hu, Mengjiao Ding, Junju Xu

Source: Frontiers in Microbiology, Vol 16 (2025)

Subject Terms: crop rotation, soil microbial communities, karst agricultural system, soil physicochemical properties, microbiome assembly, Microbiology, QR1-502

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Relation: https://www.frontiersin.org/articles/10.3389/fmicb.2025.1503636/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/07bd338ba0dc466f8a36b4fb01f7e540

Small molecule metabolites drive plant rhizosphere microbial community assembly patterns

Authors: Yanwei Ma, Heqi Wang, Yalong Kang, Tao Wen

Source: Frontiers in Microbiology, Vol 16 (2025)

Subject Terms: microbiome assembly, microbial community, rhizosphere metabolites, neutral model, ecological process, Microbiology, QR1-502

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Relation: https://www.frontiersin.org/articles/10.3389/fmicb.2025.1503537/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/93816687e2a84776991c03aabd7caae1

Initial abiotic factors as key drivers in core microbe assembly: Regulatory effects on flavor profiles in light-flavor Baijiu

Authors: Xiaoning Huang, Jiamu Kang, Yuandi Zhang, Xiaoxue Chen, Beizhong Han

Source: Food Chemistry: X, Vol 25, Iss , Pp 101982- (2025)

Subject Terms: Baijiu, Fermented grains, Microbiome assembly, Ethyl lactate, Ethyl acetate, Flavor profile, Nutrition. Foods and food supply, TX341-641, Food processing and manufacture, TP368-456

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2590157524008708; https://doaj.org/toc/2590-1575

Access URL: https://doaj.org/article/e3bbab349da34e1d93d67a45be7a782e

Oak seedling microbiome assembly under climate warming and drought

Authors: Daniel Hoefle, Milena Sommer, Birgit Wassermann, Maria Faticov, Demetrio Serra, Gabriele Berg, Ayco J.M. Tack, Ahmed Abdelfattah

Source: Environmental Microbiome, Vol 19, Iss 1, Pp 1-12 (2024)

Subject Terms: Climate change, Microbiome assembly, Quercus robur L., Phyllosphere, Rhizosphere, Environmental sciences, GE1-350, Microbiology, QR1-502

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Relation: https://doaj.org/toc/2524-6372

Access URL: https://doaj.org/article/674786cf2c4d43bca337a01c461b0198

Genome-scale resources in the infant gut symbiont Bifidobacterium breve reveal genetic determinants of colonization and host-microbe interactions

Authors: Shiver, Anthony L. ¹, Sun, Jiawei ^{1, 21}, Culver, Rebecca ^{2, 21}, Violette, Arvie ^{1, 21}, Wynter, Char ^{1, 21}, Nieckarz, Marta ^{3, 21}, Mattiello, Samara Paula ^{4, 5}, Sekhon, Prabhjot Kaur ^{4, 6, 7}, Bottacini, Francesca ^{8, 9}, Friess, Lisa ^{8, 10}, Carlson, Hans K. ¹¹, Wong, Daniel P.G.H. ¹², Higginbottom, Steven ¹³, Weglarz, Meredith ¹⁴, Wang, Weigao ¹⁵, Knapp, Benjamin D. ¹⁶, Guiberson, Emma ^{13, 17}, Sanchez, Juan ¹⁸, Huang, Po-Hsun ¹⁹, Garcia, Paulo A. ¹⁹, Buie, Cullen R. ¹⁹, Good, Benjamin H. ^{12, 18}, DeFelice, Brian ¹⁸, Cava, Felipe ³, Scaria, Joy ^{4, 6}, Sonnenburg, Justin L. ¹³, Van Sinderen, Douwe ^{8, 10}, Deutschbauer, Adam M. ^{11, 20}, Huang, Kerwyn Casey ^{1, 13, 18, 22, ∗}

Source: In Cell February 2025

Characteristics of soil microbial community assembly patterns in fields with serious occurrence of tobacco Fusarium wilt disease

Authors: Huidi Liu, Yongfeng Zhang, Hongchen Li, Shilu Chen, Jingze Zhang, Wei Ding

Source: Frontiers in Microbiology, Vol 15 (2024)

Subject Terms: Fusarium wilt disease, microbiome, microbiome assembly, microbial network, microbial interaction, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmicb.2024.1482952/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/473d1e45d112440da79442e451ab4691

The beneficial endophytic microbes enhanced tobacco defense system to resist bacterial wilt disease

Authors: Jiemeng Tao, Mengli Gu, Shizhou Yu, Jingjing Shi, Lingtong Cheng, Jingjing Jin, Peng Lu, Jianfeng Zhang, He Li, Peijian Cao

Source: Chemical and Biological Technologies in Agriculture, Vol 11, Iss 1, Pp 1-15 (2024)

Subject Terms: Bacterial wilt disease, Endophytic microbiome, Microbiome assembly, Beneficial microbe, Plant defense system, Agriculture

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Relation: https://doaj.org/toc/2196-5641

Access URL: https://doaj.org/article/d67cbafeb64643ee833196548393a193

A Streptomyces Consortium Contributes Distinct Microbial Interactions During Arabidopsis thaliana Microbiome Assembly

Authors: Alexandra D. Gates, Austin M. French, Alexander A. Demetros, Brittni R. Kelley, Sarah L. Lebeis

Source: Phytobiomes Journal, Vol 7, Iss 4, Pp 515-525 (2023)

Subject Terms: microbial interactions, plant microbiome assembly, salicylic acid, Streptomyces, Plant culture, SB1-1110, Microbial ecology, QR100-130, Plant ecology, QK900-989

File Description: electronic resource

Relation: https://doaj.org/toc/2471-2906

Access URL: https://doaj.org/article/46b58807b11c44278e6c9db8b1d1310c

Altering plant carbon allocation to stems has distinct effects on rhizosphere soil microbiome assembly, interactions, and potential functions in sorghum

Authors: Niuniu Ji, Di Liang, Anthony J. Studer, Stephen P. Moose, Angela D. Kent

Source: GCB Bioenergy, Vol 16, Iss 6, Pp n/a-n/a (2024)

Subject Terms: bioenergy crop, carbon allocation, microbial function, microbial interaction, microbiome assembly, Renewable energy sources, TJ807-830, Energy industries. Energy policy. Fuel trade, HD9502-9502.5

File Description: electronic resource

Relation: https://doaj.org/toc/1757-1693; https://doaj.org/toc/1757-1707

Access URL: https://doaj.org/article/4718e702a6bb4b2ea39b605ece5f1f02

Alternative Splicing

Contributors: Gao, Bei, Chen, Moxian, Oliver, Melvin J.

Subject Terms: rice, grain size, QTL, BSA-seq, splicing, additive effects, alternative splicing, GWAS, proteogenomics, Zea mays L., plant genotype, plant–microbe interaction, microbiome assembly, post-transcriptional regulation, alkaloids, ascorbate, phytohormones, lipids, metabolism, phenylpropanoids, plants, starch, terpenoids, FtHDACs, genome-wide, low-temperature responses, Tartary buckwheat, microRNA, moderate soil drying, inferior spikelets, MACP2, membrane attack complex/perforin-like protein, pathogen infection, salicylic acid signaling, indole glucosinolates, PpRNH1A, heat stress (HS), lipid droplets, Physcomitrium (Physcomitrella) patens, Brassica napus, transcription factors, nutrient stress, transcriptomic analysis, miRNA, galanthamine, Lycoris, SWATH-MS, Research and information: general, Biology, life sciences

File Description: image/jpeg

Access URL: https://directory.doabooks.org/handle/20.500.12854/100792
https://mdpi.com/books/pdfview/book/7254

Host genetic variation drives the differentiation in the ecological role of the native Miscanthus root-associated microbiome

Authors: Niuniu Ji, Di Liang, Lindsay V. Clark, Erik J. Sacks, Angela D. Kent

Source: Microbiome, Vol 11, Iss 1, Pp 1-13 (2023)

Subject Terms: Perennial plant microbiomes, Rhizosphere soil, Microbiome assembly, Microbial co-occurrence networks, Core microbiome, Host genetic variation, Microbial ecology, QR100-130

File Description: electronic resource

Relation: https://doaj.org/toc/2049-2618

Access URL: https://doaj.org/article/d0631d4a2a38467f95c741832f293831

Microbiome assembly mechanism and functional potential in enhanced biological phosphorus removal system enriched with Tetrasphaera-related polyphosphate accumulating organisms

Authors: Wang, Hui ^{a, b, c}, Lin, Limin ^{b, c}, Zhang, Lu ^{b, c}, Han, Ping ^e, Ju, Feng ^{b, c, d, f, ∗}

Source: In Environmental Research 15 September 2023 233

Continental scale deciphering of microbiome networks untangles the phyllosphere homeostasis in tea plant

Authors: Ping Xu, Erinne Stirling, Hengtong Xie, Wenbing Li, Xiaofei Lv, Haruna Matsumoto, Haiyan Cheng, Anan Xu, Wanyi Lai, Yuefei Wang, Zuntao Zheng, Mengcen Wang, Xingmei Liu, Bin Ma, Jianming Xu

Source: Journal of Advanced Research, Vol 44, Iss , Pp 13-22 (2023)

Subject Terms: Microbiome assembly, Co-occurrence, Trade-off, Tea plant, Phyllosphere, Homeostasis, Medicine (General), R5-920, Science (General), Q1-390

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Relation: http://www.sciencedirect.com/science/article/pii/S2090123222000832; https://doaj.org/toc/2090-1232

Access URL: https://doaj.org/article/3f79c4019bdf4d6d9b8a3d2090e63d31

Rice bacterial leaf blight drives rhizosphere microbial assembly and function adaptation

Authors: Hubiao Jiang, Jinyan Luo, Quanhong Liu, Solabomi Olaitan Ogunyemi, Temoor Ahmed, Bing Li, Shanhong Yu, Xiao Wang, Chenqi Yan, Jianping Chen, Bin Li

Source: Microbiology Spectrum, Vol 11, Iss 6 (2023)

Subject Terms: rice bacterial leaf blight, rhizosphere microbiome, microbiome assembly, metagenomics, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2165-0497

Access URL: https://doaj.org/article/449e60265b08408aa5eda2b6a30900ec

Exogenous antibiotic resistance gene contributes to intestinal inflammation by modulating the gut microbiome and inflammatory cytokine responses in mouse

Authors: Rong Tan, Min Jin, Zhengshan Chen, Yifan Shao, Yuanyuan Song, Jing Yin, Lifang Wang, Tianjiao Chen, Junwen Li, Dong Yang

Source: Gut Microbes, Vol 15, Iss 1 (2023)

Subject Terms: eARGs, gut microbiome assembly, inflammatory cytokine response, metabolic profiles, intestinal inflammation, Diseases of the digestive system. Gastroenterology, RC799-869

File Description: electronic resource

Relation: https://doaj.org/toc/1949-0976; https://doaj.org/toc/1949-0984

Access URL: https://doaj.org/article/5ae5623e0de3415dbc37239d006d7bba

Temporal metabolite responsiveness of microbiota in the tea plant phyllosphere promotes continuous suppression of fungal pathogens

Authors: Ping Xu, Xiaoyan Fan, Yuxiao Mao, Haiyan Cheng, Anan Xu, Wanyi Lai, Tianxing Lv, Yang Hu, Yanxia Nie, Xuxia Zheng, Qing Meng, Yuefei Wang, Tomislav Cernava, Mengcen Wang

Source: Journal of Advanced Research, Vol 39, Iss , Pp 49-60 (2022)

Subject Terms: Phyllosphere microbiota, Microbiome assembly, Co-adaption, Plant metabolites, Disease suppression, Medicine (General), R5-920, Science (General), Q1-390

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Relation: http://www.sciencedirect.com/science/article/pii/S2090123221001995; https://doaj.org/toc/2090-1232

Access URL: https://doaj.org/article/12c85124391f41ec8dae518d90335613

Insights into the microbiome assembly during different growth stages and storage of strawberry plants

Authors: Expedito Olimi, Peter Kusstatscher, Wisnu Adi Wicaksono, Ahmed Abdelfattah, Tomislav Cernava, Gabriele Berg

Source: Environmental Microbiome, Vol 17, Iss 1, Pp 1-15 (2022)

Subject Terms: Fragaria × ananassa, Microbiome assembly, Fruit pathogens, Bacterial communities, Fungal communities, Amplicon sequencing, Environmental sciences, GE1-350, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2524-6372

Access URL: https://doaj.org/article/68ecd8f2c2c246a7aea992a33a41043b

Aedes albopictus microbiome derives from environmental sources and partitions across distinct host tissues

Authors: Priscilla S. Seabourn, Danya E. Weber, Helen Spafford, Matthew C. I. Medeiros

Source: MicrobiologyOpen, Vol 12, Iss 3, Pp n/a-n/a (2023)

Subject Terms: Aedes albopictus, environment, microbiome assembly, tissue microbiome, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2045-8827

Access URL: https://doaj.org/article/e4f07b6404e648bebb9c493e8d8e4a02

Ecological niche selection shapes the assembly and diversity of microbial communities in Casuarina equisetifolia L.

Authors: Qi Lin, Ying Wang, Miaomiao Li, Zhixia Xu, Lei Li

Source: Frontiers in Plant Science, Vol 13 (2022)

Subject Terms: Casuarina equisetifolia, microbiome assembly, compartment niche, plant-associated microorganism, Hainan province, soil–plant continuum, Plant culture, SB1-1110

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fpls.2022.988485/full; https://doaj.org/toc/1664-462X

Access URL: https://doaj.org/article/ca7fe4590b67413a83645b759586db74