Article
Microbiology
Alexander Koliada, Vladislav Moseiko, Mariana Romanenko, Oleh Lushchak, Nadiia Kryzhanovska, Vitaly Guryanov, Alexander Vaiserman
Summary: Sex-specific differences in the phylum-level intestinal microbiota composition were observed in the Ukraine population, with females having significantly increased relative abundances of Firmicutes and Actinobacteria, while decreased Bacteroidetes compared to males. The Firmicutes to Bacteroidetes ratio was significantly higher in females, with the difference being more pronounced in individuals aged 50 years and older. Further investigation is needed to understand the mechanistic basis for these sex-specific differences in gut microbiota composition and their potential role in the development of chronic diseases.
Article
Biotechnology & Applied Microbiology
Polina Beskrovnaya, Doaa Fakih, Isabelle Morneau, Ameena Hashimi, Dainelys Guadarrama Bello, Shipei Xing, Antonio Nanci, Tao Huan, Elitza Tocheva
Summary: Endospore formation was not confirmed in Rhodobacter johrii and Serratia marcescens, with phase-bright structures identified as triacylglycerol storage granules and cellular debris aggregates, respectively. This study concludes that endospore formation remains exclusive to the phylum Firmicutes.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Sandra Alvarez-Carretero, Asif U. Tamuri, Matteo Battini, Fabricia F. Nascimento, Emily Carlisle, Robert J. Asher, Ziheng Yang, Philip C. J. Donoghue, Mario dos Reis
Summary: A Bayesian molecular-clock dating approach was developed to estimate a timetree of 4,705 mammal species using information from 72 mammal genomes. Larger phylogenomic datasets produced diversification time estimates with smaller uncertainties, allowing for precise tests of macroevolutionary hypotheses. This approach facilitates the analysis of complete genomes and thousands of species within an integrated framework to address previously intractable research questions on species diversifications.
Article
Plant Sciences
Kyu Tae Park, SeonJoo Park
Summary: The study characterized the complete chloroplast genomes of Hepatica, identifying unique gene features and selection pressures. Comparative analyses revealed insights into the phylogenetic relationships of Hepatica and its relatives through multiple comparisons and gene loss events.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Evolutionary Biology
Michael J. Sanderson, Alberto Burquez, Dario Copetti, Michelle M. McMahon, Yichao Zeng, Martin F. Wojciechowski
Summary: The study analyzes the phylogenetic structure within a species by using genome sequencing data of the saguaro cactus, revealing well-resolved and consistent phylogenetic trees across different data sets. The most likely root of the saguaro cactus is inferred to be in the east and south, supporting hypotheses of postglacial expansion. The study highlights the importance of using SNP-based methods for phylogenomic analysis within species, especially when gene flow and linkage effects are present.
SYSTEMATIC BIOLOGY
(2022)
Article
Plant Sciences
Shun Liu, Mattia Storti, Giovanni Finazzi, Chris Bowler, Richard G. G. Dorrell
Summary: Diatoms, an important group of algae, contribute significantly to marine photosynthetic activity. This study analyzed the plastid transporters in diatoms and discovered both similarities and differences compared to plant plastid transporters. Diatom-specific transporter functions, related to carbon and amino acid transport and plastid-mitochondria crosstalk, were identified. Environmental data also suggested that plastid transporters may play a role in diatom sensitivity to ocean warming.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Manuela Thienel, Johannes B. Mueller-Reif, Zhe Zhang, Vincent Ehreiser, Judith Huth, Khrystyna Shchurovska, Badr Kilani, Lisa Schweizer, Philipp E. Geyer, Maximilian Zwiebel, Julia Novotny, Enzo Luesebrink, Gemma Little, Martin Orban, Leo Nicolai, Shaza El Nemr, Anna Titova, Michael Spannagl, Jonas Kindberg, Alina L. Evans, Orpheus Mach, Matthias Vogel, Steffen Tiedt, Steffen Ormanns, Barbara Kessler, Anne Dueck, Andrea Friebe, Peter Godsk Jorgensen, Monir Majzoub-Altweck, Andreas Blutke, Amin Polzin, Konstantin Stark, Stefan Kaab, Doris Maier, Jonathan M. Gibbins, Ulrich Limper, Ole Frobert, Matthias Mann, Steffen Massberg, Tobias Petzold
Summary: This study identified a mechanism of thromboprotection in immobilized brown bears and spinal cord injury patients, involving the down-regulation of heat shock protein 47 (HSP47) in platelets. This resulted in attenuated immune cell activation and neutrophil extracellular trap formation, providing potential therapeutic targets for antithrombotic treatments.
Article
Biodiversity Conservation
Xiaofeng Liu, Junjia Luo, Mingke Zhang, Qiang Wang, Jie Liu, Die Wu, Zhixi Fu
Summary: This study sequenced the chloroplast genomes of two Parasenecio species and compared them with those of other Senecioneae species. The results showed the conservation of chloroplast genome sequences among Parasenecio and related species. Additionally, valuable plastid markers were identified, contributing to super-barcode, phylogenetic, and evolutionary studies of Parasenecio plants.
Article
Environmental Sciences
Xue Yang, Yujuan Xu, Man Jiang, Yukun Wang, Huayu Lu, Yajie Xue, Jinlong Wang, Nianxi Zhao, Yubao Gao
Summary: Biodiversity loss can affect community processes and ecosystem functioning. This study explored the impact of different levels of biodiversity on biomass production in plant communities, finding that dominant genotypic diversity plays an important role in aboveground biomass production. The relationships between community functional diversity and biomass were mostly nonlinear.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Biotechnology & Applied Microbiology
Sachiko Sakamoto, Masaru K. Nobu, Daisuke Mayumi, Satoshi Tamazawa, Hiroyuki Kusada, Hideharu Yonebayashi, Hiroki Iwama, Masayuki Ikarashi, Tatsuki Wakayama, Haruo Maeda, Susumu Sakata, Tomohiro Tamura, Nobuhiko Nomura, Yoichi Kamagata, Hideyuki Tamaki
Summary: A novel anaerobic thermophilic bacterium, strain NRmbB1(T), was isolated from a deep subsurface oil field in Japan. This bacterium showed unique cellular structure, growth conditions, and metabolic pathways. Based on chemotaxonomic, phylogenetic, and genomic characterization, a new genus, family, and order were proposed for this bacterium.
SYSTEMATIC AND APPLIED MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Morgan R. Gostel, Gisela Sancho, Nadia Roque, Mariano Donato, Vicki A. Funk
Summary: This article discusses the evolution of the tribe Gochnatieae in the sunflower family, specifically focusing on its phylogenetic and reproductive characteristics. The study reveals that Gochnatieae consists of nine genera originating from Eastern South America and expanding to other regions through dispersal from the central Andes. The article also highlights the derived reproductive traits associated with complex plant reproductive biology in this tribe.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Ecology
Yongyi Peng, Zijian Lu, Donald Pan, Ling-Dong Shi, Zhao Zhao, Qing Liu, Chuwen Zhang, Kuntong Jia, Jiwei Li, Casey R. J. Hubert, Xiyang Dong
Summary: Through the study of active and extinct stages in the Haima cold seeps area, we found that deep sea cold seep sediments harbor novel, abundant, and diverse bacterial and archaeal viruses. The dynamics of host-virus interactions are determined by diverse antiviral defense systems across different microbial genomes. Cold seep viruses are predicted to have various adaptive strategies to persist in this environment. Extremely low nucleotide diversity is observed in cold seep viral populations, influenced by factors such as microbial host, sediment depth, and cold seep stage. Most cold seep viral genes are under strong purifying selection with trajectories depending on the activity of the cold seeps. This work sheds light on the environmental adaptation mechanisms and evolutionary patterns of viruses in the sub-seafloor biosphere.
Article
Environmental Sciences
Kevin Lopez-Reyes, Luis Osorio-Olvera, Octavio Rojas-Soto, Xavier Chiappa-Carrara, Carlos Patron-Rivero, Carlos Yanez-Arenas
Summary: Modeling units based on phylogenetic relationships and including occurrence records of related species can improve the predictive capacity of niche models for estimating the invasion area of target species, particularly for species in non-environmental pseudo-equilibrium and with geographical constraints.
MARINE ENVIRONMENTAL RESEARCH
(2023)
Article
Multidisciplinary Sciences
Aileen J. Lam, Lu Rao, Yuzu Anazawa, Kyoko Okada, Kyoko Chiba, Mariah Dacy, Shinsuke Niwa, Arne Gennerich, Dan W. Nowakowski, Richard J. McKenney
Summary: KIF1A is a critical motor for cargo transport within neurons, and mutations associated with KAND can significantly affect its microtubule-binding rate. The P305L mutation negatively impacts various biophysical parameters of the motor, with the 310 helix playing a crucial role in maintaining a specific K-loop conformation.
Review
Microbiology
Claire R. Burbick, Erik Munson, Sara D. Lawhon, Amanda Zapp, Maia Villaflor, Elizabeth Thelen
Summary: Increased interest in farmed aquatic species, aquatic conservation measures, and microbial metabolic end-product utilization have led to the need for recognizing and revising novel microbial species and bacterial taxonomy. A 4-year literature review provides lists of novel and revised bacterial species from aquatic hosts, serving as a baseline for future taxonomic revisions. The majority of new and revised taxa are found within oxidase-positive and/or nonglucose fermentative Gram-negative bacilli, including members of the Tenacibaculum, Flavobacterium, and Vibrio genera. Additionally, valid and effectively published members of the Streptococcus, Erysipelothrix, and Photobacterium genera are described from a disease pathogenesis perspective.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Biochemical Research Methods
Yanxia Zhou, Pan Shen, Qiuyan Lan, Chen Deng, Yao Zhang, Yanchang Li, Wei Wei, Yihao Wang, Na Su, Fuchu He, Qiong Xie, Zhitang Lyu, Dong Yang, Ping Xu
Article
Microbiology
Zhitang Lu, Weiwei Zhang
CURRENT MICROBIOLOGY
(2012)
Article
Microbiology
Runlei Yang, Li-Ping Zhang, Li-Ge Guo, Nan Shi, Zhitang Lu, Xiumin Zhang
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2008)
Article
Microbiology
Xiumin Zhang, Li-Ping Zhang, Runlei Yang, Nan Shi, Zhitang Lu, Wen Xin Chen, Cheng-Lin Jiang, Li-Hua Xu
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2008)
Article
Soil Science
Weiwei Zhang, Kai Yang, Zhitang Lyu, Jiaojun Zhu
SOIL BIOLOGY & BIOCHEMISTRY
(2019)
Article
Biochemical Research Methods
Jinshuai Sun, Jiahui Shi, Yihao Wang, Shujia Wu, Liping Zhao, Yanchang Li, Hong Wang, Lei Chang, Zhitan Lyu, Junzhu Wu, Fengsong Liu, Wenjun Li, Fuchu He, Yao Zhang, Ping Xu
JOURNAL OF PROTEOME RESEARCH
(2019)
Article
Microbiology
Lei Sun, Panpan Wang, Dongfang Zhao, Jiashuo Wang, Qiji Wu, Lin Liu, Zhitang Lyu
Summary: Strain R196(T) is a novel species of the genus Paenibacillus, named Paenibacillus cymbidii sp. nov., with distinctive cellular polar lipids and respiratory quinone composition. The genome of R196T contains 7617 predicted protein-coding genes, with a DNA G+C content of 57.7 mol%.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Chao Li, Wuyundalai Bao, Haoyue Zhang, Zhitang Lyu, Yihua Chen, Zhengyan Guo
Summary: This study identified several AFN congeners with effective anti-MRSA activities, highlighting the influence of halogen substitution on the bioactivities of AFNs.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Yanwu Chen, Chong Xu, Chongfa Zhong, Zhitang Lyu, Junlian Liu, Zhanghuang Chen, Huanhuan Dun, Bingmu Xin, Qiong Xie
Summary: This study examined the temporal characteristics of the oropharyngeal and nasal microbiota structure in crewmembers living in a closed environment for 180 days in the Chinese Controlled Ecological Life Support System (CELSS). The results showed significant differences in the microbiota between the oropharynx and nasal cavity, as well as individual differences among occupants. The findings suggest that living in a closed environment for a prolonged period can impact the microbiota structure and diversity of the respiratory tract, with potential migration of microbiota between occupants.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Fang Ye, Xinying Gao, Zhiyi Wang, Shuman Cao, Guangcai Liang, Danni He, Zhitang Lv, Liming Wang, Pengfei Xu, Qi Zhang
Summary: Significant differences in the composition of the gut microbiome were observed between boys with ASD and neurotypical controls in this study, contributing to the understanding of gut microbiome alterations in ASD patients and opening up the possibility for early identification of the disease.
SYNTHETIC AND SYSTEMS BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Zhitang Lyu, Tingting Yu, Lichao Zhang, Xiaona Xu, Yijun Zhang, Jihong Li, Zhirong Li, Wei Zhang, Senlin Hou
Summary: The study revealed that patients with primary CBD stones have a more complex biliary microbiota, with a potential risk of dysbiosis, where the abundance of certain major acid-producing bacteria is significantly decreased, impacting biliary health and leading to stone formation.
SYNTHETIC AND SYSTEMS BIOTECHNOLOGY
(2021)
Article
Soil Science
Weiwei Zhang, Zhitang Lu, Kai Yang, Jiaojun Zhu
APPLIED SOIL ECOLOGY
(2017)
Article
Microbiology
Weili Lyu, Yunlong Wu, Ya Liu, Zhitang Lyu
GENOME ANNOUNCEMENTS
(2016)
Article
Microbiology
ZH Liu, YL Shi, YM Zhang, ZH Zhou, ZT Lu, W Li, Y Huang, C Rodríguez, M Goodfellow
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2005)