Article
Microbiology
Ilayda Akacin, Seymanur Ersoy, Osman Doluca, Mine Gungormusler
Summary: This review provides a comprehensive overview of recent literature on the utilization of TGS and NGS technologies in microbial metagenomics research. It discusses the advantages and limitations of these technologies and presents real-time examples of novel applications in clinical microbiology and public health, food and agriculture, energy and environment, arts and space.
MICROBIOLOGICAL RESEARCH
(2022)
Review
Microbiology
Suleiman Aminu, Abdulaziz Ascandari, Meriem Laamarti, Nour El Houda Safdi, Achraf El Allali, Rachid Daoud
Summary: This review provides an overview of the use of whole genome sequencing (WGS) in microbiome research, highlighting its importance in unraveling the diversity and complexity of microbial communities in different environments. It discusses the relationship between the gut microbiome and human health, the impact of human activities on microbial communities, and the investigation of microbiomes in various animal species and plant tissues.
CRITICAL REVIEWS IN MICROBIOLOGY
(2023)
Article
Immunology
Yuyang Hou, Meng Zhang, Qiannan Jiang, Yuping Yang, Jiang Liu, Ke Yuan, Zheng Sun, Xiuxiang Liu
Summary: We used a newly developed ultra-sensitive metagenomic sequencing method, 2bRAD-M, to investigate the microbial signatures of central nervous system infections in neonates. By applying this method, we identified potential biomarkers that have significantly different relative abundance based on cerebrospinal fluid examination results, which can aid in the diagnosis of neonatal bacterial meningitis.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Review
Food Science & Technology
Min Yap, Danilo Ercolini, Avelino Alvarez-Ordonez, Paul W. O'Toole, Orla O'Sullivan, Paul D. Cotter
Summary: This article introduces a community-based method, particularly the application of sequencing-based meta-omics strategies, for characterizing microbial communities along the food chain.
ANNUAL REVIEW OF FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Microbiology
Jason A. Rothman, Jenna L. Riis, Katrina R. Hamilton, Clancy Blair, Douglas A. Granger, Katrine L. Whiteson
Summary: Human oral microbial communities have significant implications for oral and systemic health due to their diversity. Understanding the differences between healthy and dysbiotic oral microbiomes is important, especially within and between families. This study investigates the changes in oral microbiome composition within individuals and the impact of factors such as environmental tobacco smoke exposure, metabolic regulation, inflammation, and antioxidant potential. The findings reveal differences in oral microbiomes between children and caregivers, with shared diversity but distinct differences, and highlight the associations between the oral microbiome and various salivary markers.
Article
Genetics & Heredity
Runzhi Zhang, Dorothy Ellis, Alejandro R. Walker, Susmita Datta
Summary: The study investigates city-specific microbial signatures by analyzing microbial compositions from different cities and successfully predicts the origins of unknown samples using machine learning methods. The model achieved a 19.60% error rate in classifying cities based on their microbial compositions and accurately labeled a significant portion of test samples from new cities as mystery samples.
FRONTIERS IN GENETICS
(2021)
Article
Microbiology
Indrani Mukhopadhya, Jennifer C. Martin, Sophie Shaw, Aileen J. McKinley, Silvia W. Gratz, Karen P. Scott
Summary: This study compares the bacterial profiles of faecal and mucosal microbiota and finds that faecal samples can be used as a convenient surrogate for rectal biopsy-associated microbiota. The results from bacterial culturing and 16S rRNA gene sequencing show similar taxonomic patterns.
Article
Genetics & Heredity
Qingyu Chen, Shili Lin, Chi Song
Summary: MiAF is a method that combines p-values from OTU-level tests adaptively to construct a community-level test. It combines the flexibility of OTU-level tests with the biological relevance of community-level tests. Simulation study and real data applications demonstrate that MiAF has comparable or better power than methods specifically designed for community-level tests.
FRONTIERS IN GENETICS
(2022)
Article
Ecology
Daniel Machado, Oleksandr M. Maistrenko, Sergej Andrejev, Yongkyu Kim, Peer Bork, Kaustubh R. Patil, Kiran R. Patil
Summary: The study shows that microbial communities cluster at different ends of the spectrum between resource competition and metabolic cooperation. Cooperative communities tend to have smaller genomes and multiple auxotrophies, whereas competitive communities have larger genomes, overlapping niches, and a high potential for antimicrobial activity.
NATURE ECOLOGY & EVOLUTION
(2021)
Review
Agriculture, Dairy & Animal Science
A. M. Osorio-Doblado, K. P. Feldmann, J. M. Lourenco, R. L. Stewart, W. B. Smith, L. O. Tedeschi, F. L. Fluharty, T. R. Callaway
Summary: The rumen microbial ecosystem, comprised of bacteria, archaea, protozoa, and fungi, plays a crucial role in the degradation of plant cell walls in ruminants fed a variety of forages. Next-generation sequencing techniques have greatly enhanced our understanding of the microbial ecology of the rumen and the specific role of carbohydrate-active enzymes in forage degradation. These advancements have also shed light on the dynamic changes in the ruminal microbial population and the impact on the assortment of fermentation products. A better understanding of the rumen's microbial population is essential for improving fiber degradation and promoting sustainable production systems.
JOURNAL OF ANIMAL SCIENCE
(2023)
Review
Genetics & Heredity
Hiral G. Chaudhari, Shobha Prajapati, Zuhour Hussein Wardah, Gopal Raol, Vimalkumar Prajapati, Rajesh Patel, Ali A. Shati, Mohammad Y. Alfaifi, Serag Eldin I. Elbehairi, R. Z. Sayyed
Summary: A large part of the Earth's biological systems consists of microorganisms, most of which have not been cultured. Traditional methods of culturing microbes have limitations, prompting the development of culture-independent molecular methods. Metagenomics has revolutionized research by revealing the diversity and novelty of microbial communities and genomes. This review focuses on the development of this field, sequencing techniques and data analysis, as well as interpretation and representation.
FRONTIERS IN GENETICS
(2023)
Article
Immunology
Maria Nikodemova, Elizabeth A. Holzhausen, Courtney L. Deblois, Jodi H. Barnet, Paul E. Peppard, Garret Suen, Kristen M. Malecki
Summary: PCR amplicon sequencing can lead to the detection of false operational taxonomic units (OTUs), which inflates estimates of gut microbial diversity. Filtering methods for removing low-abundance OTUs and the reliability of OTU detection within replicates still lack consensus. This study investigated the reliability of OTU detection and quantification accuracy in human stool specimens by applying different filtering methods.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Otorhinolaryngology
Kenneth Yan, Samuel Auger, Ashley Diaz, Julia Naman, Ramya Vemulapalli, Rifat Hasina, Evgeny Izumchenko, Benjamin Shogan, Nishant Agrawal
Summary: The study examines the oral microbiome in the context of oral cavity squamous cell carcinoma using 16S rRNA sequencing. The results show changes in bacterial populations in oral cancer patients, with increases in certain bacteria genera correlating with tumor stage. These bacteria can potentially serve as markers for tumor progression or provide insights into the tumor microenvironment.
OTOLARYNGOLOGY-HEAD AND NECK SURGERY
(2023)
Article
Multidisciplinary Sciences
Jing Chang, Xiang Li, Qingxin Xia, Shumin Yang, He Zhang, Hui Yang
Summary: Microbial communities found in breast cancer tissues may contribute to oncogenesis. Analysis of FFPE and FF tumor samples from 30 BC participants revealed consistent microbial composition and stable core bacterial communities, indicating the potential value of FFPE tissues for intratumoral microbiome analysis in breast cancer.
Article
Ecology
Manolito G. Torralba, Gajender Aleti, Weizhong Li, Kelvin Jens Moncera, Yi-Han Lin, Yanbao Yu, Michal M. Masternak, Wojciech Golusinski, Pawel Golusinski, Katarzyna Lamperska, Anna Edlund, Marcelo Freire, Karen E. Nelson
Summary: The study found a higher number of Fusobacteria, Bacteroidetes, and Firmicutes in oral squamous cell carcinoma (OSCC) tumor tissue, with an increase of Prevotella in saliva from OSCC patients and a prevalence of Corynebacterium in healthy subjects. Additionally, adhesion and virulence factors associated with Streptococcus gordonii and Fusobacterium genera were detected in OSCC tissues, suggesting potential biomarkers for disease progression.
Article
Ecology
Shu-mei Lai, Wei-chung Liu, Ferenc Jordan
ECOLOGICAL MODELLING
(2015)
Article
Multidisciplinary Sciences
Shu-li Cheng, Wen-hsien Lin, Frederick Kin Hing Phoa, Jing-shiang Hwang, Wei-chung Liu
Article
Multidisciplinary Sciences
Wei-Ping Chan, I-Ching Chen, Robert K. Colwell, Wei-Chung Liu, Cho-ying Huang, Sheng-Feng Shen
Article
Mathematical & Computational Biology
Austin W. T. Chiang, Wei-Chung Liu, Pep Charusanti, Ming-Jing Hwang
BMC SYSTEMS BIOLOGY
(2014)
Article
Multidisciplinary Sciences
Chih-Ming Hung, Pei-Jen L. Shaner, Robert M. Zink, Wei-Chung Liu, Te-Chin Chu, Wen-San Huang, Shou-Hsien Li
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2014)
Letter
Ecology
Wei-Ping Chan, I-Ching Chen, Robert K. Colwell, Wei-Chung Liu, Cho-ying Huang, Sheng-Feng Shen
JOURNAL OF BIOGEOGRAPHY
(2018)
Article
Biology
Ming Liu, Dustin R. Rubenstein, Wei-Chung Liu, Sheng-Feng Shen
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2019)
Article
Computer Science, Theory & Methods
Wei-Chung Liu, Liang-Cheng Huang, Chester Wai-Jen Liu, Ferenc Jordan
APPLIED NETWORK SCIENCE
(2020)
Article
Mathematics
Ferenc Jordan, Anett Endredi, Wei-chung Liu, Domenico D'Alelio
Article
Ecology
Wei-Chung Liu, Shu-Mei Lai, Hsuan-Wien Chen
ECOLOGICAL RESEARCH
(2017)