Some papers using SqueezeMeta (non comprehensive list)

You can find a list of papers citing SqueezeMeta in PubMed

• Uritskiy G, DiRuggiero J. Applying Genome-Resolved Metagenomics to Deconvolute the Halophilic Microbiome. Genes (Basel). 2019 Mar 14;10(3):220. doi: 10.3390/genes10030220. PMID: 30875864; PMCID: PMC6471235.
• Garcia-Grau I, Perez-Villaroya D, Bau D, Gonzalez-Monfort M, Vilella F, Moreno I, Simon C. Taxonomical and Functional Assessment of the Endometrial Microbiota in A Context of Recurrent Reproductive Failure: A Case Report. Pathogens. 2019 Oct 24;8(4):205. doi: 10.3390/pathogens8040205. PMID: 31653041; PMCID: PMC6963572.
• Donovan M, Lynch MDJ, Mackey CS, Platt GN, Washburn BK, Vera DL, Trickey DJ, Charles TC, Wang Z, Jones KM. Metagenome-Assembled Genome Sequences of Five Strains from the Microtus ochrogaster (Prairie Vole) Fecal Microbiome. Microbiol Resour Announc. 2020 Jan 9;9(2):e01310-19. doi: 10.1128/MRA.01310-19. PMID: 31919172; PMCID: PMC6952658.
• Mukherjee A, Reddy MS. Metatranscriptomics: an approach for retrieving novel eukaryotic genes from polluted and related environments. 3 Biotech. 2020 Feb;10(2):71. doi: 10.1007/s13205-020-2057-1. Epub 2020 Jan 27. PMID: 32030340; PMCID: PMC6985312.
• Macedo, Thais & Dornelles, Henrique & Marques, Ana & Delforno, Tiago & Centurion, V.B. & Oliveira, Valéria & Silva, Edson & Varesche, Maria. (2020). The influence of upflow velocity and hydraulic retention time changes on taxonomic and functional characterization in Fluidized Bed Reactor treating commercial laundry wastewater in co-digestion with domestic sewage. Biodegradation. 31. doi: 10.1007/s10532-020-09895-x.
• Lira F, Vaz-Moreira I, Tamames J, Manaia CM, Martínez JL. Metagenomic analysis of an urban resistome before and after wastewater treatment. Sci Rep. 2020 May 18;10(1):8174. doi: 10.1038/s41598-020-65031-y. PMID: 32424207; PMCID: PMC7235214.
• Costa OYA, de Hollander M, Pijl A, Liu B, Kuramae EE. Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer. Microbiome. 2020 Jun 1;8(1):76. doi: 10.1186/s40168-020-00836-7. PMID: 32482164; PMCID: PMC7265232.
• Vuillemin A, Vargas S, Coskun ÖK, Pockalny R, Murray RW, Smith DC, D'Hondt S, Orsi WD. Atribacteria Reproducing over Millions of Years in the Atlantic Abyssal Subseafloor. mBio. 2020 Oct 6;11(5):e01937-20. doi: 10.1128/mBio.01937-20. PMID: 33024037; PMCID: PMC7542362.
• Hidalgo, Kelly & Teramoto, Elias & Soriano, Adriana & Valoni, E. & Baessa, Marcus & Richnow, Hans & Vogt, Carsten & Chang, Hung & Oliveira, Valéria. (2020). Taxonomic and functional diversity of the microbiome in a jet fuel contaminated site as revealed by combined application of in situ microcosms with metagenomic analysis. Science of The Total Environment 135-152. doi: 10.1016/j.scitotenv.2019.135152.
• Delforno, Tiago & Belgini, Daiane & Hidalgo, Kelly & Centurion, V.B. & Lacerda Júnior, Gileno & Duarte, Iolanda & Varesche, Maria & Oliveira, V. (2020). Anaerobic reactor applied to laundry wastewater treatment: Unveiling the microbial community by gene and genome-centric approaches. International Biodeterioration & Biodegradation. doi: 10.1016/j.ibiod.2020.104916
• Santillan E, Phua WX, Constancias F, Wuertz S. Sustained organic loading disturbance favors nitrite accumulation in bioreactors with variable resistance, recovery and resilience of nitrification and nitrifiers. Sci Rep. 2020 Dec 7;10(1):21388. doi: 10.1038/s41598-020-78314-1. PMID: 33288775; PMCID: PMC7721871.
• Yulandi A, Suwanto A, Waturangi DE, Wahyudi AT. Shotgun metagenomic analysis reveals new insights into bacterial community profiles in tempeh. BMC Res Notes. 2020 Dec 11;13(1):562. doi: 10.1186/s13104-020-05406-6. PMID: 33308279; PMCID: PMC7731626.
• Xia X, Lee P, Cheung S, Lu Y, Liu H. Discovery of Euryhaline Phycoerythrobilin-Containing Synechococcus and Its Mechanisms for Adaptation to Estuarine Environments. mSystems. 2020 Dec 15;5(6):e00842-20. doi: 10.1128/mSystems.00842-20. PMID: 33323414; PMCID: PMC7771541.
• Centurion, V.B. & Lacerda Júnior, Gileno & Duarte, Alysson & Silva, T & Silva, Leonardo & Rosa, L & Oliveira, V. (2021). Dynamics of microbial stress responses driven by abiotic changes along a temporal gradient in Deception Island, Maritime Antarctica. Science of The Total Environment. 758. doi: 10.1016/j.scitotenv.2020.143671.
• de Abreu VAC, Perdigão J, Almeida S. Metagenomic Approaches to Analyze Antimicrobial Resistance: An Overview. Front Genet. 2021 Jan 18;11:575592. doi: 10.3389/fgene.2020.575592. PMID: 33537056; PMCID: PMC7848172.
• Wang M., Garrido-Sanz D., Sansegundo-Lobato P., Redondo-Nieto M., Conlon R., Martin M., Mali R., Liu X., Dowling D. N., Rivilla R., Germaine K. J. (2021). Soil Microbiome Structure and Function in Ecopiles Used to Remediate Petroleum-Contaminated Soil. Front Environ Science 9, 39. doi: 10.3389/fenvs.2021.624070
• Raes, E.J., Karsh, K., Sow, S.L.S. et al. Metabolic pathways inferred from a bacterial marker gene illuminate ecological changes across South Pacific frontal boundaries. Nat Commun 12, 2213 (2021). doi: [10.1038/s41467-021-22409-4] (https://doi.org/10.1038/s41467-021-22409-4)
• Saborío-Montero A, López-García A, Gutiérrez-Rivas M, Atxaerandio R, Goiri I, García-Rodriguez A, Jiménez-Montero JA, González C, Tamames J, Puente-Sánchez F, Varona L, Serrano M, Ovilo C, González-Recio O. A dimensional reduction approach to modulate the core ruminal microbiome associated with methane emissions via selective breeding. J Dairy Sci. 2021 Apr 22:S0022-0302(21)00550-6. doi: [10.3168/jds.2020-20005] (https://doi.org/10.3168/jds.2020-20005)
• Moya-Beltrán, Ana & Beard, Simón & Rojas-Villalobos, Camila & Issotta, Francisco & Gallardo, Yasna & Ulloa, José & Giaveno, Alejandra & Esposti, Mauro & Johnson, David & Quatrini, Raquel. (2021). Genomic evolution of the class Acidithiobacillia: deep-branching Proteobacteria living in extreme acidic conditions. The ISME Journal. 1-18. doi: [10.1038/s41396-021-00995-x] (https://doi.org/10.1038/s41396-021-00995-x)
• Du, Jingjie & Zayed, Ahmed & Kigerl, Kristina & Zane, Kylie & Sullivan, Matthew & Popovich, Phillip. (2021). Spinal Cord Injury Changes the Structure and Functional Potential of Gut Bacterial and Viral Communities. mSystems. 6. doi: [10.1128/mSystems.01356-20] (https://doi.org/10.1128/mSystems.01356-20)
• Hinsu, Ankit & Nilam, Tulsani & Panchal, Ketankumar & Ramesh, Pandit & Jyotsana, Basanti & Dafale, Nishant & Patil, Niteen & Purohit, Hemant & Joshi, Chaitanya & Jakhesara, Subhash. (2021). Characterizing rumen microbiota and CAZyme profile of Indian dromedary camel (Camelus dromedarius) in response to different roughages. Scientific Reports. 11. doi: [10.1038/s41598-021-88943-9] (https://doi.org/10.1038/s41598-021-88943-9)
• Kakuk B, Wirth R, Maróti G, Szuhaj M, Rakhely G, Laczi K, Kovács KL, Bagi Z. Early response of methanogenic archaea to H2 as evaluated by metagenomics and metatranscriptomics. Microb Cell Fact. 2021 Jul 3;20(1):127. doi: [10.1186/s12934-021-01618-y] (https://doi.org/10.1186/s12934-021-01618-y)
• Gil-Gil T, Ochoa-Sánchez LE, Baquero F, Martínez JL. Antibiotic resistance: Time of synthesis in a post-genomic age. Comput Struct Biotechnol J. 2021 May 21;19:3110-3124. doi: [10.1016/j.csbj.2021.05.034] (https://doi.org/10.1016/j.csbj.2021.05.034)