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Latest Articles

  • Continuous Genomic Surveillance Monitored the <em>In Vivo</em> Evolutionary Trajectories of <span class="named-content genus-species" id="named-content-1">Vibrio parahaemolyticus</span> and Identified a New Virulent Genotype
    Research Article | Ecological and Evolutionary Science
    Continuous Genomic Surveillance Monitored the In Vivo Evolutionary Trajectories of Vibrio parahaemolyticus and Identified a New Virulent Genotype

    Most human infectious diseases originate from animals. Thus, how to reduce or prevent pandemic zoonoses before they emerge in people is becoming a critical issue.

    Songzhe Fu, Qian Yang, Qingyao Wang, Bo Pang, Ruiting Lan, Dawei Wei, Baocheng Qu, Ying Liu
    19 Jan 2021
  • Phylogenetic Distribution of Plastic-Degrading Microorganisms
    Research Article | Applied and Environmental Science
    Phylogenetic Distribution of Plastic-Degrading Microorganisms

    We have collated the most complete database of microorganisms identified as being capable of degrading plastics to date. These data allow us to explore the phylogenetic distribution of these organisms and their enzymes, showing that traits for plastic degradation are predominantly not phylogenetically conserved.

    Victor Gambarini, Olga Pantos, Joanne M. Kingsbury, Louise Weaver, Kim M. Handley, Gavin Lear
    19 Jan 2021
  • Microbiome Search Engine 2: a Platform for Taxonomic and Functional Search of Global Microbiomes on the Whole-Microbiome Level
    Resource Report | Novel Systems Biology Techniques
    Microbiome Search Engine 2: a Platform for Taxonomic and Functional Search of Global Microbiomes on the Whole-Microbiome Level

    A search-based strategy is useful for large-scale mining of microbiome data sets, such as a bird’s-eye view of the microbiome data space and disease diagnosis via microbiome big data. Here, we introduce Microbiome Search Engine 2 (MSE 2), a microbiome database platform for searching query microbiomes against the existing microbiome data sets on the basis of their similarity in taxonomic structure or functional profile.

    ...
    Gongchao Jing, Lu Liu, Zengbin Wang, Yufeng Zhang, Li Qian, Chunxiao Gao, Meng Zhang, Min Li, Zhenkun Zhang, Xiaohan Liu, Jian Xu, Xiaoquan Su
    19 Jan 2021
  • Comparative Genomic Analysis of <em>Mycobacteriaceae</em> Reveals Horizontal Gene Transfer-Mediated Evolution of the CRISPR-Cas System in the <span class="named-content genus-species" id="named-content-1">Mycobacterium tuberculosis</span> Complex
    Research Article | Ecological and Evolutionary Science
    Comparative Genomic Analysis of Mycobacteriaceae Reveals Horizontal Gene Transfer-Mediated Evolution of the CRISPR-Cas System in the Mycobacterium tuberculosis Complex

    Comparative genomic analysis of prokaryotes has led to a better understanding of the biology of several pathogenic microorganisms. One such clinically important pathogen is M. tuberculosis, the leading cause of bacterial infection worldwide.

    Anoop Singh, Mohita Gaur, Vishal Sharma, Palak Khanna, Ankur Bothra, Asani Bhaduri, Anupam Kumar Mondal, Debasis Dash, Yogendra Singh, Richa Misra
    19 Jan 2021
  • Computational Analysis of Microbial Flow Cytometry Data
    Minireview | Applied and Environmental Science
    Computational Analysis of Microbial Flow Cytometry Data

    Flow cytometry is an important technology for the study of microbial communities. It grants the ability to rapidly generate phenotypic single-cell data that are both quantitative, multivariate and of high temporal resolution.

    Peter Rubbens, Ruben Props
    19 Jan 2021
  • Caught between Two Genes: Accounting for Operonic Gene Structure Improves Prokaryotic RNA Sequencing Quantification
    Commentary | Novel Systems Biology Techniques
    Caught between Two Genes: Accounting for Operonic Gene Structure Improves Prokaryotic RNA Sequencing Quantification

    RNA sequencing (RNA-seq) has matured into a reliable and low-cost assay for transcriptome profiling and has been deployed across a range of systems. The computational tool space for the analysis of RNA-seq data has kept pace with advances in sequencing.

    Taylor Reiter
    12 Jan 2021
  • <em>Candida</em> Administration Worsens Uremia-Induced Gut Leakage in Bilateral Nephrectomy Mice, an Impact of Gut Fungi and Organismal Molecules in Uremia
    Research Article | Host-Microbe Biology
    Candida Administration Worsens Uremia-Induced Gut Leakage in Bilateral Nephrectomy Mice, an Impact of Gut Fungi and Organismal Molecules in Uremia

    The impact of fungi in the intestine on acute uremia was demonstrated by the oral administration of Candida albicans in mice with the removal of both kidneys. Because fungi in the mouse intestine are less abundant than in humans, a Candida-administered mouse model has more resemblance to patient conditions.

    Wimonrat Panpetch, Chitrasak Kullapanich, Cong Phi Dang, Peerapat Visitchanakun, Wilasinee Saisorn, Jutamas Wongphoom, Dhammika Leshan Wannigama, Arthid Thim-uam, Kanitha Patarakul, Naraporn Somboonna, Somying Tumwasorn, Asada Leelahavanichkul
    12 Jan 2021
  • New Provisional Function of OmpA from <em>Acinetobacter</em> sp. Strain SA01 Based on Environmental Challenges
    Research Article | Applied and Environmental Science
    New Provisional Function of OmpA from Acinetobacter sp. Strain SA01 Based on Environmental Challenges

    Acinetobacter OmpA is known as a multifaceted protein with multiple functions, including emulsifying properties. Bioemulsifiers are surface-active compounds that can disperse hydrophobic compounds in water and help increase the bioavailability of hydrophobic hydrocarbons to be used by degrading microorganisms.

    Shahab Shahryari, Mahbubeh Talaee, Kamahldin Haghbeen, Lorenz Adrian, Hojatollah Vali, Hossein Shahbani Zahiri, Kambiz Akbari Noghabi
    12 Jan 2021
  • Dynamics and Microevolution of <em>Vibrio parahaemolyticus</em> Populations in Shellfish Farms
    Research Article | Ecological and Evolutionary Science
    Dynamics and Microevolution of Vibrio parahaemolyticus Populations in Shellfish Farms

    Globally, V. parahaemolyticus-related gastroenteritis outbreaks caused by seafood consumption represent an increasing threat to human health. Despite advances in our understanding of the global epidemiology of pandemic V. parahaemolyticus, fundamental questions about the key driving forces for the...

    Songzhe Fu, Qingyao Wang, Yixiang Zhang, Qian Yang, Jingwei Hao, Ying Liu, Bo Pang
    12 Jan 2021
  • Complementary Roles of Wood-Inhabiting Fungi and Bacteria Facilitate Deadwood Decomposition
    Editor's Pick Research Article | Ecological and Evolutionary Science
    Complementary Roles of Wood-Inhabiting Fungi and Bacteria Facilitate Deadwood Decomposition

    Wood represents a globally important stock of C, and its mineralization importantly contributes to the global C cycle. Microorganisms play a key role in deadwood decomposition, since they possess enzymatic tools for the degradation of recalcitrant plant polymers.

    Vojtěch Tláskal, Vendula Brabcová, Tomáš Větrovský, Mayuko Jomura, Rubén López-Mondéjar, Lummy Maria Oliveira Monteiro, João Pedro Saraiva, Zander Rainier Human, Tomáš Cajthaml, Ulisses Nunes da Rocha, Petr Baldrian
    12 Jan 2021

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