Review
Biochemistry & Molecular Biology
Pei Yee Tiew, Oliver W. Meldrum, Sanjay H. Chotirmall
Summary: Microbiomics has made significant advancements in the past decade due to the availability of next-generation sequencing (NGS) and multi-omic technologies. Integration of NGS and multi-omic datasets allows for comprehensive assessment of endophenotypes in chronic respiratory diseases like chronic obstructive pulmonary disease (COPD). Valuable insights have been gained into the role of microbial communities in COPD onset, progression, prognosis, and treatment response. Identifying specific microbes and metabolic signatures associated with COPD can lead to new therapeutic interventions and prognosis-related biomarkers. However, the analysis and interpretation of the large amount of data generated by these technologies remain challenging, and standardized methods are lacking.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Fisheries
Tina Kollannoor Johny, Rinu Madhu Puthusseri, Sarita Ganapathy Bhat
Summary: The fish gut is a complex ecosystem influenced by various factors, and the gut microbiota plays important roles in the physiological functions of the host. With technological advancements, the application of culture-independent techniques in studying fish gut microbiota is promising for a better understanding.
AQUACULTURE RESEARCH
(2021)
Article
Microbiology
Mary Hannah Swaney, Shelby Sandstrom, Lindsay R. Kalan
Summary: The skin microbiome plays a crucial role in maintaining skin health, and cobamide sharing may mediate dynamics within skin microbial communities.
Article
Multidisciplinary Sciences
Nuttachai Kulthammanit, Tikumphorn Sathirapatya, Poonyapat Sukawutthiya, Hasnee Noh, Kornkiat Vongpaisarnsin, Duangdao Wichadakul
Summary: Short tandem repeats (STRs) are commonly found in the human genome and used for forensic science. However, there is currently no open-source software platform that integrates the collection, management, and analysis of STR data from next-generation sequencing (NGS). To address this gap, we introduce STRategy, a web-based application that provides essential STR data management and analysis capabilities.
Review
Microbiology
Jake M. Robinson, Zohar Pasternak, Christopher E. Mason, Eran Elhaik
Summary: The rise of microbiomics and metagenomics in forensic investigations is driven by advances in technology and methods, offering great potential, yet facing challenges such as limited sample sizes, low model accuracies, and overly idealized environmental settings.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Engineering, Environmental
Emily Garner, Benjamin C. Davis, Erin Milligan, Matthew Forrest Blair, Ishi Keenum, Ayella Maile-Moskowitz, Jin Pan, Mariah Gnegy, Krista Liguori, Suraj Gupta, Aaron J. Prussin, Linsey C. Marr, Lenwood S. Heath, Peter J. Vikesland, Liqing Zhang, Amy Pruden
Summary: The emergence of NGS technologies has revolutionized the water industry's ability to address complex microbiological challenges, although faced with barriers like cost and expertise. Research has focused on the applications of NGS in water, wastewater, and recycled water, highlighting key contributions and future directions for advancement.
Article
Infectious Diseases
Rebecca Yee, Florian P. Breitwieser, Stephanie Hao, Belita N. A. Opene, Rachael E. Workman, Pranita D. Tamma, Jennifer Dien-Bard, Winston Timp, Patricia J. Simner
Summary: Antimicrobial resistance poses a threat to public health, necessitating efficient surveillance methods like metagenomic next-generation sequencing (mNGS). This approach showed promise in detecting multidrug-resistant organisms and provides a rapid and unbiased diagnostic tool for microbiome and resistome investigations.
EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES
(2021)
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)
Article
Medicine, General & Internal
Zhonghui Ma, Su Yan, Haoxin Dong, Huifen Wang, Yonggang Luo, Xi Wang
Summary: Brain abscesses are associated with an increased long-term risk of new seizures and mortality, with common microorganisms including bacteria, fungi, and mycoplasma. We present a case of a 75-year-old man with a brain abscess caused by an oral pathogen, Prevotella denticola, where metagenomics sequencing was critical in determining targeted antibiotic therapy.
FRONTIERS IN MEDICINE
(2021)
Review
Cell Biology
Heloise Tudela, Sandrine P. Claus, Maya Saleh
Summary: The gut microbiota, a diverse community of microorganisms in the gastrointestinal tract, has a significant impact on health and disease. Keystone species, essential microbes for microbiota balance, play crucial roles in maintaining essential functions and their identification is crucial for the development of microbiome-based therapeutics. Understanding the functions of keystone species is a major step towards comprehending microbiome dynamics in disease.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Zhenli Diao, Dongsheng Han, Rui Zhang, Jinming Li
Summary: This review summarizes the potential applications and challenges of metagenomic next-generation sequencing (mNGS) in the diagnosis of lower respiratory tract infections (LRIs), aiming to promote the integration of mNGS into the management of patients with respiratory tract infections in a clinical setting.
JOURNAL OF ADVANCED RESEARCH
(2022)
Review
Infectious Diseases
Caitlin Sande, Zoe J. Boston, Lindsay R. Kalan, Meghan B. Brennan
Summary: The use of molecular microbiology techniques for diagnosing infection complicating diabetic foot ulcers is still a concern, but studies on metagenomics and metatranscriptomics show promise in accelerating the development of diagnostic assays.
CURRENT INFECTIOUS DISEASE REPORTS
(2023)
Review
Biochemical Research Methods
Matteo Comin, Barbara Di Camillo, Cinzia Pizzi, Fabio Vandin
Summary: The study of microbial communities relies on comparing metagenomic next-generation sequencing data sets, facing challenges such as species identification and quantification, computation of distances between samples, and identification of features associated with a phenotype. Solutions involve reference-based methods using a database of reference genomes and reference-free methods working directly on sequencing reads.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Medicine, Legal
Shubham Yadav, Vijay Tripathi, Vaibhav Saran
Summary: Characterization of human saliva through Next-Generation Sequencing has revealed the influence of habits, such as smoking, alcohol consumption, and vegan diet, on the microbial composition and diversity of the salivary microbiome.
FORENSIC SCIENCE INTERNATIONAL
(2023)
Review
Biochemistry & Molecular Biology
Konstantina Athanasopoulou, Panagiotis G. G. Adamopoulos, Andreas Scorilas
Summary: Over 10(14) symbiotic microorganisms in a healthy human body are responsible for important synthesis and support of the immune system. However, microbial deregulation can lead to various diseases. The human gastrointestinal tract is a favorable environment for diverse microbes. The gut microbiome, the largest microbiome community in the human body, has been extensively studied for its medical significance. Advances in sequencing techniques have enabled the detection of microbiomes and opened new avenues in studying human microbiota. The present review emphasizes the complexity of the gastrointestinal tract microbiome and its implications in cellular homeostasis and human diseases.