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
Immunology
Xiao-guang Cao, Shu-sheng Zhou, Chun-yan Wang, Kui Jin, Hua-dong Meng
Summary: This study demonstrates that NGS is accurate and efficient in diagnosing sepsis, and the combination of NGS and ALB for early screening is more effective. NGS and ALB are identified as independent prediction factors for sepsis, with the combined diagnostic approach being more accurate.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Ecology
Zi-Wen Yang, Yu Men, Jing Zhang, Zhi-Hui Liu, Jiu-Yang Luo, Yan-Hui Wang, Wen-Jun Li, Qiang Xie
Summary: The study found that air dried preservation method had poor effects on insect microbiome samples, while RNAlater was not suitable for longer field works. CTAB and ethanol were recommended as more effective and cost-efficient preservatives. Additionally, NGS sequencing of the V4 region of the 16S rRNA gene had lower resolution compared to TGS sequencing, potentially leading to misestimations of microbial community compositions.
Article
Immunology
Min Kong, Wei Li, Qingsheng Kong, Haixin Dong, Aizhong Han, Liqing Jiang
Summary: This study describes a case of a child infected with tuberculosis after being wounded. The use of metagenomic next-generation sequencing (mNGS) helped in identifying the specific pathogen and facilitating early treatment, leading to improved prognosis.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Review
Infectious Diseases
Koay Chun Giok, Rohit Kunnath Menon
Summary: It is beneficial to use mechanical debridement augmented with antibiotics for the treatment of peri-implantitis. The microbial profile plays a key role in selecting the appropriate antibiotics. Further studies with standardization and universal clinical parameters are needed for a better understanding of peri-implantitis.
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)
Article
Immunology
Jiachun Su, Xu Han, Xiaogang Xu, Wenchao Ding, Ming Li, Weiqin Wang, Mi Tian, Xiyuan Chen, Binbin Xu, Zhongqing Chen, Jinyi Yuan, Xiaohua Qin, Dongfang Lin, Ruilan Wang, Ye Gong, Liping Pan, Jun Wang, Minggui Wang
Summary: The clinical value of using metagenomic next-generation sequencing (mNGS) to detect tumors in patients with suspected infections has been demonstrated.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Medical Laboratory Technology
Chendi Jing, Hongbin Chen, Yong Liang, Ying Zhong, Qi Wang, Lifeng Li, Shijun Sun, Yifan Guo, Ruobing Wang, Zhi Jiang, Hui Wang
Summary: The mNGS workflow showed a high clinical sensitivity of 87.1%, improved clinical specificity of 80.2%, and reduced false-positive results by utilizing multiple control groups. This optimization can enhance the utility of mNGS as a powerful tool for identifying pathogens in bloodstream infections.
CLINICAL CHEMISTRY
(2021)
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
Medical Laboratory Technology
Zhenli Diao, Yuanfeng Zhang, Yuqing Chen, Yanxi Han, Lu Chang, Yu Ma, Lei Feng, Tao Huang, Rui Zhang, Jinming Li
Summary: This study evaluated the performance of mNGS assays in detecting pathogens in lower respiratory infections and identified sources of false-positive and false-negative results. The findings provide valuable insights for the improvement of method development and quality control in clinical mNGS laboratories.
CLINICAL CHEMISTRY
(2023)
Article
Ophthalmology
Junfeng Zhu, Honghe Xia, Ruqing Tang, Tsz Kin Ng, Fen Yao, Xulong Liao, Qi Zhang, Xixuan Ke, Tingkun Shi, Haoyu Chen
Summary: This study investigated the use of metagenomic next-generation sequencing (mNGS) in identifying pathogens in endophthalmitis. The results showed that mNGS had a higher positive rate than traditional culture methods and could provide information on antibiotic resistance and visual prognosis.
RETINA-THE JOURNAL OF RETINAL AND VITREOUS DISEASES
(2022)
Review
Biology
Heena Satam, Kandarp Joshi, Upasana Mangrolia, Sanober Waghoo, Gulnaz Zaidi, Shravani Rawool, Ritesh P. Thakare, Shahid Banday, Alok K. Mishra, Gautam Das, Sunil K. Malonia
Summary: Next-generation sequencing (NGS) is a powerful tool that can sequence millions of DNA fragments simultaneously, providing detailed information about genomes, genetic variations, gene activity, and changes in gene behavior. Recent advancements have focused on improving sequencing speed and accuracy, reducing costs, and enhancing data analysis. These advancements have great potential for advancing genomics research and improving our understanding of diseases and personalized healthcare.
Article
Immunology
Chengxin Liu, Juhua Yang, Huiting Huang, Shaofeng Zhan, Xintian Xia
Summary: Infection of Nocardia gipuzkoensis is a relatively uncommon form of pulmonary nocardiosis, usually occurring in patients with immune deficiency. We report a case of a 23-year-old female with a 10-year history of cough and sputum production, diagnosed with bronchiectasis. The infection was identified using metagenomic next-generation sequencing and whole genome sequencing, and was controlled with appropriate medication.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemical Research Methods
Brendan O'Fallon, Jacob Durtschi, Ana Kellogg, Tracey Lewis, Devin Close, Hunter Best
Summary: This study proposes two algorithmic adaptations to improve the accuracy of CNV detection in a Hidden Markov Model (HMM) context. First, it improves the accuracy by computing target- and copy number-specific emission distributions. Second, it enhances the sensitivity for small CNV calls using the Pointwise Maximum a posteriori (PMAP) HMM decoding procedure. The prototype implementation, called Cobalt, shows similar sensitivity to other CNV detection tools but significantly reduces false positive detections.
BMC BIOINFORMATICS
(2022)
Article
Urology & Nephrology
Maria Camila Suarez Arbelaez, Joseph M. Israeli, Craig D. Tipton, Justin Loloi, Nicholas Deebel, Joon Yau Leong, Ranjith Ramasamy
Summary: This study investigated the impact of vasectomy on the semen microbiome by comparing semen samples before and after the procedure. It was found that vasectomy resulted in a decrease in microbiome diversity and changes in the relative abundance of bacterial species in semen. Further research is needed to understand the clinical significance of these changes.
EUROPEAN UROLOGY FOCUS
(2023)