Review
Biochemistry & Molecular Biology
Eric Banan-Mwine Daliri, Fred Kwame Ofosu, Ramachandran Chelliah, Byong H. Lee, Deog-Hwan Oh
Summary: The application of multi-omic technologies in gut microbiome studies has unveiled the comprehensive interaction between commensals in health and disease. However, challenges remain in identifying the origin and function of certain proteins and metabolites in gut samples, which may be overcome by combining different omics techniques. Future perspectives in this area include overcoming challenges and advancing our understanding of the gut microbiome through the integration of various omic approaches.
Article
Microbiology
Chun-Xu Xue, Heyu Lin, Xiao-Yu Zhu, Jiwen Liu, Yunhui Zhang, Gary Rowley, Jonathan D. Todd, Meng Li, Xiao-Hua Zhang
Summary: Metagenomics and metatranscriptomics are powerful methods for uncovering key micro-organisms and processes driving biogeochemical cycling. However, databases and normalization models for depicting biogeochemical pathways are lacking. This study presents DiTing, a tool for inferring and comparing biogeochemical pathways from metagenomic/metatranscriptomic data, which has been successfully applied to a wide range of datasets.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Engineering, Marine
Cora Hoerstmann, Sylke Wohlrab, Uwe John
Summary: High-throughput sequencing technologies have advanced our understanding of microbial diversity in the oceans, but research on microbial eukaryotes (protists) lags behind. This review discusses the challenges and opportunities of high-throughput sequencing methods for studying the evolutionary, ecological, and functional aspects of oceanic protists. These approaches allow for a deeper understanding of the functional role of protists and the changes in marine ecosystems.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2022)
Article
Soil Science
Qicheng Bei, Jingjing Peng, Werner Liesack
Summary: The study elucidated the genetic potential and functional activity of Ignavibacteria in straw-amended paddy soils from Italy, revealing their versatility and adaptation to varying oxygen conditions in the ecosystem.
SOIL BIOLOGY & BIOCHEMISTRY
(2021)
Article
Microbiology
Daria Shafranskaya, Varsha Kale, Rob Finn, Alla L. Lapidus, Anton Korobeynikov, Andrey D. Prjibelski
Summary: While metagenome sequencing provides insights on microbial communities, metatranscriptome analysis is useful for studying functional activity. However, the complexity, dynamic range, and lack of computational methods for assembling metatranscriptomes pose challenges. This study presents MetaGT, a pipeline that combines metatranscriptomic and metagenomic data to improve assembly coverage and completeness. Results show significant improvement compared to existing methods. The pipeline, implemented in NextFlow, is available athttps://github.com/ablab/metaGT.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Renaud Van Damme, Martin Hoelzer, Adrian Viehweger, Bettina Mueller, Erik Bongcam-Rudloff, Christian Brandt
Summary: Metagenomics has revolutionized microbiology, but analyzing metagenome-assembled genomes remains challenging. MUFFIN, a bioinformatics workflow, integrates short and long reads to reconstruct bacterial species and their functions with high reproducibility and efficiency. MUFFIN is a user-friendly tool that automates complex analysis steps and provides valuable insights into microbial communities.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Lina Aitmanaite, Karolis Sirmonaitis, Giancarlo Russo
Summary: This review summarizes the contributions of metagenomics and metatranscriptomics to the understanding of the microbial environment associated with various types of cancers. It highlights the advantages of metatranscriptomics in assessing microbial functions and suggests ways to advance the knowledge of the cancer bacterial environment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Joao C. Sequeira, Miguel Rocha, M. Madalena Alves, Andreia F. Salvador
Summary: Omics and meta-omics technologies provide powerful approaches to explore microbial functions. However, the analysis of large and complex datasets is often challenging. In this study, three novel bioinformatics tools were developed to facilitate functional annotation and metabolic pathway analysis. These tools are user-friendly and valuable resources for interpreting microbial activities in nature and biotechnological processes.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Genetics & Heredity
Susana Martinez Arbas, Susheel Bhanu Busi, Pedro Queiros, Laura de Nies, Malte Herold, Patrick May, Paul Wilmes, Emilie E. L. Muller, Shaman Narayanasamy
Summary: Multi-omic studies have become increasingly prevalent in microbial communities, allowing for a deeper understanding of community structure and function. Longitudinal multi-omic microbiome datasets offer advantages in understanding community dynamics.
FRONTIERS IN GENETICS
(2021)
Article
Microbiology
Victoria Pascal Andreu, Hannah E. Augustijn, Koen van den Berg, Justin J. J. van der Hooft, Michael A. Fischbach, Marnix H. Medema
Summary: Microbial gene clusters encoding biosynthesis of metabolites are crucial for microbial ecosystems. BiG-MAP is a bioinformatic tool that profiles gene cluster abundance and expression levels in microbiome samples, allowing for hypothesis generation on functional roles and associations with phenotypes of interest.
Article
Microbiology
Billy Taj, Mobolaji Adeolu, Xuejian Xiong, Jordan Ang, Nirvana Nursimulu, John Parkinson
Summary: Whole microbiome RNASeq (metatranscriptomics) is a powerful technology for functional analysis of microbial communities. MetaPro is a flexible and scalable data analysis pipeline that effectively processes and analyzes metatranscriptomic datasets. It outperforms current state-of-the-art pipelines in terms of performance and functionality.
Article
Gastroenterology & Hepatology
Jinlong Ru, Mohammadali Khan Mirzaei, Jinling Xue, Xue Peng, Li Deng
Summary: ViroProfiler is a computer analysis tool for analyzing shotgun viral metagenomic data. It can be run on a local or cloud computing environment. It uses containerization technology to ensure computational reproducibility and facilitate collaborative research.
Article
Biochemical Research Methods
Hunyong Cho, Yixiang Qu, Chuwen Liu, Boyang Tang, Ruiqi Lyu, Bridget M. Lin, Jeffrey Roach, M. Andrea Azcarate-Peril, Apoena Aguiar Ribeiro, Michael Love, Kimon Divaris, Di Wu
Summary: Understanding the function of the human microbiome is important, but statistical methods for metatranscriptomics are still in their early stages. A comprehensive evaluation of 10 differential analysis methods was conducted to address this gap. The logistic-beta (LB) test showed the highest sensitivity and controlled type I error well, while the MAST test had inflated type I error. The LB and log-normal (LN) tests successfully identified genes associated with childhood dental disease in a study.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biotechnology & Applied Microbiology
Felix Van der Jeugt, Rien Maertens, Aranka Steyaert, Pieter Verschaffelt, Caroline De Tender, Peter Dawyndt, Bart Mesuere
Summary: This study developed a tool suite called UMGAP for shotgun metagenomics taxonomic profiling, which achieved competitive performance with state-of-the-art tools. UMGAP utilizes protein coding regions to analyze the data, leading to low runtime, manageable memory footprint, high accuracy, and interactive visualizations for easy exploration.
Article
Biotechnology & Applied Microbiology
Ting Huang, Zhen-Ming Lu, Ming-Ye Peng, Li-Juan Chai, Xiao-Juan Zhang, Jin-Song Shi, Qi Li, Zheng-Hong Xu
Summary: Complex microorganisms in food fermentation can be challenging for standardized production, but constructing a defined starter can improve fermentation efficiency. This study used multi-omics techniques to identify vital species in autochthonous vinegar starter and designed a defined microbial community for efficient cereal vinegar fermentation.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Sunho Park, Seung-Jun Kim, Donghyeon Yu, Samuel Pena-Llopis, Jianjiong Gao, Jin Suk Park, Beibei Chen, Jessie Norris, Xinlei Wang, Min Chen, Minsoo Kim, Jeongsik Yong, Zabi Wardak, Kevin Choe, Michael Story, Timothy Starr, Jae-Ho Cheong, Tae Hyun Hwang
Article
Urology & Nephrology
Karam Aboudehen, Min Soo Kim, Matthew Mitsche, Kristina Garland, Norma Anderson, Lama Noureddine, Marco Pontoglio, Vishal Patel, Yang Xie, Russell DeBose-Boyd, Peter Igarashi
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2016)
Article
Nutrition & Dietetics
Hannah G. Piper, Di Fan, Laura A. Coughlin, Evi X. Ho, Margaret M. McDaniel, Nandini Channabasappa, Jiwoong Kim, Minsoo Kim, Xiaowei Zhan, Yang Xie, Andrew Y. Koh
JOURNAL OF PARENTERAL AND ENTERAL NUTRITION
(2017)
Article
Multidisciplinary Sciences
Wenfang Chen, Haley Hill, Alana Christie, Min Soo Kim, Eboni Holloman, Andrea Pavia-Jimenez, Farrah Homayoun, Yuanqing Ma, Nirav Patel, Paul Yell, Guiyang Hao, Qurratulain Yousuf, Allison Joyce, Ivan Pedrosa, Heather Geiger, He Zhang, Jenny Chang, Kevin H. Gardner, Richard K. Bruick, Catherine Reeves, Tae Hyun Hwang, Kevin Courtney, Eugene Frenkel, Xiankai Sun, Naseem Zojwalla, Tai Wong, James P. Rizzi, Eli M. Wallace, John A. Josey, Yang Xie, Xian-Jin Xie, Payal Kapur, Renee M. McKay, James Brugarolas
Article
Microbiology
Andrew Y. Koh
Article
Oncology
Arthur E. Frankel, Laura A. Coughlin, Jiwoong Kim, Thomas W. Froehlich, Yang Xie, Eugene P. Frenkel, Andrew Y. Koh
Editorial Material
Microbiology
Tiffany R. Simms-Waldrip, Andrew Y. Koh
CELL HOST & MICROBE
(2018)
Article
Cell Biology
Issei S. Shimada, Sun-Hee Hwang, Bandarigoda N. Somatilaka, Xin Wang, Patryk Skowron, Jiwoong Kim, Min Kim, John M. Shelton, Veena Rajaram, Zhenyu Xuan, Michael D. Taylor, Saikat Mukhopadhyay
Article
Multidisciplinary Sciences
Wenhan Zhu, Maria G. Winter, Mariana X. Byndloss, Luisella Spiga, Breck A. Duerkop, Elizabeth R. Hughes, Lisa Buttner, Everton de Lima Romao, Cassie L. Behrendt, Christopher A. Lopez, Luis Sifuentes-Dominguez, Kayci Huff-Hardy, R. Paul Wilson, Caroline C. Gillis, Cagla Tukel, Andrew Y. Koh, Ezra Burstein, Lora V. Hooper, Andreas J. Baumler, Sebastian E. Winter
Article
Oncology
Mitchell S. von Itzstein, Amrit S. Gonugunta, Thomas Sheffield, Jade Homsi, Jonathan E. Dowell, Andrew Y. Koh, Prithvi Raj, Farjana Fattah, Yiqing Wang, Vijay S. Basava, Shaheen Khan, Jason Y. Park, Vinita Popat, Jessica M. Saltarski, Yvonne Gloria-McCutchen, David Hsiehchen, Jared Ostmeyer, Yang Xie, Quan-Zhen Li, Edward K. Wakeland, David E. Gerber
Summary: Patients treated with antibiotics have worse outcomes from cancer immunotherapy, potentially due to the impact of antibiotics on the gut microbiome. This study found significant differences in immune parameters, including antibodies and cytokines, according to antibiotic exposure.
Review
Medical Laboratory Technology
Andrew Y. Koh
CLINICAL CHEMISTRY
(2017)
Article
Hematology
Tiffany R. Simms-Waldrip, Gauri Sunkersett, Laura A. Coughlin, Milan R. Savani, Carlos Arana, Jiwoong Kim, Minsoo Kim, Xiaowei Zhan, David E. Greenberg, Yang Xie, Stella M. Davies, Andrew Y. Koh
BIOLOGY OF BLOOD AND MARROW TRANSPLANTATION
(2017)