Literature
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Recommended papers from Semantic Scholar, ranked by journal impact.
Last synced: Oct 19, 2026
Journal Articles
Past 30 days · ranked by 2-year mean citedness
Prehistoric global migration of vanishing gut microbes with humans.
Matthew M. Carter, Zhi-Ru Liu, M. Olm, Melanie A. Martin, D. Sprockett, Parsa Ghadermazi, Benjamin C. Trumble, H. Kaplan, J. Stieglitz, D. Rodriguez, D. Relman, E. Sonnenburg, M. Gurven, Benjamin H. Good, J. Sonnenburg
Domesticated bacterial origin genes regulate homeostasis of the insect gut microbiome and empower adaptation
NEWZhen-Jia Zhang, Yu-Bo Zhang, Kun Zhao, Guang-Yuan Cheng, Zhi-Hao Lu, Dong-Ju Wang, Yi-Qun Liu, Jian-Guo Wu, Li-Ying Wang, Li-Sheng Zhang, Xin-Hai Ye, Li Yu, Wei Zhang, Yi Li
gutMDisorder v3.0: an updated database for dysbiosis of the gut and oral microbiota in phenotypes and interventions.
Si-Yuan Guan, Chang-Lu Qi, Xing-Wang Liu, Bai-Feng Li, Yuan-Ming Zhang, Hong-Wei Gao, Qiu-Han Chen, Liang Cheng, Xue Zhang
The human gut microbiome primes fever after vaccination.
Kelsey E. Huus, Hirohito Abo, Yi-Han Tan, Ezgi Atay, Héloïse Rytter, Ronald Keller, Silke Dauser, Dai Long Vu, Meghan B. Azad, R. Knight, Alfred Ke, L. Lotoski, M.-A. Langlois, Rong Liu, Alexander V. Tyakht, Nicholas D. Youngblut, Sang-Moo Kang, J. Parsonnet, L. Maier, B. Chassaing, Peter G. Kremsner, Andrew T. Gewirtz, Meral Esen, R. Ley, Julian J. Gabor, J. M. Gaile, W. A. Fleischmann, Alex S. Siebner, Geerten Smeenk, J. Flügge, Roberta Allgayer De Moraes, Dennis Jakob, Alina Prokipchuk, Carolin Wilhelm
A global mitochondrial genomic atlas illuminates freshwater microeukaryote diversity
Lucas Serra Moncadas, H. Ruscheweyh, J. Woodhouse, M. Salcher, Yusuke Okazaki, D. Ngugi, Michael Pester, T. Posch, R. Ghai, H. Grossart, S. Sunagawa, Jakob Pernthaler, A. Andrei
Five-country analysis of geographic and dietary drivers of gut microbiome composition and genomic variation
Lora Khatib, Renee E. Oles, Alejandra Ríos Hernández, Tyler Myers, Jian-Shu Zhao, Megha Kumar, Ana Laroya, V. Tolosa-Enguís, Nobuko Matsunami, Daisuke Suzuki, Nodoka Chiba, Katharine E. Gilbert, Promi Das, Jon G. Sanders, Lucas Patel, Nicole S. Litwin, Brent Nowinski, Amanda Birmingham, Sawyer Farmer, C. Brennan, MacKenzie M. Bryant, Caitlin Tribelhorn, Karenina Sanders-Bodai, Charles Cowart, Oliver Nizet, Edgar A. Diaz, P. Veiga, Sudarshan A. Shetty, J. Knol, C. Lay, Hana Koutnikova, Soline Chaumont, J. Tap, Aurélie Cotillard, Muriel Derrien, M. Laiola, Antonio González, A. Tovar, Nimbe Torres, Y. Sanz, Takuji Yamada, D. McDonald, Se-Jin Song, A. Bartko, Rob Knight
Author Correction: Non-catalytic ubiquitin binding by A20 prevents psoriatic arthritis-like disease and inflammation.
Bahram Razani, M. Whang, Francis S. Kim, Mary C. Nakamura, Xiao-Fei Sun, R. Advincula, Jessie A. Turnbaugh, M. Pendse, Priscilia Tanbun, Philip Achacoso, P. Turnbaugh, Barbara A. Malynn, Averil Ma
Phylogeny-agnostic strain-level prediction of phage-host interactions from genomes using machine learning.
A. Noonan, Lucas Morinière, E. O. Rivera-Lopez, Krish Patel, Melina Pena, Madeline Svab, A. Kazakov, A. Deutschbauer, E. Dudley, V. Mutalik, A. Arkin
A high-resolution spatial model of the primate gut microbiome defines niche-specific functions and host-adapted microbial metabolism.
NEWShu-Wen Hou, Yue-Song Jiang, Deng-Wei Zhang, Z. Xu, Yong-Xin Li, Xi-Qiang Liu, Hai-Tao Zhang, Jia-Chao Zhang, Q. Zhai, Chuan Zhang, Xin-Rui Wang, Shi Huang
Ethanol exposure is associated with spatial and taxon-specific gut microbiota remodeling characterized by ecological adaptation rather than broad activation of microbial ethanol metabolism
Ming-Liang Li, Jie-Qi Mao, Shuang-Ping Liu, Hao-Jie Yu, Hui Qin, Xiao-Gang Liu, Rong-Kun Tu, Shu-Guang Chen, Zi-Ming Liu, Su-Yi Zhang, Jian Mao
Phage-based depletion of Variovorax reveals interactions within intact microbiomes
Tomas Hessler, Dawn Chiniquy, Benjamin A. Adler, Jordan Hoff, Eliana Tucker, R. Huddy, Rohan Sachdeva, Shu-Fei Lei, Susan T. L. Harrison, R. Barrangou, Spencer Diamond, A. Deutschbauer, J. Banfield
The grammar of the pangenome: terms, concepts, methods, and emerging patterns—a general framework for comparative genomics and genome biology
A. Chasapi, Alexandros Michailidis, L. Schriml, Claudio Donati, N. Kyrpides, Christos A. Ouzounis
A pangenomic method for establishing a synthetic somatic variant resource in HapMap mixtures.
NEWNahyun Kong, Zi-Tian Tang, Andrew Ruttenberg, Juan F. Macias-Velasco, Ze-Fan Li, Emma Casey, Wen-Jin Zhang, Ben-Peng Miao, Zi-Lan Xin, Qi-Chen Fu, Haeorum Park, X. Zhuo, Elvisa Mehinovic, Edward A. Belter, Chad Tomlinson, John E. Garza, Shi-Hua Dong, Benjamin K. Johnson, Mary F. Majewski, Theron Palmer, Yu-Chen Cheng, Tina Lindsay, Tim Schedl, Dao-Feng Li, Hui Shen, Robert S. Fulton, Ting Wang, Sheng-Chih Jin
Decoding the lncRNA landscape in bovine mastitis: insights into immune regulation and gene networks underlying host response
V. Bisutti, D. Giannuzzi, A. Vanzin, G. Giannotta, A. Cecchinato, G. Polizel, V. Asselstine, Á. Cánovas, S. Pegolo
Structural Variants in the Human Genome Associated With Gut Microbiome and Blood Metabolic Traits With Potential Causal Links
Qun Zhou, Ke-Qing Wang, Jun-Hong Chen, Hao-Yu Wang, Xin-Jiang Tan, Xuan-Lin Huang, Zhi-Yin Lin, Xun Xu, Xin Jin, Shao-Qiao Zhang, Liang Xiao, Yuan-Qiang Zou, Tao Zhang, Xiao-Min Liu
Omnidirectional Interaction Networks Modulating Phenotypic Plasticity in the Gut Microbiota Towards Ulcerative Colitis
Hui-Zhen Li, Jia-Yi Li, Ang Dong, Xiao-Yan Guo, Qiu-Yue Tu, Ze-Lin Feng, Hao-Jia Lin, Yan-Ru Zhang, Yuxuan Hao, Hui-Ying Gong, Yi-Han Meng, Yu Wang, Shing-Tung Yau, Xiao-Cang Cao, Rong-Ling Wu, Xin-Juan Liu
Gut Microbial Topology and Metabolic Signatures Associated With Colorectal Neoplasia
K. Song, You-Wen Qin, Jia-Hui Luo, Li-Ping Liu, Chen-Yu Luo, Yin-Bin Qiu, Yi-Yi Zhong, Huan-Zi Zhong, Kui Wu, Meng Ni, Dong Wu, Min Dai, Shi-Da Zhu, Hong-Da Chen
Pan-NLRome profiling of NLR neighborhoods reveals extensive diversity in melon and boosts GWAS-based resistance gene discovery
J. Belinchon-Moreno, A. Bérard, A. Canaguier, Isabelle Le-Clainche, P. Mistral, Karine Leyre, Vincent Rittener-Ruff, J. Lagnel, D. Hinsinger, Patricia Faivre-Rampant, N. Boissot
Integrative genotype-environment association and single-cell transcriptomic analyses identify candidate mechanisms of environmental adaptation in pigs.
Dong Li, Tian-Tian Yuan, Xiang Li, Yu Quan, Xue-Kai Tian, Ye Cheng, Yu-Long Wang, Xing-Long Wu, Bo-Yuan Sun, Wan-Sheng Liu, Yu Jiang, Rong-Rong Ding, M. Groenen, M. Derks, Tai-Yong Yu
Independently modulated genes in Streptococcus pneumoniae TIGR4 reveal transcriptional rewiring in antibiotic-adapted and antibiotic-sensitive strains
Ayako Bando, Toshiki Tabuchi, Y. Hirose, E. Catoiu, Jayanth Krishnan, Masayuki Ono, Eri Ikeda, Saugat Poudel, Mao Sugiyama, Arisa Mori, Yuma Nishimura, Rene Tamura, Bernhard O. Palsson, Victor Nizet, Shigetada Kawabata
Fecal Metabolomics-Based Dietary Profiling Reveals Food Markers of HIV Brain Health Disorders.
Crystal X. Wang, Harsha Gouda, T. Scheurink, J. Zemlin, Christine E. Spaven, Helena Mannochio-Russo, Jennifer E. Iudicello, R. Heaton, David J. Moore, S. Letendre, M. Cherner, D. Franklin, Monica Guma, Andrew H. Miller, R. Knight, Pieter C. Dorrestein, R. J. Ellis
Understanding pathophysiology of gallstone disease: a multi-omic analysis focused on adult women with obesity.
NEWJ. Hoozemans, P. D. de Jonge, M. Guman, S. Haal, Ö. Aydin, A. Meijnikman, F. Bäckhed, M. D. de Brauw, Y. Acherman, M. Nieuwdorp, A. Groen, V. Gerdes
Preprints
Past 10 days · bioRxiv, medRxiv, arXiv, etc.
Genus-wide re-speciation of Corynebacterium and genomic characterisation of 87 sinus isolates resolves taxonomic conflicts and identifies four candidate novel species
NEWIsabella Burdon, James P. Psaltis, Nick Vrodos, Jeffrey Sung, Lindsay Durr, Emma F. Barry, C. Cooksley, S. Vreugde, P. Wormald, A. Psaltis
Metabolic reorganization shapes the dynamics of a water kefir microbial community
NEWMarine Chambeaudie, Delphine Mazé, M. Cariou, Evelyne Duvernois-Berthet, J. Mozziconacci, Ekaterina Tulaeva, Mathilde Courel, E. Delagoutte, F. Lopes, C. Lavelle, J. Boulé, Alexandra Joubert
FastaLake selects compact metaproteomic databases from large sequence reservoirs by de novo peptide lookup
Peter V. Treit, F. Rosenberger, Philip Hartout, Mikhail Lebedev, Jin-Qiu Xiao, M. Zwiebel, P. Geyer, Ankit Sinha, G. Wallmann, Vincenth Brennsteiner, K. Korff, E. Rodriguez, Wen-Feng Zeng, Maximilian T. Strauss, M. Keller, Michael Kuhn, J. Trebicka, C. Junot, M. Arumugam, J. Grembi, D. Shalon, K. Huang, Karsten Borgwardt, J. Müller-Reif, Matthias Mann
Urban Vietnam at the microbiome transition: Co-existing enterotypes reflect the global industrialization patterns
Thanh Thien Le, Joshua Tran, Linh Hong Thi Mai, Dao Bich Thi Tran, Dat Quoc Nguyen, Quynh Mai Nguyen, G. M. Vũ, M. Truong, Manh Khanh Dinh, Hao The Chung, Thanh Hong Nguyen, Chi Du Thi Tran, Huấn Đức Phạm, H. T. Pham, Mười Xuân Nguyễn, Thuy Xuan Nguyen, H. D. Viet, May Ngoc Le, T. Nguyen, Jennifer Le, Jack A. Gilbert, Xuan-Hung Nguyen
Targeted Depletion of rRNAs and Tobamoviruses Enhances Viral Discovery in Wastewater Metatranscriptomes
María A. Bautista, Tulika Bhardwaj, Dylan J. Barbera, Samuel J. Rulli, J. Zorz, J. McCalder, Chloe Papparis, Xiao-Li Pang, Bonita E. Lee, Judy Y. Qiu, Rhonda S. Clark, N. Acosta, Christine O' Grady, M. Parkins, Casey R. J. Hubert