Article
Microbiology
Farnaz Fouladi, Jacqueline B. Young, Anthony A. Fodor
Summary: This study introduces a fast and scalable algorithm for inferring sequence variants in 16S rRNA gene data sets, utilizing a HashMap-based approach and normal distribution combined with LOESS regression. The method is computationally efficient and produces conservative sets of variants well supported by reference databases.
Article
Agriculture, Dairy & Animal Science
Xin Yang, Mingzhe Fu, Zhengqing Yu, Junwei Wang, Junke Song, Guanghui Zhao
Summary: The study in Shaanxi province, northwestern China, reported the occurrence of Anaplasma infection among dairy, cashmere, and meat goats, and identified significant differences in prevalence among production categories, species, regions, and ages. The findings emphasized the urgent need for One Health-based intervention approaches to block the transmission between humans and animals.
Article
Environmental Sciences
Pitchiah Sivaperumal, Kannan Kamala, Kumaran Subramanian, Wilson Aruni, Rajeshkumar Shanmugam, Rajendran Rajaram
Summary: Baseline assessments of marine microbial studies around Nuclear Power Plant (NPP) sites are limited. This study focused on the distribution and diversity of marine actinobacteria and their potential remediation ability. The results showed high diversity of marine actinobacteria, with dominance of the genus Streptomyces, and the identification of a potential strain capable of producing EPS and remediating uranium radionuclides.
ENVIRONMENTAL RESEARCH
(2022)
Article
Ecology
Robert Starke, Victor Satler Pylro, Daniel Kumazawa Morais
Summary: Sequencing 16S rRNA gene amplicons is commonly used to study prokaryotic communities, but gene copy normalization (GCN) does not improve the accuracy of results. The study questions the use of GCN for metataxonomic surveys until a more comprehensive catalogue of copy numbers becomes available.
Article
Biochemistry & Molecular Biology
Yuya Nakamura, Shinya Suzuki, Shinnosuke Murakami, Yuichiro Nishimoto, Koichi Higashi, Naoki Watarai, Junpei Umetsu, Chiharu Ishii, Yutaro Ito, Yuka Mori, Mamiko Kohno, Takuji Yamada, Shinji Fukuda
Summary: This study investigated the intestinal microbiome and metabolome profiles related to the effectiveness of B. longum BB536 supplementation in increasing bowel movement frequency. The findings suggest that these profiles might be used as potential markers for improved bowel movement after B. longum BB536 supplementation.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biotechnology & Applied Microbiology
Suchi Parvin Biki, Shobuz Mahmud, Sumaia Akhter, Md Jiaur Rahman, Jessica J. Rix, Md Adnan Al Bachchu, Maruf Ahmed
Summary: In this study, bacteria were separated from landfill soil and their ability to degrade LDPE was evaluated. Ralstonia sp. strain SKM2 and Bacillus sp. strain SM1 were identified as effective LDPE-degrading microorganisms, causing weight loss and pH changes in the media. Structural changes in LDPE sheet were observed under microscope and FTIR analysis showed alterations in carbon bonds and groups.
ENVIRONMENTAL TECHNOLOGY & INNOVATION
(2021)
Article
Microbiology
Richard Bigge, Boyke Bunk, Wolfram W. Rudolph, Florian Gunzer, Sina M. Coldewey, Thomas Riedel, Percy Schroettner
Summary: Recent publications show that A. radioresistens can cause infections in humans, although it is rarely reported in routine diagnostics. This might be due to misidentification by conventional methods and the lack of clinical relevance and consistent inclusion in diagnostic results. To investigate the medical significance of this bacterium and establish reliable identification methods, a collection of 21 well-documented reference strains was created. Comparison of three widely used methods (MALDI-TOF MS, VITEK 2, and sequencing of housekeeping genes) revealed that MALDI-TOF MS and sequencing of housekeeping genes provide secure and reliable identification of A. radioresistens, while VITEK 2 resulted in misidentification for some strains.
Article
Immunology
Kai Xia, Renyuan Gao, Xiaocai Wu, Jing Sun, Jian Wan, Tianqi Wu, Jakub Fichna, Lu Yin, Chunqiu Chen
Summary: Crohn's disease (CD) is a chronic inflammatory bowel disease with an increasing global incidence. Microbial dysbiosis has been recognized as a key factor contributing to CD. This study found distinct microbial dysbiosis in the oral cavity, sputum, and ileum of CD patients, with alterations in microbiota diversity and composition. Additionally, the microbiota changes varied across disease stages.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Immunology
Yinhua Huang, Zhijie Wang, Hongjie Ma, Shangli Ji, Zhongping Chen, Zekai Cui, Jiansu Chen, Shibo Tang
Summary: The study revealed compositional alterations of gut microbiota in patients with type 2 diabetes and diabetic retinopathy, as well as identified bacterial families that could distinguish different groups, which might serve as non-invasive biomarkers for clinical and differential diagnosis.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Gastroenterology & Hepatology
Jinhuan Yang, Qikuan He, Fei Lu, Kaiwen Chen, ZhiHao Ni, Haoyue Wang, Chen Zhou, Yaosheng Zhang, Bo Chen, Zhiyuan Bo, Jialiang Li, Haitao Yu, Yi Wang, Gang Chen
Summary: Oral, gut, and tumor microbiota play important roles in gastrointestinal malignancies such as hepatocellular carcinoma (HCC). This study aims to investigate the durability of the oral-gut-tumor microbiome and its diagnostic performance in HCC. The results show that specific oral and gut genera can distinguish HCC from controls, with improved diagnostic performance when combined with serum levels of alpha-fetoprotein (AFP). In addition, dominant microbiota species were confirmed in hepatic tumor and non-tumor tissues.
Article
Microbiology
Hubiao Jiang, Xinyan Xu, Yuan Fang, Solabomi Olaitan Ogunyemi, Temoor Ahmed, Xuqing Li, Yong Yang, Chengqi Yan, Jianping Chen, Bin Li
Summary: In this study, 16S rRNA gene amplicon sequencing was used to investigate the impact of rice bacterial leaf blight (BLB) on the rice rhizosphere microbial community. The results showed that the alpha diversity index of the microbial community decreased significantly during the onset of BLB and gradually recovered to normal levels. Beta diversity analysis indicated that BLB had a significant effect on community composition. Furthermore, there were significant differences in the taxonomic composition between healthy and diseased groups, with certain genera being more abundant in diseased rhizospheres such as Streptomyces, Sphingomonas, and Flavobacterium. Additionally, the size and complexity of the rhizosphere co-occurrence network increased after disease onset, and hub microbes like Rhizobiaceae and Gemmatimonadaceae played important roles in maintaining network stability. Overall, this study provides important insights into the response of the rhizosphere microbial community to BLB and offers valuable data and ideas for using rhizosphere microbes to control BLB.
MICROBIOLOGICAL RESEARCH
(2023)
Article
Parasitology
Sandor Hornok, Andrei D. Mihalca, Jeno Kontschan, Nora Takacs, Denis Fedorov, Olivier Plantard, Attila D. Sandor
Summary: This study provides high-resolution digital pictures and molecular data of male and female I. rugicollis for the first time, and morphological comparison with I. cornutus could not resolve uncertainties in the latter species' validity. Further molecular comparisons with new specimens of I. cornutus are needed to confirm its status. This study represents the first comprehensive molecular phylogenetic analysis of western Palearctic Pholeoixodes species, including I. rugicollis, and confirms the phylogenetic position of the subgenus Eschatocephalus within Pholeoixodes.
PARASITES & VECTORS
(2023)
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
Plant Sciences
Carmen Haro, Manuel Anguita-Maeso, Madis Metsis, Juan A. Navas-Cortes, Blanca B. Landa
Summary: The study assessed the impact of different DNA extraction kits and primer pairs on bacterial community assessment in olive xylem sap, indicating that the choice of extraction method significantly influences the results.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Microbiology
Rui Yin, Yan-Jun Yi, Zhuo Chen, Guan-Jun Chen, Yan-Xia Zhou, Zong-Jun Du
Summary: A novel Gram-negative bacterium, Flavihalobacter algicola gen. nov., sp. nov., designated Dm15(T), isolated from marine alga in Weihai, China, showed unique characteristics such as growth at a wide range of temperature and salinity, as well as the ability to degrade alginate. It represents a distinct lineage within the family Flavobacteriaceae, with specific genes for cellulase and alginate lyase contributing to its phenotypic characteristics.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Shin Ae Lee, Yiseul Kim, Mee-Kyung Sang, Jaekyeong Song, Soon-Wo Kwon, Hang-Yeon Weon
JOURNAL OF MICROBIOLOGY
(2019)
Article
Multidisciplinary Sciences
Yong-Hak Kim, Yunhee Choi, Yu Yeong Oh, Nam-Chul Ha, Jaekyeong Song
Article
Microbiology
Jun Heo, Moriyuki Hamada, Hayoung Cho, Hang-Yeon Weon, Jeong-Seon Kim, Seong-Beom Hong, Soo-Jin Kim, Soon-Wo Kwon
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2019)
Article
Microbiology
Jun Heo, Hang-Yeon Weon, Hayoung Cho, Seung-Beom Hong, Jeong-Seon Kim, Soo-Jin Kim, Soon-Wo Kwon
JOURNAL OF MICROBIOLOGY
(2020)
Article
Biotechnology & Applied Microbiology
Cheol Lee, Juhwan Lee, Hyunho Cho, Jaekyeong Song, Hojung Jung, Xiao Ma, Jihyo Hwang
BIOMED RESEARCH INTERNATIONAL
(2019)
Article
Microbiology
Munusamy Madhaiyan, Venkatakrishnan Sivaraj Saravanan, Jochen Blom, Theo H. M. Smits, Fabio Rezzonico, Soo-Jin Kim, Hang-Yeon Weon, Soon-Wo Kwon, William B. Whitman, Lianghui Ji
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2020)
Article
Microbiology
Shin Ae Lee, Jun Heo, Tae-Wan Kim, Mee-Kyung Sang, Jaekyeong Song, Soon-Wo Kwon, Hang-Yeon Weon
Summary: A novel bacterium, designated as Chitinophaga agrispecies, was isolated from reclaimed land soil in the Republic of Korea. Phylogenetic and physiological analysis supported its affiliation to the Chitinophaga genus. This bacterium exhibited specific characteristics in terms of growth conditions, genome content, and fatty acid composition.
ARCHIVES OF MICROBIOLOGY
(2021)
Article
Microbiology
Shin Ae Lee, Jun Heo, Tae-Wan Kim, Mee-Kyung Sang, Jaekyeong Song, Soon-Wo Kwon, Hang-Yeon Weon
CURRENT MICROBIOLOGY
(2020)
Article
Microbiology
Shin Ae Lee, Tae-Wan Kim, Jun Heo, Mee-Kyung Sang, Jaekyeong Song, Soon-Wo Kwon, Hang-Yeon Weon
JOURNAL OF MICROBIOLOGY
(2020)
Correction
Microbiology
Ohgew Kweon, Seong-Jae Kim, James P. Freeman, Jaekyeong Song, Songjoon Baek, Carl E. Cerniglia
Article
Multidisciplinary Sciences
Shin Ae Lee, Jeong Myeong Kim, Yiseul Kim, Jae-Ho Joa, Seong-Soo Kang, Jae-Hyung Ahn, Mincheol Kim, Jaekyeong Song, Hang-Yeon Weon
SCIENTIFIC REPORTS
(2020)
Article
Microbiology
Shin Ae Lee, Tae-Wan Kim, Mee-Kyung Sang, Jaekyeong Song, Soon-Wo Kwon, Hang-Yeon Weon
Summary: KIS59-12(T) is a novel bacterium isolated from soil in Hodo island, Boryeong, Republic of Korea, belonging to the genus Arachidicoccus and proposed to be named Arachidicoccus soli sp. nov. It shares high sequence similarities with other Arachidicoccus species, while showing differences in genomic and chemotaxonomic characteristics.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Biology
Yunhee Choi, Ha Pham, Mai Phuong Nguyen, Le Viet Ha Tran, Jueun Kim, Songhwa Kim, Chul Won Lee, Jaekyeong Song, Yong-Hak Kim
Summary: The conjugative plasmid pBV71 plays a crucial role in promoting cell morphogenesis, biofilm formation, and antibiotic resistance in Bacillus velezensis strain GH1-13. Cells with or without pBV71 exhibit different phenotypes and antibiotic sensitivities.
COMMUNICATIONS BIOLOGY
(2021)
Article
Agriculture, Multidisciplinary
Sung-Je Yoo, Hang-Yeon Weon, Jaekyeong Song, Mee Kyung Sang
INTERNATIONAL JOURNAL OF AGRICULTURE AND BIOLOGY
(2020)
Article
Agriculture, Multidisciplinary
Da Jeong Shin, Sung-Je Yoo, Jeum Kyu Hong, Hang-Yeon Weon, Jaekyeong Song, Mee Kyung Sang
PLANT PATHOLOGY JOURNAL
(2019)
