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
Microbiology
Hyo-Lim Hong, Laure Flurin, Kerryl E. E. Greenwood-Quaintance, Matthew J. J. Wolf, Bobbi S. S. Pritt, Andrew P. P. Norgan, Robin Patel
Summary: The performance of 16S rRNA gene PCR/sequencing of heart valves was compared with conventional IE diagnostics. The sequencing method can identify pathogens in patients with blood culture-negative IE by analyzing the 16S rRNA gene sequence.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Microbiology
Botond Bendeguz Suranyi, Benjamin Zwirzitz, Csilla Mohacsi-Farkas, Tekla Engelhardt, Konrad J. Domig
Summary: In order to enhance agricultural productivity and feed the growing population, irrigation is crucial. However, the use of poorly characterized water sources increases the prevalence of foodborne diseases. Therefore, analyzing microorganisms in irrigation water can help prevent such cases.
Article
Biotechnology & Applied Microbiology
Sho Shimada, Ryosuke Nakai, Kotaro Aoki, Norifumi Shimoeda, Giichiro Ohno, Sakae Kudoh, Satoshi Imura, Kentaro Watanabe, Yasunari Miyazaki, Yoshikazu Ishii, Kazuhiro Tateda
Summary: In this study, waterborne pathogens, particularly Legionella spp., were analyzed in the Antarctic environment. The results showed a variety of Legionella spp. distributed widely in Antarctica, suggesting diverse unknown species in cold environments. Human-made environments were found to alter the Legionella community, with known pathogenic variants mainly localized in the station.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Jungnam Lee, Hye Jung Jeong, Hanul Kim, Jin-Seok Park
Summary: This study investigates the changes in microbiome compositions and metabolic signature associated with CBD stones. The researchers analyzed the microbial diversity and composition, as well as the metabolic profile of bile samples from patients using DNA sequencing and metabolomics analysis. They also conducted in vivo experiments on mice and observed systemic inflammation and extracellular trap formation in the CBD stone group. The findings highlight the importance of biliary dysbiosis and bile metabolites in CBD stone development and may have implications for diagnostic and therapeutic strategies.
Article
Immunology
Madiha Fida, Sarwat Khalil, Omar Abu Saleh, Douglas W. Challener, Muhammad Rizwan Sohail, Joshua N. Yang, Bobbi S. Pritt, Audrey N. Schuetz, Robin Patel
Summary: This study retrospectively analyzed 566 specimens from 460 patients and found a higher positivity rate of 16S rRNA PCR/sequencing in clinically infected patients with low impact on clinical care. Specimens with positive Gram stain were more likely to have a positive PCR result. Cardiovascular specimens yielded higher PCR positivity, while musculoskeletal specimens were more likely to have positive bacterial cultures.
CLINICAL INFECTIOUS DISEASES
(2021)
Article
Immunology
Jin Li, Qiu Zhong, Mei-Yun Shang, Min Li, Yuan-Su Jiang, Jia-Jun Zou, Shan-Shan Ma, Qing Huang, Wei-Ping Lu
Summary: In this study, a simple and visual device combined with lateral flow strip-based recombinase polymerase amplification (LF-RPA) was developed for the identification of Burkholderia pseudomallei. The LF-RPA assay showed good performance in amplifying target DNA at a temperature range of 30-45 degrees C and completed the entire reaction in a short time. It had a low limit of detection for B. pseudomallei genomic DNA, comparable to real-time PCR. The newly developed LF-RPA system was also successfully used to retrospectively confirm clinical B. pseudomallei isolates.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Microbiology
Laura E. Tibbs-Cortes, Bienvenido W. Tibbs-Cortes, Stephan Schmitz-Esser
Summary: This study analyzed the microbiota of tardigrades from apple orchards in central Iowa, United States, and found that tardigrades have a distinct microbiota from their environment. They also identified tardigrade-associated taxa that belong to genera known to contain phytopathogens. This suggests the presence of putative endosymbionts and phytopathogens in the microbiota of wild tardigrades in North America.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Kerstin Locher, Corrie R. Belanger, Eric Eckbo, Melissa Caza, Billie Velapatino, Marthe K. Charles
Summary: In this study, a fast, simplified, and largely automated protocol for 16S sequencing was validated using 99 clinical bacterial isolates. The protocol combines real-time PCR and automated amplicon sequencing, with sequence analysis and result interpretation performed using an automated R-based script. The protocol achieves a high accuracy rate of nearly 99% compared to routine laboratory identification methods. This simplified sequencing protocol is suitable for frontline clinical microbiology laboratories.
MICROBIOLOGY SPECTRUM
(2022)
Article
Environmental Sciences
R. G. Bulgarelli, M. F. A. Leite, M. De Hollander, P. Mazzafera, S. A. L. Andrade, E. E. Kuramae
Summary: The availability of soil phosphorus can affect plant growth, root-soil interactions, and rhizosphere microbial community composition. This study investigated the rhizosphere microbial communities of 24 species of eucalypts under low or sufficient soil phosphorus availability. It was found that eucalypt species identity was the main factor determining the composition of the rhizosphere microbial community, while the effect of phosphorus availability varied among species.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Microbiology
Annie Wing-Tung Lee, Chloe Toi-Mei Chan, Lily Lok-Yee Wong, Cheuk-Yi Yip, Wing-Tung Lui, Kai-Chun Cheng, Jake Siu-Lun Leung, Lam-Kwong Lee, Ivan Tak-Fai Wong, N. G. Timothy Ting-Leung, Hiu-Yin Lao, Gilman Kit-Hang Siu
Summary: Microbes in the built environment have been identified as a potential source of infectious diseases. The use of long-read taxonomic tools for microbial evaluations using nanopore sequencing has shown promising results. This study analyzed the performance of different taxonomic classifiers for microbial community analysis and provided recommendations for species-level classification and culturable species identification using 16S-nanopore dataset.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Claudie Lamoureux, Laure Surgers, Vincent Fihman, Guillaume Gricourt, Vanessa Demontant, Elisabeth Trawinski, Melissa N'Debi, Camille Gomart, Guilhem Royer, Nathalie Launay, Jeanne-Marie Le Glaunec, Charlotte Wemmert, Giulia La Martire, Geoffrey Rossi, Raphael Lepeule, Jean-Michel Pawlotsky, Christophe Rodriguez, Paul-Louis Woerther
Summary: This study compared the performance of shotgun metagenomics (SMg) and Sanger sequencing in bacterial detection and identification, showing that SMg had significantly better performance at the species level. This technology has the potential to replace Sanger sequencing in infectious disease diagnosis.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Ming -Han Li, Jin-Xin Meng, Wei Wang, Ma He, Zi-Yu Zhao, Ning Ma, Qing-Bo Lv, Yi-Feng Qin, Quan Zhao, Hong -Bo Ni, Xiao-Xuan Zhang
Summary: This study examined the diversity of bacteria and fungi in the gut microbiota of commercial broilers raised in cages. The results showed that the composition of the gut microbiota was influenced by age, with increasing richness and diversity as the broilers grew older. The gut microbiota had a unique structure in the early days after birth, and then underwent significant changes during periods of rapid growth and weight gain. Furthermore, certain bacteria and fungi played key roles in the gut microbiota of broilers, and their loss may impact the intestinal homeostasis of broilers.
Article
Plant Sciences
Mahmoud N. Menshawy, Ahmed M. Abdel-Hamid, Samy K. Mohamed, Mo'men H. El-Katatny
Summary: Nine cellulolytic bacteria were isolated from agricultural residues compost, and five of them showed the ability to degrade cellulose and xylan. These bacteria were also capable of depolymerizing rice straw and sugarcane bagasse. Among them, CX2 and CX9 exhibited the highest production of CMC-ase and xylanase on both substrates.
SOUTH AFRICAN JOURNAL OF BOTANY
(2022)
Article
Agriculture, Dairy & Animal Science
Hui Jiang, Shaoming Fang, Hui Yang, Congying Chen
Summary: This study revealed a close relationship between gut microbiota and residual feed intake in pigs, with specific bacteria such as Ruminococcusflavefaolens enriched in high-FE pigs and Prevotella spp. enriched in high-RFI pigs. Functional analysis showed that the low-RFI pigs had a higher abundance of pathways related to amino acid metabolism, while the high-RFI pigs lacked these pathways.
JOURNAL OF ANIMAL SCIENCE
(2021)