Article
Engineering, Chemical
Mikhail Y. Syromyatnikov, Ekaterina Y. Nesterova, Maria Gladkikh, Anna A. Tolkacheva, Olga Bondareva, Vladimir M. Syrov, Nina A. Pryakhina, Vasily N. Popov
Summary: This study demonstrates the use of high-throughput sequencing for quality control and safety evaluation of microbial bioformulations, revealing discrepancies between the actual bacterial composition and what is declared by the manufacturers in some samples.
Article
Microbiology
Xinfu Li, Qiang Xiong, Hui Zhou, Baocai Xu, Yun Sun
Summary: By investigating the microbial communities on sterilized smoked bacon, it was found that bacterial counts increased significantly within the first 15 days of storage, with the microbiota developing into more similar communities over time. At the end of the storage period, samples inoculated with Serratia liquefaciens had the highest abundance of the bacterium, while samples inoculated with Carnobacterium maltaromaticum and Leuconostoc mesenteroides showed sharp increases in abundance of these species.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Heng Zheng, Peng Zhang, Jing Qin, Jiani Guo, Jun Deng
Summary: This study used high-throughput sequencing to analyze the diversity and community structures of endophytic bacteria in Gastrodia elata tuber. A total of 1,265 endophytic ASVs were found, and the core microbiota were identified. The study also found that the beta diversity of endophytic bacteria in Gastrodia elata tuber was higher in the Guizhou region compared to the Hubei region.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Agriculture, Dairy & Animal Science
Lufen Feng, Chongmiao Zhu, Pengke Xia, Hongyu Wang, Yong Su, Weiyun Zhu
Summary: Using high-throughput sequencing, this study investigated the development of intestinal lactic acid bacteria (LAB) in piglets. The results showed significant changes in the structure and predominant species of LAB from birth to weaning, which is of great significance for understanding the impact of LAB on the health of piglets.
ANIMAL BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
K. Snehaa, Taru Singh, Sajad Ahmad Dar, Shafiul Haque, Vishnampettai G. Ramachandran, Rumpa Saha, Dheeraj Shah, Shukla Das
Summary: This study investigated the prevalence and regional variation of EPEC in paediatric population suffering from diarrhea in East Delhi, India, showing a changing trend of aEPEC over tEPEC in children less than 5 years with diarrhea, emerging as a drug resistant enteropathogen.
BIOMEDICAL JOURNAL
(2021)
Article
Agriculture, Dairy & Animal Science
Guanjie Lu, Zhe Wang, Baofeng Zhang, Zhichao Zhou, Defu Hu, Dong Zhang
Summary: This study used high-throughput 16S rRNA sequencing technology to identify the types and abundance of pathogenic bacteria in abscess disease samples. It found that the dominant pathogenic bacteria were Trueperella pyogenes, Fusobacterium necrophorum, and Bacteroides fragilis. The study also suggested that high-throughput sequencing technology has the potential to replace traditional bacterial culture and targeted PCR methods.
Article
Food Science & Technology
Ye Won Hong, Ga-Hee Ban, Dongryeoul Bae, Sun Ae Kim
Summary: This study investigated the microbial communities of olive flounder and related environmental samples from six different sources. The results showed that the composition of fish microbiomes was influenced by geographical location and the stages of the supply chain, and certain bacteria were closely associated with sanitation control. This study provides important insights into the olive flounder and its environmental microbiomes, and suggests control measures to improve food safety.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Marie-Pierre Chapuis, Laure Benoit, Maxime Galan
Summary: Obtaining high-quality nucleic acids is crucial for studying bacterial communities associated with animal hosts. This study compared five DNA extraction protocols for animal samples using different methods, including mechanical or enzymatic lysis. The results showed that none of the methods fully eliminated bias, but one method with enzymatic lysis had lower bias. Standardization of DNA extraction is important for comparing microbiome results across different samples.
MOLECULAR ECOLOGY RESOURCES
(2023)
Review
Microbiology
Tara E. Ness, Andrew DiNardo, Maha R. Farhat
Summary: High throughput sequencing (HTS) can detect the presence of Mycobacterium tuberculosis DNA in clinical samples and provide information on drug susceptibility. Multiple studies have laid the groundwork for exploring the clinical application of HTS in tuberculosis diagnosis. This article presents the workflow challenges, strengths, and limitations of different sequencing platforms, as well as the tools used for analysis, to provide a framework for further innovations in the field.
Article
Food Science & Technology
Mikhail Syromyatnikov, Ekaterina Nesterova, Maria Gladkikh, Vasily Popov
Summary: The unregulated probiotic market can have serious health consequences. High-throughput sequencing was used to analyze commercially available probiotics, revealing the presence of additional bacterial genera not declared by the manufacturers. These changes in bacterial composition can negatively impact the taste, storage, and transportation of products, as well as the health benefits for humans.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Review
Medicine, General & Internal
Xuejun He, Ningzhi Zhang, Wenye Cao, Yiqiao Xing, Ning Yang
Summary: Advancements in high-throughput sequencing (HTS) technology have provided new insights into the etiology, signaling pathways, and biomarkers of ocular diseases, aiding in improving their diagnosis and research.
JOURNAL OF CLINICAL MEDICINE
(2022)
Article
Biotechnology & Applied Microbiology
Ying Qi, Sheng-qi Zang, Juan Wei, Hong-chuan Yu, Zhao Yang, Hui-min Wu, Ying Kang, Hui Tao, Miao-fang Yang, Lei Jin, Ke Zen, Fang-Yu Wang
Summary: The study evaluated variations in salivary microbiota in IBD patients and healthy controls, finding dysbiosis in IBD characterized by changes in microbiota biodiversity and composition, and significant increases in certain oral biofilm-forming bacteria. Levels of inflammatory cytokines associated with IBD were also found to be elevated and correlated with specific bacteria, with functional variations identified in genetic information processing, carbohydrate metabolism, and protein processing in endoplasmic reticulum in IBD.
Article
Food Science & Technology
Li Zhang, Ying Wang, Yunhao Ma, Jieying Deng, Yongsheng Ni, Baocai Xu
Summary: Culture-dependent methods and high-throughput sequencing technology were used to analyze the spoilage bacteria in braised chickens stored at low temperature. The bacterial diversity decreased while the relative abundance increased during storage. Lactobacillus, Brochothrix, Leuconostoc, Carnobacterium, and Enterobacteriaceae were found to be the dominant microorganisms. By using the random forest method, the source of the samples could be accurately predicted at different taxonomic levels with high accuracy.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Aziz M. Al'Khafaji, Jonathan T. Smith, Kiran V. Garimella, Mehrtash Babadi, Victoria Popic, Moshe Sade-Feldman, Michael Gatzen, Siranush Sarkizova, Marc A. Schwartz, Emily M. Blaum, Allyson Day, Maura Costello, Tera Bowers, Stacey Gabriel, Eric Banks, Anthony A. Philippakis, Genevieve M. Boland, Paul C. Blainey, Nir Hacohen
Summary: Full-length RNA-sequencing methods using long-read technologies are limited in throughput. We introduce MAS-ISO-seq, a technique that programmably concatenates cDNAs for long-read sequencing, increasing throughput by >15-fold to nearly 40 million cDNA reads per run. Applied to single-cell RNA sequencing of tumor-infiltrating T cells, MAS-ISO-seq showed a 12- to 32-fold increase in the discovery of differentially spliced genes.
NATURE BIOTECHNOLOGY
(2023)
Article
Biology
James K. Bonfield, John Marshall, Petr Danecek, Heng Li, Valeriu Ohan, Andrew Whitwham, Thomas Keane, Robert M. Davies
Summary: This paper introduces a software library for programmatic access to sequencing alignment and variant formats, derived from SAMtools and BCFtools applications, with many improvements and new features added. Performance has significantly improved since the original Samtools release, with wide adoption and integration into different languages.