Article
Biotechnology & Applied Microbiology
Stephan Schmeing, Mark D. Robinson
Summary: In high-throughput sequencing data, performance comparisons between computational tools are crucial, and ReSeq improves the authenticity of synthetic data by including systematic errors, a fragment-based coverage model, and sampling-matrix estimates based on two-dimensional margins, leading to more accurate performance evaluations.
Article
Environmental Sciences
Weizhi Yan, Na Wang, Dong Wei, Chengyu Liang, Xiaomiao Chen, Li Liu, Jiping Shi
Summary: This study used high-throughput sequencing technology to investigate the microbial community structure and diversity in a cattle farm wastewater treatment plant, revealing significant impacts of different stages on microbial community structure. The results also showed that total phosphorus is the most important factor regulating microbial community composition, and nitrogen metabolic pathway and transformation mechanism were elucidated.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2021)
Article
Food Science & Technology
Xiaoyu Xu, Yuanyuan Miao, Huan Wang, Juan Du, Chenqiang Wang, Xuewei Shi, Bin Wang
Summary: This study utilized high-throughput sequencing and high-performance liquid chromatography to investigate the diversity of epiphytic microbial communities and physicochemical indicators in different wine grape varieties. The results showed that the grape variety significantly influences the structure of surface microbial communities.
Article
Genetics & Heredity
Nasserdine Papa Mze, Idir Kacel, Mamadou Beye, Raphael Tola, Mariema Sarr, Leonardo Basco, Herve Bogreau, Philippe Colson, Pierre-Edouard Fournier
Summary: A rapid and cost-effective sequencing protocol is proposed to validate its reliability by comparing the SARS-CoV-2 genome sequences obtained using the modified Illumina COVIDSeq protocol with the standard protocol. The modified protocol saves time and costs, providing high-quality results comparable to the standard protocol.
Article
Microbiology
Hiu-Yin Lao, Timothy Ting-Leung Ng, Ryan Yik-Lam Wong, Celia Sze-Ting Wong, Lam-Kwong Lee, Denise Sze-Hang Wong, Chloe Toi-Mei Chan, Stephanie Hoi-Ching Jim, Jake Siu-Lun Leung, Hazel Wing-Hei Lo, Ivan Tak-Fai Wong, Miranda Chong-Yee Yau, Jimmy Yiu-Wing Lam, Alan Ka-Lun Wu, Gilman Kit-Hang Siu
Summary: In this study, two 16S rRNA gene sequencing tests based on the Illumina and Nanopore sequencing technologies were compared to identify clinical isolates that cannot be identified by MALDI-TOF MS. The results showed that the Nanopore workflow had a higher taxonomic resolution at the species level.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Rose Chinly Mae H. Ortega, Sharon Rose M. Tabugo, Joey Genevieve T. Martinez, Chinee S. Padasas, Jose L. Balcazar
Summary: This study assessed the bacterial community structure in the skin of Barbour's seahorses, with a focus on the Aeromonadaceae family. The presence of Aeromonas genus in the seahorses' skin and its relationship with the surrounding sediment were analyzed. The findings provide baseline information for future research on the role of Aeromonas species in seahorse microbiota and health. Importance rating: 7 out of 10.
Article
Orthopedics
Du Wang, Qingcong Zheng, Qi Lv, Yuanqing Cai, Yun Zheng, Huidong Chen, Wenming Zhang
Summary: The study characterized seawater bacterioplankton communities in Changle city using Illumina MiSeq sequencing and bacterial culture techniques. The predominant bacteria phyla included Cyanobacteria, Proteobacteria, and Bacteroidetes. Assessing the biodiversity of seawater bacterioplankton helps in understanding their composition and differences.
ORTHOPAEDIC SURGERY
(2022)
Article
Fisheries
Yufeng Si, Jinxuan Wen, Yao Xu, Patarida Roengjit, Hao Wang
Summary: The 16S rRNA high throughput sequencing technology is increasingly used to discover pathogenic bacteria, with Edwardsiella identified as the main causative pathogen in the diseased turbot outbreak in China. This cost-effective and rapid technology helps in accurate pathogen identification and disease research.
AQUACULTURE REPORTS
(2021)
Article
Genetics & Heredity
Daniela Gaio, Kay Anantanawat, Joyce To, Michael Liu, Leigh Monahan, Aaron E. Darling
Summary: We developed a low-cost method called Hackflex for generating Illumina-compatible sequencing libraries, which can produce up to 14 times more libraries for the same cost compared to the standard Nextera Flex protocol. The libraries generated using Hackflex showed high-quality and uniform coverage. We also introduced new sample barcodes that can be multiplexed with standard Illumina barcodes. This method allows researchers to construct more libraries within a given budget, enabling more data and facilitating research programs that require sequencing of large numbers of libraries.
MICROBIAL GENOMICS
(2022)
Article
Biotechnology & Applied Microbiology
S. Vishnupriya, T. Jabir, K. P. Krishnan, A. A. Mohamed Hatha
Summary: Kongsfjorden, an Arctic fjord, is experiencing changes in bacterial community structure of sediments due to glacier melt and Atlantification driven by accelerated warming in the Arctic. The dominant phyla in the sediments are Proteobacteria, Bacteroidetes, and Epsilonbacteraeota, with alpha- and gamma-Proteobacteria class dominating in surface sediments and delta-Proteobacteria in subsurface sediments. Total organic carbon is suggested to be a major factor affecting bacterial diversity, and bacterial communities are predicted to be involved in the degradation of complex organic compounds and biosynthesis of secondary metabolites.
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yiran Hou, Rui Jia, Bing Li, Jian Zhu
Summary: This study investigated the effects of apex predators on bacterioplankton communities in aquaculture ponds and revealed the differences in composition and function, as well as the mechanisms of assembly. The results showed that apex predators increased the abundance of organic matter degradation bacteria and decreased pathogens. Furthermore, apex predator disturbances increased environmental adaptation and reduced functional redundancy and stability in bacterioplankton communities.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Claudia Gutierrez-Garcia, Shiek S. S. J. Ahmed, Sathishkumar Ramalingam, Dhivya Selvaraj, Aashish Srivastava, Sujay Paul, Ashutosh Sharma
Summary: This study utilized high-throughput sequencing technology to analyze the miRNA profile of Murraya koenigii and identified miRNAs associated with secondary metabolite biosynthesis. The results showed that these miRNAs targeted key enzymes in the terpenoid backbone and flavonoid biosynthesis pathways. The sequencing results were validated by qPCR. This is the first report of the miRNA profile of Murraya koenigii, providing valuable information for studying the involvement of miRNAs in secondary metabolism.
Article
Food Science & Technology
Ying-Ying Huang, Zhang-Cheng Liang, Xiao-Zi Lin, Zhi-Gang He, Xiang-Yun Ren, Wei-Xin Li, Istvan Molnar
Summary: This study investigated the fungal microbiome compositions of Hong Qu glutinous rice wine and identified key fungi responsible for fermentation characteristics. The findings showed significant differences in fermentation characteristics among different regional varieties of HQ, providing valuable insights for controlling fungal community structures and designing fermentation processes for HQ wines with desirable characteristics.
FOOD RESEARCH INTERNATIONAL
(2021)
Article
Engineering, Chemical
Wanting Li, Jie Cui, Jiafeng Li, Jian Guo, Tao Huang, Jiaojiao Zhang, Hao Hu, Xingquan Liu
Summary: This study collected rice samples from granaries in different directions and storage time. High-throughput ITS sequencing analysis revealed the changes in fungi community during rice storage, with Ascomycota, Basidiomycota, and Mucoromycota as the main fungi present. Aspergillus sp. was the predominant fungi, and other fungi species varied during storage. The study highlighted the importance of improving granary ventilation systems and maintaining a uniform atmosphere to control fungi growth.
Article
Agronomy
Lumeng Chao, Xiaodan Ma, Munkhzul Tsetsegmaa, Yaxin Zheng, Hanting Qu, Yuan Dai, Jingpeng Li, Yuying Bao
Summary: This study investigated the changes in soil microbial communities during grassland degradation and the role of these communities in vegetation restoration succession. The results showed that pH was the most critical factor affecting soil microbial communities in severely degraded grassland, while soil moisture content and soil enzyme activities had a greater impact in non-degraded and less degraded grasslands. The findings provide valuable information for reducing grassland degradation and promoting vegetation restoration succession.