Works about METAGENOMICS

Results: 5000

Do Malassezia yeasts colonize the guts of people living with HIV?

Published in:

PLoS ONE, 2025, v. 20, n. 5, p. 1, doi. 10.1371/journal.pone.0322982

By:

Abdillah, Abdourahim;
Ravaux, Isabelle;
Mokhtari, Saadia;
Ranque, Stéphane

Publication type:

Article

Recent Advances in Adaptation Genomics in Fumarole Fields: An Overlooked Extreme Environment.

Published in:

Plant & Cell Physiology, 2025, v. 66, n. 4, p. 496, doi. 10.1093/pcp/pcae122

By:

Nagasawa, Koki;
Setoguchi, Hiroaki;
Sakaguchi, Shota

Publication type:

Article

Distinct microbial communities drive methane cycling in below- and above-ground compartments of tropical cloud forests growing on peat.

Published in:

Environmental Microbiome, 2025, v. 20, n. 1, p. 1, doi. 10.1186/s40793-025-00718-1

By:

Kazmi, Fahad Ali;
Mander, Ülo;
Khanongnuch, Ramita;
Öpik, Maarja;
Ranniku, Reti;
Soosaar, Kaido;
Masta, Mohit;
Tenhovirta, Salla A. M.;
Kasak, Kuno;
Ah-Peng, Claudine;
Espenberg, Mikk

Publication type:

Article

A pan-crop metagenomic exploration of microbial communities linked to pesticide and xenobiotic degradation pathways in agricultural microbiomes.

Published in:

Discover Agriculture, 2025, v. 3, n. 1, p. 1, doi. 10.1007/s44279-025-00237-0

By:

Prabha, Ratna;
Samota, Mahesh K.;
Verma, M. K.;
Gupta, Shailendra;
Rai, Anil;
Dubey, S. C.;
Singh, D. P.

Publication type:

Article

HPD-Kit: a comprehensive toolkit for pathogen detection and analysis.

Published in:

Frontiers in Cellular & Infection Microbiology, 2025, p. 1, doi. 10.3389/fcimb.2025.1580165

By:

Que, Tengcheng;
Li, Wen;
Zhang, Zhining;
He, Yunlin;
He, Kangming;
Qiu, Hong;
Huang, Juan;
Lu, Zhiwei;
Jiang, Chunlan;
Huang, Yongjian;
Huang, Hui;
Wu, Qiuyu;
Chen, Panyu;
Hu, Yanling;
Liu, Wenjian

Publication type:

Article

Estimating similarity and distance using FracMinHash.

Published in:

Algorithms for Molecular Biology, 2025, v. 20, n. 1, p. 1, doi. 10.1186/s13015-025-00276-8

By:

Rahman Hera, Mahmudur;
Koslicki, David

Publication type:

Article

CoverM: read alignment statistics for metagenomics Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf147

By:

Aroney, Samuel T N;
Newell, Rhys J P;
Nissen, Jakob N;
Camargo, Antonio Pedro;
Tyson, Gene W;
Woodcroft, Ben J

Publication type:

Article

A NOVL DETECTION OF BACTERIAL COMMUNITY IN VAGINA BY METAGENOMIC AND MOLECULAR DETECTION OF A NEW LOCAL STRAIN OF MYCOPLASMA GENITALIUM.

Published in:

Obstetrics & Gynaecology Forum, 2024, v. 34, n. 3, p. 1781

By:

Mahmood, Sarah Badri;
Alrawi, Amera Mahmood

Publication type:

Article

Beneficial soil microbiome profiles assembled using tetramycin to alleviate root rot disease in Panax notoginseng.

Published in:

Frontiers in Microbiology, 2025, p. 1, doi. 10.3389/fmicb.2025.1571684

By:

Liu, Lianjin;
Wang, Zongqing;
Luo, Cheng;
Deng, Yinglong;
Wu, Wentao;
Jin, Yongping;
Wang, Yuxuan;
Huang, Hongping;
Wei, Zhaoxia;
Zhu, Youyong;
He, Xiahong;
Guo, Liwei

Publication type:

Article

Metagenomic Next-Generation Sequencing Improves the Diagnosis Efficiency of Mixed Periprosthetic Joint Infections.

Published in:

Infection & Drug Resistance, 2025, v. 18, p. 2165, doi. 10.2147/IDR.S516650

By:

Zhou, Zibo;
Song, Yanhua;
Yan, Yafang;
Zheng, Yan

Publication type:

Article

DNA extraction protocols for animal fecal material on blood spot cards.

Published in:

PLoS ONE, 2025, v. 20, n. 5, p. 1, doi. 10.1371/journal.pone.0313808

By:

Llarena, Ann-Katrin;
Haverkamp, Thomas H. A.;
Gulliksen, Wenche Støldal;
Herstad, Kristin;
Holst-Jensen, Arne;
Skjerve, Eystein;
Rannem, Lisbeth;
Rodriguez-Campos, Sabrina;
Øines, Øivind

Publication type:

Article

Beyond clinical genomics: addressing critical gaps in One Health AMR surveillance.

Published in:

Frontiers in Microbiology, 2025, p. 1, doi. 10.3389/fmicb.2025.1596720

By:

Vallejo-Espín, Diana;
Galarza-Mayorga, Jael;
Lalaleo, Liliana;
Calero-Cáceres, William

Publication type:

Article

Asparagopsis taxiformis mitigates ruminant methane emissions via microbial modulation and inhibition of methyl-coenzyme M reductase.

Published in:

Frontiers in Microbiology, 2025, p. 1, doi. 10.3389/fmicb.2025.1586456

By:

Li, Shuai;
Sun, Yi;
Cao, Siguang;
Guo, Tongjun;
Tong, Xiong;
Zhang, Zhifei;
Sun, Jiajie;
Yang, Yufeng;
Wang, Qing;
Li, Dagang;
Min, Li

Publication type:

Article

Letter to Editor: Addressing Methodological and Interpretative Gaps in the Study on Bowel Preparation and Gut Microbiotad.

Published in:

Journal of Gastroenterology & Hepatology, 2025, v. 40, n. 5, p. 1330, doi. 10.1111/jgh.16957

By:

Sathian, Brijesh;
Al Hamad, Hanadi;
Iqbal, Javed

Publication type:

Article

The gut microbiome is associated with disease‐free survival in stage I–III colorectal cancer patients.

Published in:

International Journal of Cancer, 2025, v. 157, n. 1, p. 64, doi. 10.1002/ijc.35342

By:

Byrd, Doratha A.;
Damerell, Victoria;
Gomez Morales, Maria F.;
Hogue, Stephanie R.;
Lin, Tengda;
Ose, Jennifer;
Himbert, Caroline;
Ilozumba, Mmadili N.;
Kahlert, Christoph;
Shibata, David;
Toriola, Adetunji T.;
Li, Christopher I.;
Figueiredo, Jane;
Stephens, W. Zac;
Warby, Christy A.;
Hardikar, Sheetal;
Siegel, Erin M.;
Round, June;
Ulrich, Cornelia M.;
Gigic, Biljana

Publication type:

Article

Whole genome comparisons reveal gut-to-lung translocation of Escherichia coli and Burkholderia cenocepacia in two cases of ventilator-associated pneumonia in ICU patients.

Published in:

Respiratory Research, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12931-025-03204-x

By:

Gao, Huihui;
Xu, Lei;
Liu, Yixin;
Wang, Xiaolong;
Zhu, Siyuan;
Lin, Huai;
Gao, Yuting;
Mao, Daqing;
Lu, Xing;
Luo, Yi

Publication type:

Article

Metagenomic analysis of NIPT raw data suggests high negative predictive value for congenital cytomegalovirus infection screening.

Published in:

Ultrasound in Obstetrics & Gynecology, 2025, v. 65, n. 5, p. 653, doi. 10.1002/uog.29221

By:

Bourgon, N.;
Padioleau, I.;
Guibon, J.;
Fourgeaud, J.;
Lermine, A.;
Meurice, G.;
Guilleminot, T.;
Bussieres, L.;
Leruez‐Ville, M.;
Dupont, J.‐M.;
Ville, Y.

Publication type:

Article

白酒酿造功能微生物的多样性及其应用研究进展.

Published in:

China Brewing, 2025, v. 44, n. 4, p. 7, doi. 10.11882/j.issn.0254-5071.2025.04.002

By:

夏序春;
班世栋;
罗小叶;
王晓丹

Publication type:

Article

Contribution of shotgun metagenomics in the diagnosis of a subcutaneous phaeohyphomycosis caused by Parathyridaria percutanea.

Published in:

British Journal of Dermatology, 2025, v. 192, n. 5, p. 948, doi. 10.1093/bjd/ljaf018

By:

Monpierre, Lorra;
Angebault, Cécile;
Hua, Camille;
Merio, Léa;
Ortonne, Nicolas;
Lafont, Emmanuel;
Foulet, Françoise;
Botterel, Françoise

Publication type:

Article

Distribution status and influencing factors of antibiotic resistance genes in the Chaohu Lake, China.

Published in:

PeerJ, 2025, p. 1, doi. 10.7717/peerj.19384

By:

Zhang, Yan;
Ding, Guoao;
Gao, Yue;
Li, Ying;
Zhou, Peng;
Wu, Li;
Zhou, Minghui;
Wang, Jingjing;
Tang, Jun

Publication type:

Article

Feature selection with vector-symbolic architectures: a case study on microbial profiles of shotgun metagenomic samples of colorectal cancer.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 2, p. 1, doi. 10.1093/bib/bbaf177

By:

Cumbo, Fabio;
Truglia, Simone;
Weitschek, Emanuel;
Blankenberg, Daniel

Publication type:

Article

FGeneBERT: function-driven pre-trained gene language model for metagenomics.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 2, p. 1, doi. 10.1093/bib/bbaf149

By:

Duan, Chenrui;
Zang, Zelin;
Xu, Yongjie;
He, Hang;
Li, Siyuan;
Liu, Zihan;
Lei, Zhen;
Zheng, Ju-Sheng;
Li, Stan Z

Publication type:

Article

A review of neural networks for metagenomic binning.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 2, p. 1, doi. 10.1093/bib/bbaf065

By:

Herazo-Álvarez, Jair;
Mora, Marco;
Cuadros-Orellana, Sara;
Vilches-Ponce, Karina;
Hernández-García, Ruber

Publication type:

Article

Genomic characterisation of novel extremophile lineages from the thalassohaline lake Dziani Dzaha expands the metabolic repertoire of the PVC superphylum.

Published in:

Environmental Microbiome, 2025, v. 20, n. 1, p. 1, doi. 10.1186/s40793-025-00699-1

By:

Vigneron, Adrien;
Cloarec, Lilian A.;
Brochier-Armanet, Céline;
Flandrois, Jean Pierre;
Troussellier, Marc;
Bernard, Cécile;
Agogué, Hélène;
Oger, Philippe M.;
Hugoni, Mylène

Publication type:

Article

Impact of microbiological molecular methodologies on adaptive sampling using nanopore sequencing in metagenomic studies.

Published in:

Environmental Microbiome, 2025, v. 20, n. 1, p. 1, doi. 10.1186/s40793-025-00704-7

By:

Herbert, Josephine;
Thompson, Stanley;
Beckett, Angela H.;
Robson, Samuel C.

Publication type:

Article

Metagenomic and Molecular Detection of Novel Fecal Viruses in Free-Ranging Agile Wallabies.

Published in:

EcoHealth, 2023, v. 20, n. 4, p. 427, doi. 10.1007/s10393-023-01659-2

By:

Okoh, God'spower Richard;
Ariel, Ellen;
Whitmore, David;
Horwood, Paul F.

Publication type:

Article

Metagenomic Analysis Reveals Previously Undescribed Bat Coronavirus Strains in Eswatini.

Published in:

EcoHealth, 2021, v. 18, n. 4, p. 421, doi. 10.1007/s10393-021-01567-3

By:

Shapiro, Julie Teresa;
Mollerup, Sarah;
Jensen, Randi Holm;
Olofsson, Jill Katharina;
Nguyen, Nam-phuong D.;
Hansen, Thomas Arn;
Vinner, Lasse;
Monadjem, Ara;
McCleery, Robert A.;
Hansen, Anders J.

Publication type:

Article

Where Next for Microbiome Research?

Published in:

PLoS Biology, 2015, v. 13, n. 1, p. 1, doi. 10.1371/journal.pbio.1002050

By:

Waldor, Matthew K.;
Tyson, Gene;
Borenstein, Elhanan;
Ochman, Howard;
Moeller, Andrew;
Finlay, B. Brett;
Kong, Heidi H.;
Gordon, Jeffrey I.;
Nelson, Karen E.;
Dabbagh, Karim;
Smith, Hamilton

Publication type:

Article

Minimizing the deep coalescence cost.

Published in:

Journal of Bioinformatics & Computational Biology, 2018, v. 16, n. 5, p. N.PAG, doi. 10.1142/S0219720018400218

By:

Dąbkowski, Dawid;
Tabaszewski, Paweł;
Górecki, Paweł

Publication type:

Article

Metagenome sequence clustering with hash-based canopies.

Published in:

Journal of Bioinformatics & Computational Biology, 2017, v. 15, n. 6, p. -1, doi. 10.1142/S0219720017400066

By:

Rahman, Mohammad Arifur;
LaPierre, Nathan;
Rangwala, Huzefa;
Barbara, Daniel

Publication type:

Article

Introduction to selected papers from the 8th International Conference on Bioinformatics and Computational Biology (BICOB 2016).

Published in:

Journal of Bioinformatics & Computational Biology, 2017, v. 15, n. 3, p. -1, doi. 10.1142/S0219720017020024

By:

Haspel, Nurit;
Ioerger, Thomas;
Al-Mubaid, Hisham

Publication type:

Article

An accurate and fast alignment-free method for profiling microbial communities.

Published in:

Journal of Bioinformatics & Computational Biology, 2017, v. 15, n. 3, p. -1, doi. 10.1142/S0219720017400017

By:

Pham, Diem-Trang;
Gao, Shanshan;
Phan, Vinhthuy

Publication type:

Article

Grid-Assembly: An oligonucleotide composition-based partitioning strategy to aid metagenomic sequence assembly.

Published in:

Journal of Bioinformatics & Computational Biology, 2015, v. 13, n. 3, p. -1, doi. 10.1142/S0219720015410048

By:

Ghosh, Tarini Shankar;
Mehra, Varun;
Mande, Sharmila S.

Publication type:

Article

Comparative metagenome analysis of an Alaskan glacier.

Published in:

Journal of Bioinformatics & Computational Biology, 2014, v. 12, n. 2, p. -1, doi. 10.1142/S0219720014410030

By:

Choudhari, Sulbha;
Lohia, Ruchi;
Grigoriev, Andrey

Publication type:

Article

LARGE-SCALE METAGENOMIC SEQUENCE CLUSTERING ON MAP-REDUCE CLUSTERS.

Published in:

Journal of Bioinformatics & Computational Biology, 2013, v. 11, n. 1, p. -1, doi. 10.1142/S0219720013400015

By:

YANG, XIAO;
ZOLA, JAROSLAW;
ALURU, SRINIVAS

Publication type:

Article

METAGENOMIC TAXONOMIC CLASSIFICATION USING EXTREME LEARNING MACHINES.

Published in:

Journal of Bioinformatics & Computational Biology, 2012, v. 10, n. 5, p. -1, doi. 10.1142/S0219720012500151

By:

RASHEED, ZEEHASHAM;
RANGWALA, HUZEFA

Publication type:

Article

An Atypical Naturally Split Intein Engineered for Highly Efficient Protein Labeling.

Published in:

Angewandte Chemie, 2014, v. 126, n. 5, p. 1330, doi. 10.1002/ange.201307969

By:

Thiel, Ilka V.;
Volkmann, Gerrit;
Pietrokovski, Shmuel;
Mootz, Henning D.

Publication type:

Article

Challenges of metagenomics and single-cell genomics approaches for exploring cyanobacterial diversity.

Published in:

Photosynthesis Research, 2015, v. 126, n. 1, p. 135, doi. 10.1007/s11120-014-0066-9

By:

Davison, Michelle;
Hall, Eric;
Zare, Richard;
Bhaya, Devaki

Publication type:

Article

High-throughput amplicon sequencing demonstrates extensive diversity of xylanase genes in the sediment of soda lake Dabusu.

Published in:

Biotechnology Letters, 2019, v. 41, n. 3, p. 409, doi. 10.1007/s10529-019-02646-w

By:

Wang, Guozeng;
Ren, Yaxin;
Ng, Tzi Bun;
Streit, Wolfgang R.;
Ye, Xiuyun

Publication type:

Article

Characterization of an inhibitor-resistant endo-1,4-β-mannanase from the gut microflora metagenome of Hermetia illucens.

Published in:

Biotechnology Letters, 2018, v. 40, n. 9/10, p. 1377, doi. 10.1007/s10529-018-2596-2

By:

Song, Jaeeun;
Kim, Su-Yeon;
Kim, Dae-Hyuk;
Lee, Young-Seok;
Sim, Joon-Soo;
Hahn, Bum-Soo;
Lee, Chang-Muk

Publication type:

Article

Direct cloning, expression of a thermostable xylanase gene from the metagenomic DNA of cow dung compost and enzymatic production of xylooligosaccharides from corncob.

Published in:

Biotechnology Letters, 2015, v. 37, n. 9, p. 1877, doi. 10.1007/s10529-015-1857-6

By:

Sun, Ming-zhe;
Zheng, Hong-chen;
Meng, Ling-cai;
Sun, Jun-she;
Song, Hui;
Bao, Yun-juan;
Pei, Hai-sheng;
Yan, Zheng;
Zhang, Xiu-qing;
Zhang, Jing-sheng;
Liu, Yi-han;
Lu, Fu-ping

Publication type:

Article

New dioxygenase from metagenomic library from Brazilian soil: insights into antibiotic resistance and bioremediation.

Published in:

Biotechnology Letters, 2015, v. 37, n. 9, p. 1809, doi. 10.1007/s10529-015-1861-x

By:

Santos, Débora;
Istvan, Paula;
Noronha, Eliane;
Quirino, Betânia;
Krüger, Ricardo

Publication type:

Article

Cloning and characterization of a novel GH44 family endoglucanase from mangrove soil metagenomic library.

Published in:

Biotechnology Letters, 2014, v. 36, n. 8, p. 1701, doi. 10.1007/s10529-014-1531-4

By:

Mai, Zhimao;
Su, Hongfei;
Yang, Jian;
Huang, Sijun;
Zhang, Si

Publication type:

Article

Expression and characterization of a thermostable penicillin G acylase from an environmental metagenomic library.

Published in:

Biotechnology Letters, 2014, v. 36, n. 3, p. 617, doi. 10.1007/s10529-013-1403-3

By:

Zhang, Qian;
Xu, Hui;
Zhao, Jing;
Zeng, Runying

Publication type:

Article

Discovery of a novel esterase subfamily sharing an identified arm sequence (ArmEst) by gene-specific metagenomic PCR.

Published in:

Biotechnology Letters, 2013, v. 35, n. 11, p. 1937, doi. 10.1007/s10529-013-1293-4

By:

Zhang, Ao;
Zhao, Rong;
Jin, Peng;
Ma, Lifang;
Xiong, Xiaolong;
Xie, Tian;
Pei, Xiaolin;
Yu, Li;
Yin, Xiaopu;
Wang, Qiuyan

Publication type:

Article

Metagenomic cloning and characterization of Na/H antiporter genes taken from sediments in Chaerhan Salt Lake in China.

Published in:

Biotechnology Letters, 2013, v. 35, n. 4, p. 619, doi. 10.1007/s10529-012-1122-1

By:

Wang, Xiaoyu;
Xu, Feng;
Chen, Sanfeng

Publication type:

Article

Bioactive compounds synthesized by non-ribosomal peptide synthetases and type-I polyketide synthases discovered through genome-mining and metagenomics.

Published in:

Biotechnology Letters, 2012, v. 34, n. 8, p. 1393, doi. 10.1007/s10529-012-0919-2

By:

Nikolouli, Katerina;
Mossialos, Dimitris

Publication type:

Article

Life at extreme elevations on Atacama volcanoes: the closest thing to Mars on Earth?

Published in:

Antonie van Leeuwenhoek, 2018, v. 111, n. 8, p. 1389, doi. 10.1007/s10482-018-1066-0

By:

Schmidt, S. K.;
Gendron, E. M. S.;
Vincent, K.;
Solon, A. J.;
Sommers, P.;
Schubert, Z. R.;
Vimercati, L.;
Porazinska, D. L.;
Darcy, J. L.;
Sowell, P.

Publication type:

Article

Distinct taxonomic and functional composition of soil microbiomes along the gradient forest-restinga-mangrove in southeastern Brazil.

Published in:

Antonie van Leeuwenhoek, 2018, v. 111, n. 1, p. 101, doi. 10.1007/s10482-017-0931-6

By:

Mendes, Lucas William;
Tsai, Siu Mui

Publication type:

Article

Further analysis reveals new gut microbiome markers of type 2 diabetes mellitus.

Published in:

Antonie van Leeuwenhoek, 2017, v. 110, n. 3, p. 445, doi. 10.1007/s10482-016-0805-3

By:

Wang, Xiaokai;
Xu, Xiaoqiang;
Xia, Yan

Publication type:

Article