Metatranscriptomic profiling reveals pathogen and host response signatures of pediatric acute sinusitis and upper respiratory infection

Authors: Andrew C. Doxey, Nooran Abu Mazen, Max Homm, Vivian Chu, Manjot Hunjan, Briallen Lobb, Sojin Lee, Marcia Kurs-Lasky, John V. Williams, William MacDonald, Monika Johnson, Jeremy A. Hirota, Nader Shaikh

Source: Genome Medicine, Vol 17, Iss 1, Pp 1-22 (2025)

Subject Terms: Acute sinusitis, Host response, Upper respiratory infections, Pediatrics, Metatranscriptomics, RNA-seq, Medicine, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1756-994X

Access URL: https://doaj.org/article/dbda58e75ab845e8b0a9a4d177ee6a28

Increased methane production associated with community shifts towards Methanocella in paddy soils with the presence of nanoplastics

Authors: Zhibin He, Yarong Hou, Ying Li, Qicheng Bei, Xin Li, Yong-Guan Zhu, Werner Liesack, Matthias C. Rillig, Jingjing Peng

Source: Microbiome, Vol 12, Iss 1, Pp 1-15 (2024)

Subject Terms: Plastics, Carbon flow, Methane, Fatty acids, FT-ICR-MS, MAGs, Metatranscriptomics, Microbial ecology, QR100-130

File Description: electronic resource

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

Access URL: https://doaj.org/article/d2d7a3a650bd44568c60dae57d6aedbb

Microbial functional pathways based on metatranscriptomic profiling enable effective saliva-based health assessments for precision wellness

Authors: Eric Patridge, Anmol Gorakshakar, Matthew M. Molusky, Oyetunji Ogundijo, Angel Janevski, Cristina Julian, Lan Hu, Momchilo Vuyisich, Guruduth Banavar

Source: Computational and Structural Biotechnology Journal, Vol 23, Iss , Pp 834-842 (2024)

Subject Terms: Saliva, Metatranscriptomics, Oral microbiome, Functional pathways, Oropharyngeal disease, Precision wellness, Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2001037024000199; https://doaj.org/toc/2001-0370

Access URL: https://doaj.org/article/fe01fe84d48e4c86815a9b6c99c9e33d

Fatal tick-borne encephalitis virus infection in Dalmatian puppy-dogs after putative vector independent transmission

Authors: Kara L. D. Dawson, Giuliana Rosato, Simone Egloff, Carole Burgener, Anna Oevermann, Paula Grest, Monika Hilbe, Torsten Seuberlich

Source: Veterinary Quarterly, Vol 44, Iss 1, Pp 1-7 (2024)

Subject Terms: Tick-borne encephalitis virus, puppies, metatranscriptomics, high-throughput sequencing, Veterinary medicine, SF600-1100

File Description: electronic resource

Relation: https://doaj.org/toc/0165-2176; https://doaj.org/toc/1875-5941

Access URL: https://doaj.org/article/ee64f0ed643c45a094d6914aaf5841c1

Multi-Omics Analysis of Mouse Fecal Microbiome Reveals Supplier-Dependent Functional Differences and Novel Metagenome-Assembled Genomes

Authors: Zachary L. McAdams, Susheel Bhanu Busi, Kevin L. Gustafson, Nathan Bivens, Craig L. Franklin, Paul Wilmes, Aaron C. Ericsson

Source: Applied Microbiology, Vol 4, Iss 4, Pp 1600-1615 (2024)

Subject Terms: gut microbiome, metagenomics, metatranscriptomics, The Jackson Laboratory, Inotiv, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.mdpi.com/2673-8007/4/4/109; https://doaj.org/toc/2673-8007

Access URL: https://doaj.org/article/8871f314fc894561bd456a337ebdd18d

Lineage-dependent partitioning of activities in chemoclines defines Woesearchaeota ecotypes in an extreme aquatic ecosystem

Authors: Lilian A. Cloarec, Thomas Bacchetta, Maxime Bruto, Christophe Leboulanger, Vincent Grossi, Céline Brochier-Armanet, Jean-Pierre Flandrois, Adrian Zurmely, Cécile Bernard, Marc Troussellier, Hélène Agogué, Magali Ader, Christine Oger-Desfeux, Philippe M. Oger, Adrien Vigneron, Mylène Hugoni

Source: Microbiome, Vol 12, Iss 1, Pp 1-16 (2024)

Subject Terms: Archaeal genomic diversity, Woesearchaeales, Ecotypes, Metagenomics, Metatranscriptomics, Extreme lake, Microbial ecology, QR100-130

File Description: electronic resource

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

Access URL: https://doaj.org/article/ea3170c80ca34f419a4216242c093204

Environmental matrix and moisture influence soil microbial phenotypes in a simplified porous media incubation

Authors: Josué Rodríguez-Ramos, Natalie Sadler, Elias K. Zegeye, Yuliya Farris, Samuel Purvine, Sneha Couvillion, William C. Nelson, Kirsten S. Hofmockel

Source: mSystems, Vol 10, Iss 3 (2025)

Subject Terms: model soil microbial community, metagenomics, metaproteomics, metatranscriptomics, carbon use efficiency, chitin metabolism, Microbiology, QR1-502

File Description: electronic resource

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

Access URL: https://doaj.org/article/2369538e6fdc4440848579b285360d05

Transcriptional and microbial profile of gastric cancer patients infected with Epstein-Barr virus

Authors: Klezzer de Oliveira Carneiro, Taíssa Maíra Thomaz Araújo, Ronald Matheus Da Silva Mourão, Samir Mansour Moraes Casseb, Samia Demachki, Fabiano Cordeiro Moreira, Ândrea Kely Campos Ribeiro Dos Santos, Geraldo Ishak, Daniel de Souza Avelar Da Costa, Leandro Magalhães, Amanda Ferreira Vidal, Rommel Mario Rodriguez Burbano, Paulo Pimentel de Assumpção

Source: Frontiers in Oncology, Vol 15 (2025)

Subject Terms: gastric cancer, EBV, metatranscriptomics, gastric microbiome, carcinogenesis, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fonc.2025.1530430/full; https://doaj.org/toc/2234-943X

Access URL: https://doaj.org/article/aa36a2b77f154d13b82c3c35885137ec

Editorial: New techniques in microbiome research - volume II: Host-microbiome interactions using ‘meta-omics’ techniques

Authors: Tao Lin

Source: Frontiers in Cellular and Infection Microbiology, Vol 15 (2025)

Subject Terms: microbiome, human health and diseases, new techniques, META-OMICS, metagenomics, metatranscriptomics, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fcimb.2025.1541881/full; https://doaj.org/toc/2235-2988

Access URL: https://doaj.org/article/0eb494ac24f54f2b81e576155b604f71

Identification of novel fructo-oligosaccharide bacterial consumers by pulse metatranscriptomics in a human stool sample

Authors: Catherine Prattico, Emmanuel Gonzalez, Lharbi Dridi, Shiva Jazestani, Kristin E. Low, D. Wade Abbott, Corinne F. Maurice, Bastien Castagner

Source: mSphere, Vol 10, Iss 1 (2025)

Subject Terms: gut microbiome, prebiotics, metatranscriptomics, FOS, galactomannan, CAZymes, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2379-5042

Access URL: https://doaj.org/article/4fb97ba82971402792f1ab440aa53f31

Cover crop root exudates impact soil microbiome functional trajectories in agricultural soils

Authors: Valerie A. Seitz, Bridget B. McGivern, Mikayla A. Borton, Jacqueline M. Chaparro, Meagan E. Schipanski, Jessica E. Prenni, Kelly C. Wrighton

Source: Microbiome, Vol 12, Iss 1, Pp 1-22 (2024)

Subject Terms: Phytohormone, Plant growth promoting, Metagenome-assembled genome (MAG), Liquid chromatography-mass spectrometry (LC–MS), Metatranscriptomics, Sorghum bicolor, Microbial ecology, QR100-130

File Description: electronic resource

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

Access URL: https://doaj.org/article/e5ed763d98ae45a2bf35fc2147441e33

Metagenomic analyses of a consortium for the bioremediation of hydrocarbons polluted soils

Authors: Emiliana Pandolfo, David Durán-Wendt, Ruben Martínez-Cuesta, Mónica Montoya, Laura Carrera-Ruiz, David Vazquez-Arias, Esther Blanco-Romero, Daniel Garrido-Sanz, Miguel Redondo-Nieto, Marta Martin, Rafael Rivilla

Source: AMB Express, Vol 14, Iss 1, Pp 1-16 (2024)

Subject Terms: Bacterial consortium, Bioremediation, Total petroleum hydrocarbons, Metagenomics, Metatranscriptomics, Biotechnology, TP248.13-248.65, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2191-0855

Access URL: https://doaj.org/article/fccefe95e2d44718907b756e786e2e89

Microbial inoculum effects on the rumen epithelial transcriptome and rumen epimural metatranscriptome in calves

Authors: P. Fregulia, T. Park, W. Li, L. M. Cersosimo, G. I. Zanton

Source: Scientific Reports, Vol 14, Iss 1, Pp 1-14 (2024)

Subject Terms: Early inoculation, Metatranscriptomics, Transcriptomics, Dairy calves, Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/5766ba25257b4dc993c27212554885ed

Mg²⁺ and magnesium ammonium phosphate (MAP)-induced anammox granulation for comparable nitrogen removal: Implementation pathways and microbial mechanisms

Authors: Shi, Huiqun ^{a, b, 1}, Ren, Xiaoyi ^{a, c, 1}, Yang, Ruili ^d, Wang, Jinsong ^e, Xu, Huaihao ^{a, c}, Liao, Xinqing ^{a, c}, Lou, Yaoyin ^a, Chen, Shaohua ^a, Ye, Xin ^{a, ⁎}, Wang, Xiaojun ^{a, ⁎}

Source: In Water Research 15 March 2025 272

Distance to the water table shapes the diversity and activity of DNA and RNA viruses in a subalpine peatland

Authors: Xiong, Ziye ^a, Qiu, Xuan ^{a, ⁎}, Xiang, Xing ^b, Cai, Lanlan ^c, Wang, Nian ^d, Huang, Xianyu ^a, Wang, Hongmei ^a

Source: In Environment International March 2025 197

Metatranscriptomics reveals gene expression dynamics during an anatoxin-a producing Dolichospermum bloom in a western coastal lake

Authors: Linz, David M. ^a, Struewing, Ian ^a, Sienkiewicz, Nathan ^a, Labiosa, Rochelle ^b, Lu, Jingrang ^{a, ⁎}

Source: In Chemosphere March 2025 372

Complexity of the lichen symbiosis revealed by metagenome and transcriptome analysis of Xanthoria parietina

Authors: Tagirdzhanova, Gulnara ^{1, 8}, Scharnagl, Klara ^{1, 2}, Sahu, Neha ¹, Yan, Xia ¹, Bucknell, Angus ¹, Bentham, Adam R. ^{1, 7}, Jégousse, Clara ¹, Ament-Velásquez, Sandra Lorena ³, Onuț-Brännström, Ioana ⁴, Johannesson, Hanna ^{5, 6}, MacLean, Dan ¹, Talbot, Nicholas J. ^{1, 9, 10, ∗}

Source: In Current Biology 24 February 2025 35(4):799-817

Integrated metagenomics and metatranscriptomics analyses reveal the impacts of different Lactiplantibacillus plantarum strains on microbial communities and metabolic profiles in pickled bamboo shoots

Authors: Wu, Yuhui ^{a, b}, You, Yuming ^c, Wu, Liangru ^d, Du, Muying ^a, Ibrahim, Amel ^e, Suo, Huayi ^a, Zhang, Fusheng ^a, Zheng, Jiong ^{a, d, ⁎}

Source: In Food Chemistry 1 February 2025 464 Part 2

Microbial community and functional shifts across agricultural and urban landscapes within a Lake Erie watershed

Authors: Chen, Yu-Ting ^{a, b}, Reid, Tom ^c, Weisener, Christopher ^{a, ⁎}

Source: In Journal of Environmental Management January 2025 373

pH-dependent medium-chain fatty acid synthesis in waste activated sludge fermentation: Metabolic pathway regulation

Authors: Wang, Yun ^{a, 1}, Wu, Shu-Lin ^{b, 1}, Wei, Wei ^c, Wu, Lan ^c, Huang, Sansi ^c, Dai, Xiaohu ^{a, ⁎⁎}, Ni, Bing-Jie ^{d, ⁎}

Source: In Journal of Environmental Management January 2025 373