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Archive

January/February 2021; Volume 6,Issue 1

Perspective

  • Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities
    Perspective | Applied and Environmental Science
    Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities

    Microbiome samples are inherently defined by the environment in which they are found. Therefore, data that provide context and enable interpretation of measurements produced from biological samples, often referred to as metadata, are critical.

    Pajau Vangay, Josephine Burgin, Anjanette Johnston, Kristen L. Beck, Daniel C. Berrios, Kai Blumberg, Shane Canon, Patrick Chain, John-Marc Chandonia, Danielle Christianson, Sylvain V. Costes, Joan Damerow, William D. Duncan, Jose Pablo Dundore-Arias, Kjiersten Fagnan, Jonathan M. Galazka, Sean M. Gibbons, David Hays, Judson Hervey, Bin Hu, Bonnie L. Hurwitz, Pankaj Jaiswal, Marcin P. Joachimiak, Linda Kinkel, Joshua Ladau, Stanton L. Martin, Lee Ann McCue, Kayd Miller, Nigel Mouncey, Chris Mungall, Evangelos Pafilis, T. B. K. Reddy, Lorna Richardson, Simon Roux, Lynn M. Schriml, Justin P. Shaffer, Jagadish Chandrabose Sundaramurthi, Luke R. Thompson, Ruth E. Timme, Jie Zheng, Elisha M. Wood-Charlson, Emiley A. Eloe-Fadrosh
    23 Feb 2021

Commentary

  • 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

Minireview

  • 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

Resource Report

  • 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

Methods and Protocols

  • Identifying Potentially Beneficial Genetic Mutations Associated with Monophyletic Selective Sweep and a Proof-of-Concept Study with Viral Genetic Data
    Methods and Protocols | Ecological and Evolutionary Science
    Identifying Potentially Beneficial Genetic Mutations Associated with Monophyletic Selective Sweep and a Proof-of-Concept Study with Viral Genetic Data

    In biology, research on evolution is important to understand the significance of genetic mutation. When there is a significantly beneficial mutation, a population of species with the mutation prospers and predominates, in a process called “selective sweep.” However, there are few methods that can find such a mutation causing selective sweep from genetic data.

    Yuki Furuse
    23 Feb 2021
  • Quantifying Variation in Bacterial Reproductive Fitness: a High-Throughput Method
    Methods and Protocols | Novel Systems Biology Techniques
    Quantifying Variation in Bacterial Reproductive Fitness: a High-Throughput Method

    Reproductive fitness of bacteria is a major factor in the evolution and persistence of antimicrobial resistance and may play an important role as a pathogen factor in severe infections. With a computational approach to quantify fitness in bacteria growing competitively on agar plates, our high-throughput method has been designed to obtain additional phenotypic data for antimicrobial resistance analysis at a low cost.

    ...
    Pascal M. Frey, Julian Baer, Judith Bergada-Pijuan, Conor Lawless, Philipp K. Bühler, Roger D. Kouyos, Katherine P. Lemon, Annelies S. Zinkernagel, Silvio D. Brugger
    2 Feb 2021

Research Articles

  • Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus
    Research Article | Applied and Environmental Science
    Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus

    Recent genomic analyses have revealed that anaerobic gut fungi possess both the largest number and highest diversity of lignocellulolytic enzymes of all sequenced fungi, explaining their ability to decompose lignocellulosic substrates, e.g., agricultural waste, into fermentable sugars. Despite their potential, the development of engineering methods for these organisms has been slow due to their complex life cycle, understudied...

    St. Elmo Wilken, Jonathan M. Monk, Patrick A. Leggieri, Christopher E. Lawson, Thomas S. Lankiewicz, Susanna Seppälä, Chris G. Daum, Jerry Jenkins, Anna M. Lipzen, Stephen J. Mondo, Kerrie W. Barry, Igor V. Grigoriev, John K. Henske, Michael K. Theodorou, Bernhard O. Palsson, Linda R. Petzold, Michelle A. O’Malley
    16 Feb 2021
  • Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2
    Research Article
    Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2

    In the current study, we presented a global view of mutational pattern observed in SARS-CoV-2 virus transmission. This provided a who-infect-whom geographical model since the early pandemic.

    Vipin Gupta, Shazia Haider, Mansi Verma, Nirjara Singhvi, Kalaisaran Ponnusamy, Md. Zubbair Malik, Helianthous Verma, Roshan Kumar, Utkarsh Sood, Princy Hira, Shiva Satija, Yogendra Singh, Rup Lal
    23 Feb 2021
  • Twists and Turns in the Salicylate Catabolism of <em>Aspergillus terreus</em>, Revealing New Roles of the 3-Hydroxyanthranilate Pathway
    Research Article | Molecular Biology and Physiology
    Twists and Turns in the Salicylate Catabolism of Aspergillus terreus, Revealing New Roles of the 3-Hydroxyanthranilate Pathway

    Aspergilli are versatile cell factories used in industry for the production of organic acids, enzymes, and pharmaceutical drugs. To date, bio-based production of organic acids relies on food substrates.

    Tiago M. Martins, Celso Martins, Paula Guedes, Cristina Silva Pereira
    26 Jan 2021
  • Metabolic Interactions between <em>Brachypodium</em> and <span class="named-content genus-species" id="named-content-1">Pseudomonas fluorescens</span> under Controlled Iron-Limited Conditions
    Research Article | Host-Microbe Biology
    Metabolic Interactions between Brachypodium and Pseudomonas fluorescens under Controlled Iron-Limited Conditions

    Rhizosphere bacteria influence the growth of their host plant by consuming and producing metabolites, nutrients, and antibiotic compounds within the root system that affect plant metabolism. Under Fe-limited growth conditions, different plant and microbial species have distinct Fe acquisition strategies, often involving the secretion of strong Fe-binding chelators that scavenge Fe and facilitate uptake.

    Rene M. Boiteau, Lye Meng Markillie, David W. Hoyt, Dehong Hu, Rosalie K. Chu, Hugh D. Mitchell, Ljiljana Pasa-Tolic, Janet K. Jansson, Christer Jansson
    5 Jan 2021
  • Consumption of Dietary Fiber from Different Sources during Pregnancy Alters Sow Gut Microbiota and Improves Performance and Reduces Inflammation in Sows and Piglets
    Research Article | Host-Microbe Biology
    Consumption of Dietary Fiber from Different Sources during Pregnancy Alters Sow Gut Microbiota and Improves Performance and Reduces Inflammation in Sows and Piglets

    Although the direct effects of dietary fiber on gut microbiota composition have been studied extensively, systematic evaluation of different fiber sources on gut health and inflammatory responses of sows and their offspring has rarely been conducted. Excessive reactive oxygen species produced by overactive metabolic processes during late pregnancy and lactation of sows leads to increased endotoxin levels, disordered gut microbiota,...

    Boshuai Liu, Xiaoyan Zhu, Yalei Cui, Wenjing Wang, Hua Liu, Zidan Li, Zhiguo Guo, Sen Ma, Defeng Li, Chengzhang Wang, Yinghua Shi
    26 Jan 2021
  • <span class="named-content genus-species" id="named-content-1">Dinoroseobacter shibae</span> Outer Membrane Vesicles Are Enriched for the Chromosome Dimer Resolution Site <em>dif</em>
    Research Article | Molecular Biology and Physiology
    Dinoroseobacter shibae Outer Membrane Vesicles Are Enriched for the Chromosome Dimer Resolution Site dif

    Gram-negative bacteria continually form vesicles from their outer membrane (outer membrane vesicles [OMVs]) during normal growth. OMVs frequently contain DNA, and it is unclear how DNA can be shuffled from the cytoplasm to the OMVs.

    Hui Wang, Nicole Beier, Christian Boedeker, Helena Sztajer, Petra Henke, Meina Neumann-Schaal, Johannes Mansky, Manfred Rohde, Jörg Overmann, Jörn Petersen, Frank Klawonn, Martin Kucklick, Susanne Engelmann, Jürgen Tomasch, Irene Wagner-Döbler
    12 Jan 2021
  • Complex Response of the Chlorarachniophyte <span class="named-content genus-species" id="named-content-1">Bigelowiella natans</span> to Iron Availability
    Research Article | Molecular Biology and Physiology
    Complex Response of the Chlorarachniophyte Bigelowiella natans to Iron Availability

    Despite low iron availability in the ocean, marine phytoplankton require considerable amounts of iron for their growth and proliferation. While there is a constantly growing knowledge of iron uptake and its role in the cellular processes of the most abundant marine photosynthetic groups, there are still largely overlooked branches of the eukaryotic tree of life, such as the chlorarachniophytes.

    Eva Kotabova, Ronald Malych, Juan José Pierella Karlusich, Elena Kazamia, Meri Eichner, Jan Mach, Emmanuel Lesuisse, Chris Bowler, Ondřej Prášil, Robert Sutak
    9 Feb 2021
  • Transcription Inhibitors with XRE DNA-Binding and Cupin Signal-Sensing Domains Drive Metabolic Diversification in <em>Pseudomonas</em>
    Research Article | Molecular Biology and Physiology
    Transcription Inhibitors with XRE DNA-Binding and Cupin Signal-Sensing Domains Drive Metabolic Diversification in Pseudomonas

    Bacteria of the Pseudomonas genus, including the major human pathogen Pseudomonas aeruginosa, are known for their complex regulatory networks and high number of transcription factors, which contribute to their impressive adaptive ability. However, even in the most studied species, most of the regulators are still uncharacterized.

    Julian Trouillon, Michel Ragno, Victor Simon, Ina Attrée, Sylvie Elsen
    12 Jan 2021
  • Genomic and Chemical Diversity of <span class="named-content genus-species" id="named-content-1">Bacillus subtilis</span> Secondary Metabolites against Plant Pathogenic Fungi
    Research Article | Ecological and Evolutionary Science
    Genomic and Chemical Diversity of Bacillus subtilis Secondary Metabolites against Plant Pathogenic Fungi

    Secondary or specialized metabolites with antimicrobial activities define the biocontrol properties of microorganisms. Members of the Bacillus genus produce a plethora of secondary metabolites, of which nonribosomally produced lipopeptides in particular display strong antifungal activity.

    Heiko T. Kiesewalter, Carlos N. Lozano-Andrade, Mario Wibowo, Mikael L. Strube, Gergely Maróti, Dan Snyder, Tue Sparholt Jørgensen, Thomas O. Larsen, Vaughn S. Cooper, Tilmann Weber, Ákos T. Kovács
    23 Feb 2021
  • A Novel Group of Promiscuous Podophages Infecting Diverse Gammaproteobacteria from River Communities Exhibits Dynamic Intergenus Host Adaptation
    Research Article | Ecological and Evolutionary Science
    A Novel Group of Promiscuous Podophages Infecting Diverse Gammaproteobacteria from River Communities Exhibits Dynamic Intergenus Host Adaptation

    In natural environments, phages coexist and interact with a broad variety of bacteria, posing a conundrum for narrow-host-range phage maintenance in diverse communities. This context is rarely considered in the study of host-phage interactions, typically focused on narrow-host-range viruses and their infectivity in target bacteria isolated from sources distinct to where the phages were retrieved from.

    Daniel Cazares, Adrian Cazares, Wendy Figueroa, Gabriel Guarneros, Robert A. Edwards, Pablo Vinuesa
    2 Feb 2021
  • Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community
    Research Article | Applied and Environmental Science
    Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community

    This study represents a comprehensive community-wide genome-centered metagenome analysis of biological soil crust (BSC) communities in arid environments, providing insights into the distribution of genes encoding different energy generation mechanisms, as well as survival strategies, among populations in an arid soil ecosystem. It reveals the metabolic potential of several uncultured and previously unsequenced microbial genera, families...

    Dimitri V. Meier, Stefanie Imminger, Osnat Gillor, Dagmar Woebken
    12 Jan 2021
  • Associations of Genetic Variants Contributing to Gut Microbiota Composition in Immunoglobin A Nephropathy
    Research Article | Host-Microbe Biology
    Associations of Genetic Variants Contributing to Gut Microbiota Composition in Immunoglobin A Nephropathy

    The gut microbiota and host genetics are implicated in the pathogenesis of IgAN. Recent studies have confirmed that microbial compositions are heritable (microbiome quantitative trait loci [QTL]).

    Jia-Wei He, Xu-Jie Zhou, Ya-Feng Li, Yan-Na Wang, Li-Jun Liu, Su-Fang Shi, Xiao-Hong Xin, Rong-Shan Li, Mario Falchi, Ji-Cheng Lv, Hong Zhang
    12 Jan 2021
  • Manipulation of IRE1-Dependent MAPK Signaling by a Vibrio Agonist-Antagonist Effector Pair
    Editor's Pick Research Article | Host-Microbe Biology
    Manipulation of IRE1-Dependent MAPK Signaling by a Vibrio Agonist-Antagonist Effector Pair

    Vibrio parahaemolyticus is a seafood-borne pathogen that encodes two type 3 secretion systems (T3SS). The first system, T3SS1, is thought to be maintained in all strains of V. parahaemolyticus to maintain survival in the environment, whereas the second system, T3SS2, is linked to clinical isolates...

    Nicole J. De Nisco, Amanda K. Casey, Mohammed Kanchwala, Alexander E. Lafrance, Fatma S. Coskun, Lisa N. Kinch, Nick V. Grishin, Chao Xing, Kim Orth
    9 Feb 2021
  • Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce
    Research Article | Host-Microbe Biology
    Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce

    A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present.

    Andreas N. Schneider, John Sundh, Görel Sundström, Kerstin Richau, Nicolas Delhomme, Manfred Grabherr, Vaughan Hurry, Nathaniel R. Street
    16 Feb 2021
  • Endogenous Metabolites Released by Sanitized Sprouting Alfalfa Seed Inhibit the Growth of <span class="named-content genus-species" id="named-content-1">Salmonella enterica</span>
    Research Article | Applied and Environmental Science
    Endogenous Metabolites Released by Sanitized Sprouting Alfalfa Seed Inhibit the Growth of Salmonella enterica

    Warm, humid, and nutrient-rich conditions that are used to produce sprouts encourage Salmonella enterica to proliferate. However, many disparate sanitation methods exist, and there is currently no single treatment that can guarantee pathogen-free seeds.

    Ga-Hee Ban, Yue Dai, Tao Huan, Alfred Ke, Pascal Delaquis, Siyun Wang
    9 Feb 2021
  • Long-Term Bacterial and Fungal Dynamics following Oral Lyophilized Fecal Microbiota Transplantation in <span class="named-content genus-species" id="named-content-1">Clostridioides difficile</span> Infection
    Research Article | Therapeutics and Prevention
    Long-Term Bacterial and Fungal Dynamics following Oral Lyophilized Fecal Microbiota Transplantation in Clostridioides difficile Infection

    Clostridioides difficile infection (CDI) is a substantial health concern worldwide, complicated by patterns of increasing antibiotic resistance that may impact primary treatment. Orally administered fecal microbiota transplantation (FMT) is efficacious in the management of recurrent CDI, with specific bacterial species known to influence clinical outcomes.

    ...
    Craig Haifer, Sudarshan Paramsothy, Thomas J. Borody, Annabel Clancy, Rupert W. Leong, Nadeem O. Kaakoush
    2 Feb 2021
  • FADU: a Quantification Tool for Prokaryotic Transcriptomic Analyses
    Research Article | Host-Microbe Biology
    FADU: a Quantification Tool for Prokaryotic Transcriptomic Analyses

    Most currently available quantification tools for transcriptomics analyses have been designed for human data sets, in which full-length transcript sequences, including the untranslated regions, are well annotated. In most prokaryotic systems, full-length transcript sequences have yet to be characterized, leading to prokaryotic transcriptomics analyses being performed based on only the coding sequences.

    Matthew Chung, Ricky S. Adkins, John S. A. Mattick, Katie R. Bradwell, Amol C. Shetty, Lisa Sadzewicz, Luke J. Tallon, Claire M. Fraser, David A. Rasko, Anup Mahurkar, Julie C. Dunning Hotopp
    12 Jan 2021
  • A High-Throughput Method for Identifying Novel Genes That Influence Metabolic Pathways Reveals New Iron and Heme Regulation in <span class="named-content genus-species" id="named-content-1">Pseudomonas aeruginosa</span>
    Research Article | Novel Systems Biology Techniques
    A High-Throughput Method for Identifying Novel Genes That Influence Metabolic Pathways Reveals New Iron and Heme Regulation in Pseudomonas aeruginosa

    The ability to simultaneously and more directly correlate genes with metabolite levels on a global level would provide novel information for many biological platforms yet has thus far been challenging. Here, we describe a method to help address this problem, which we dub “Met-Seq” (metabolite-coupled Tn sequencing).

    David G. Glanville, Caroline Mullineaux-Sanders, Christopher J. Corcoran, Brian T. Burger, Saheed Imam, Timothy J. Donohue, Andrew T. Ulijasz
    2 Feb 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
  • National Prevalence of <span class="named-content genus-species" id="named-content-1">Salmonella enterica</span> Serotype Kentucky ST198 with High-Level Resistance to Ciprofloxacin and Extended-Spectrum Cephalosporins in China, 2013 to 2017
    Research Article | Clinical Science and Epidemiology
    National Prevalence of Salmonella enterica Serotype Kentucky ST198 with High-Level Resistance to Ciprofloxacin and Extended-Spectrum Cephalosporins in China, 2013 to 2017

    Ciprofloxacin and extended-spectrum cephalosporins are the choice for treatment of severe nontyphoidal S. enterica infections in adults. S. enterica serotype Kentucky ST198 has gained epidemiological importance globally, because the clone is frequently resistant to both of these high-level-...

    Honghu Chen, Jingjie Song, Xianying Zeng, Dandan Chen, Rongchang Chen, Chen Qiu, Kai Zhou
    12 Jan 2021
  • Genomic Insights into Adaptations of Trimethylamine-Utilizing Methanogens to Diverse Habitats, Including the Human Gut
    Editor's Pick Research Article | Host-Microbe Biology
    Genomic Insights into Adaptations of Trimethylamine-Utilizing Methanogens to Diverse Habitats, Including the Human Gut

    Methanomassiliicoccales are less-known members of the human gut archaeome. Members of this order use methylated amines, including trimethylamine, in methane production.

    Jacobo de la Cuesta-Zuluaga, Tim D. Spector, Nicholas D. Youngblut, Ruth E. Ley
    9 Feb 2021
  • Gradient Internal Standard Method for Absolute Quantification of Microbial Amplicon Sequencing Data
    Research Article | Applied and Environmental Science
    Gradient Internal Standard Method for Absolute Quantification of Microbial Amplicon Sequencing Data

    To solve the problem of amplicon sequencing cannot discern the microbiota absolute abundance, we proposed a gradient internal standard absolute quantification method. We used Chinese liquor fermentation as a model system to demonstrate the reliability and accuracy of the method.

    Shilei Wang, Qun Wu, Ying Han, Rubing Du, Xiaoyong Wang, Yao Nie, Xiaowei Du, Yan Xu
    12 Jan 2021
  • Nonadditive Transcriptomic Signatures of Genotype-by-Genotype Interactions during the Initiation of Plant-Rhizobium Symbiosis
    Research Article | Host-Microbe Biology
    Nonadditive Transcriptomic Signatures of Genotype-by-Genotype Interactions during the Initiation of Plant-Rhizobium Symbiosis

    A sustainable way for meeting the need of an increased global food demand should be based on a holobiont perspective, viewing crop plants as intimately associated with their microbiome, which helps improve plant nutrition, tolerance to pests, and adverse climate conditions. However, the genetic repertoire needed for efficient association with plants by the microbial symbionts is still poorly understood.

    Camilla Fagorzi, Giovanni Bacci, Rui Huang, Lisa Cangioli, Alice Checcucci, Margherita Fini, Elena Perrin, Chiara Natali, George Colin diCenzo, Alessio Mengoni
    12 Jan 2021
  • Chaperone-Mediated Stress Sensing in <span class="named-content genus-species" id="named-content-1">Mycobacterium tuberculosis</span> Enables Fast Activation and Sustained Response
    Research Article | Molecular Biology and Physiology
    Chaperone-Mediated Stress Sensing in Mycobacterium tuberculosis Enables Fast Activation and Sustained Response

    Gene regulatory networks controlling stress response in mycobacterial species have been linked to persistence switches that enable bacterial dormancy within a host. However, the mechanistic basis of switching and stress sensing is not fully understood.

    Satyajit D. Rao, Pratik Datta, Maria Laura Gennaro, Oleg A. Igoshin
    16 Feb 2021
  • Pangenome Analytics Reveal Two-Component Systems as Conserved Targets in ESKAPEE Pathogens
    Research Article | Host-Microbe Biology
    Pangenome Analytics Reveal Two-Component Systems as Conserved Targets in ESKAPEE Pathogens

    The ESKAPEE pathogens are the leading cause of health care-associated infections worldwide. Two-component systems (TCSs) can be used as effective targets against pathogenic bacteria since they are ubiquitous and manage various vital functions such as antibiotic resistance, virulence, biofilms, quorum sensing, and pH balance, among others.

    Akanksha Rajput, Yara Seif, Kumari Sonal Choudhary, Christopher Dalldorf, Saugat Poudel, Jonathan M. Monk, Bernhard O. Palsson
    26 Jan 2021
  • Impaired Intestinal <span class="named-content genus-species" id="named-content-1">Akkermansia muciniphila</span> and Aryl Hydrocarbon Receptor Ligands Contribute to Nonalcoholic Fatty Liver Disease in Mice
    Editor's Pick Research Article | Host-Microbe Biology
    Impaired Intestinal Akkermansia muciniphila and Aryl Hydrocarbon Receptor Ligands Contribute to Nonalcoholic Fatty Liver Disease in Mice

    Our findings indicate that the gut-liver signaling axis contributes to saccharin/sucralose consumption-induced NAFLD. Supplementation with metformin or fructo-oligosaccharide is a potential therapeutic strategy for NAFLD treatment. In addition, we also developed a new nutritional strategy by using a natural sweetener (neohesperidin dihydrochalcone [NHDC]) as a substitute for NAS and free sugars.

    Zunji Shi, Hehua Lei, Gui Chen, Peihong Yuan, Zheng Cao, Hooi-Leng Ser, Xuehang Zhu, Fang Wu, Caixiang Liu, Manyuan Dong, Yuchen Song, Yangyang Guo, Chuan Chen, Kexin Hu, Yifan Zhu, Xin-an Zeng, Jinlin Zhou, Yujing Lu, Andrew D. Patterson, Limin Zhang
    23 Feb 2021
  • Temporal Stability and Genetic Diversity of 48-Year-Old T-Series Phages
    Research Article | Host-Microbe Biology
    Temporal Stability and Genetic Diversity of 48-Year-Old T-Series Phages

    T-series bacteriophages have been used throughout the world for various molecular biology researches, which were critical for establishing the fundamentals of molecular biology, from the structure of DNA to advanced gene-editing tools. These model bacteriophages help keep research data consistent and comparable between laboratories.

    Dinesh Subedi, Jeremy J. Barr
    16 Feb 2021
  • Characterization of Bicistronic Transcription in Budding Yeast
    Research Article | Ecological and Evolutionary Science
    Characterization of Bicistronic Transcription in Budding Yeast

    Operons, where a single mRNA transcript encodes multiple adjacent proteins, are a widespread feature of bacteria and archaea. In contrast, the genes of eukaryotes are generally considered monocistronic.

    Baojun Wu, Murray P. Cox
    23 Feb 2021
  • Production and Excretion of Polyamines To Tolerate High Ammonia, a Case Study on Soil Ammonia-Oxidizing Archaeon “<em>Candidatus</em> Nitrosocosmicus agrestis”
    Research Article | Molecular Biology and Physiology
    Production and Excretion of Polyamines To Tolerate High Ammonia, a Case Study on Soil Ammonia-Oxidizing Archaeon “Candidatus Nitrosocosmicus agrestis”

    Ammonia tolerance of AOA is usually much lower than that of the AOB, which makes the AOB rather than AOA a predominant ammonia oxidizer in agricultural soils, contributing to global N2O emission. Recently, some AOA species from the genus “Ca. Nitrosocosmicus” were also found to have high ammonia tolerance.

    Liangting Liu, Mengfan Liu, Yiming Jiang, Weitie Lin, Jianfei Luo
    16 Feb 2021
  • Fungal Communities Are Important Determinants of Bacterial Community Composition in Deadwood
    Research Article | Ecological and Evolutionary Science
    Fungal Communities Are Important Determinants of Bacterial Community Composition in Deadwood

    Understanding the interactive dynamics between fungal and bacterial communities is important to gain predictive knowledge on ecosystem functioning. However, little is known about the mechanisms behind fungal-bacterial associations and the directionality of species interactions.

    Iñaki Odriozola, Nerea Abrego, Vojtěch Tláskal, Petra Zrůstová, Daniel Morais, Tomáš Větrovský, Otso Ovaskainen, Petr Baldrian
    5 Jan 2021
  • Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification
    Research Article | Molecular Biology and Physiology
    Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification

    Nitrate-reducing bacteria (NRB) and sulfate-reducing bacteria (SRB) colonize diverse anoxic environments, including soil subsurface, groundwater, and wastewater. NRB and SRB compete for resources, and their interplay has major implications on the global cycling of nitrogen and sulfur species, with undesirable outcomes in some contexts.

    Anne E. Otwell, Alex V. Carr, Erica L. W. Majumder, Maryann K. Ruiz, Regina L. Wilpiszeski, Linh T. Hoang, Bill Webb, Serdar Turkarslan, Sean M. Gibbons, Dwayne A. Elias, David A. Stahl, Gary Siuzdak, Nitin S. Baliga
    9 Feb 2021
  • Essential Amino Acid Enrichment and Positive Selection Highlight Endosymbiont's Role in a Global Virus-Vectoring Pest
    Editor's Pick Research Article | Host-Microbe Biology
    Essential Amino Acid Enrichment and Positive Selection Highlight Endosymbiont's Role in a Global Virus-Vectoring Pest

    Xiphinematobacter spp. are distinctly evolved intracellular symbionts in the phylum Verrucomicrobia, which includes the important human gut-associated microbe Akkermansia muciniphila and many highly abundant free-living soil microbes. Like Akkermansia sp., Xiphinematobacter sp. is obligately associated with the gut of its hosts,...

    Kaitlyn N. Myers, Daniel Conn, Amanda M. V. Brown
    2 Feb 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
  • 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
  • Microbiota Assessments for the Identification and Confirmation of Slit Defect-Causing Bacteria in Milk and Cheddar Cheese
    Research Article | Applied and Environmental Science
    Microbiota Assessments for the Identification and Confirmation of Slit Defect-Causing Bacteria in Milk and Cheddar Cheese

    Food production involves numerous control points for microorganisms to ensure quality and safety. These control points (e.g., pasteurization) are difficult to develop for fermented foods wherein some microbial contaminants are also expected to provide positive contributions to the final product and spoilage microbes may constitute only a small proportion of all microorganisms present.

    Zhengyao Xue, Jason T. Brooks, Zachary Quart, Eric T. Stevens, Mary E. Kable, Jessie Heidenreich, Jeremy McLeod, Maria L. Marco
    9 Feb 2021
  • Endophytic Lifestyle of Global Clones of Extended-Spectrum β-Lactamase-Producing Priority Pathogens in Fresh Vegetables: a Trojan Horse Strategy Favoring Human Colonization?
    Research Article | Clinical Science and Epidemiology
    Endophytic Lifestyle of Global Clones of Extended-Spectrum β-Lactamase-Producing Priority Pathogens in Fresh Vegetables: a Trojan Horse Strategy Favoring Human Colonization?

    Extended-spectrum β-lactamases (ESBL)-producing Enterobacterales are a leading cause of human and animal infections, being classified as critical priority pathogens by the World Health Organization. Epidemiological studies have shown that spread of ESBL-producing bacteria is not a problem restricted to hospitals, but also represents a growing problem involving environmental and food safety.

    Ralf Lopes, Danny Fuentes-Castillo, Herrison Fontana, Larissa Rodrigues, Karine Dantas, Louise Cerdeira, Isabel Henriques, Nilton Lincopan
    9 Feb 2021
  • Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylation in <span class="named-content genus-species" id="named-content-1">Candida albicans</span>
    Research Article | Host-Microbe Biology
    Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylation in Candida albicans

    C. albicans is one of the most commonly reported fungal pathogens in mucosal and systemic infections. A better understanding of its growth habits and metabolic processes in the host should help improve defense strategies.

    Hailin Zheng, Nana Song, Xiaowei Zhou, Huan Mei, Dongmei Li, Xiaofang Li, Weida Liu
    2 Feb 2021
  • Assessing Biodegradability of Chemical Compounds from Microbial Community Growth Using Flow Cytometry
    Research Article | Applied and Environmental Science
    Assessing Biodegradability of Chemical Compounds from Microbial Community Growth Using Flow Cytometry

    The manifold effects of potentially toxic compounds on microbial communities are often difficult to discern. Some compounds may be transformed or completely degraded by few or multiple strains in the community, whereas others may present inhibitory effects.

    B. D. Özel Duygan, S. Rey, S. Leocata, L. Baroux, M. Seyfried, J. R. van der Meer
    9 Feb 2021
  • Data Analysis Strategies for Microbiome Studies in Human Populations—a Systematic Review of Current Practice
    Research Article | Clinical Science and Epidemiology
    Data Analysis Strategies for Microbiome Studies in Human Populations—a Systematic Review of Current Practice

    The human microbiome has emerged as an important factor in the development of health and disease. Growing interest in this topic has led to an increasing number of studies investigating the human microbiome using high-throughput sequencing methods.

    Sven Kleine Bardenhorst, Tom Berger, Frank Klawonn, Marius Vital, André Karch, Nicole Rübsamen
    23 Feb 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
  • 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
  • Quantifying Live Microbial Load in Human Saliva Samples over Time Reveals Stable Composition and Dynamic Load
    Research Article | Host-Microbe Biology
    Quantifying Live Microbial Load in Human Saliva Samples over Time Reveals Stable Composition and Dynamic Load

    Human microbiomes are dynamic ecosystems often composed of hundreds of unique microbial taxa. To detect fluctuations over time in the human oral microbiome, we developed a novel workflow to quantify live microbial cells with flow cytometry in parallel with next-generation sequencing, and applied this method to over 150 unstimulated, timed saliva samples.

    Clarisse Marotz, James T. Morton, Perris Navarro, Joanna Coker, Pedro Belda-Ferre, Rob Knight, Karsten Zengler
    16 Feb 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
  • Machine Learning Reveals Time-Varying Microbial Predictors with Complex Effects on Glucose Regulation
    Research Article | Host-Microbe Biology
    Machine Learning Reveals Time-Varying Microbial Predictors with Complex Effects on Glucose Regulation

    Recent studies have shown a clear link between gut microbiota and type 2 diabetes. However, current results are based on cross-sectional studies that aim to determine the microbial dysbiosis when the disease is already prevalent.

    Oliver Aasmets, Kreete Lüll, Jennifer M. Lang, Calvin Pan, Johanna Kuusisto, Krista Fischer, Markku Laakso, Aldons J. Lusis, Elin Org
    16 Feb 2021
  • Heritable Gut Microbiome Associated with <em>Salmonella enterica</em> Serovar Pullorum Infection in Chickens
    Research Article | Host-Microbe Biology
    Heritable Gut Microbiome Associated with Salmonella enterica Serovar Pullorum Infection in Chickens

    The present study investigated the association among the host genome, the gut microbiome, and S. Pullorum infection in chickens. The results suggested that the gut microbial structure is altered in S. Pullorum-infected chickens.

    Jinmei Ding, Hao Zhou, Lingxiao Luo, Lu Xiao, Kaixuan Yang, Lingyu Yang, Yuming Zheng, Ke Xu, Chuan He, Chengxiao Han, Huaixi Luo, Chao Qin, Fisayo T. Akinyemi, Caiju Gu, Zhenxiang Zhou, Qizhong Huang, He Meng
    5 Jan 2021
  • Deciphering a Marine Bone-Degrading Microbiome Reveals a Complex Community Effort
    Research Article | Applied and Environmental Science
    Deciphering a Marine Bone-Degrading Microbiome Reveals a Complex Community Effort

    Bones are an underexploited, yet potentially profitable feedstock for biotechnological advances and value chains, due to the sheer amounts of residues produced by the modern meat and poultry processing industry. In this metagenomic study, we decipher the microbial pathways and enzymes that we postulate to be involved in bone degradation in the marine environment.

    Erik Borchert, Antonio García-Moyano, Sergio Sanchez-Carrillo, Thomas G. Dahlgren, Beate M. Slaby, Gro Elin Kjæreng Bjerga, Manuel Ferrer, Sören Franzenburg, Ute Hentschel
    9 Feb 2021
  • A 16S rRNA Gene and Draft Genome Database for the Murine Oral Bacterial Community
    Research Article | Host-Microbe Biology
    A 16S rRNA Gene and Draft Genome Database for the Murine Oral Bacterial Community

    Mouse model studies are frequently used in oral microbiome research, particularly to investigate diseases such as periodontitis and caries, as well as other related systemic diseases. We have reported here the details of the development of a curated reference database to characterize the oral microbial community in laboratory and some wild mice.

    Susan Joseph, Joseph Aduse-Opoku, Ahmed Hashim, Eveliina Hanski, Ricarda Streich, Sarah C. L. Knowles, Amy B. Pedersen, William G. Wade, Michael A. Curtis
    9 Feb 2021
  • 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
  • Evaluation of CRISPR Diversity in the Human Skin Microbiome for Personal Identification
    Research Article | Host-Microbe Biology
    Evaluation of CRISPR Diversity in the Human Skin Microbiome for Personal Identification

    Microbial community diversity analysis can be utilized to characterize the personal microbiome that varies between individuals. CRISPR sequences, which reflect virome structure, in the human skin environment may be highly personalized similar to the structures of individual viromes.

    Kochi Toyomane, Ryo Yokota, Ken Watanabe, Tomoko Akutsu, Ai Asahi, Satoshi Kubota
    2 Feb 2021
  • Harnessing Machine Learning To Unravel Protein Degradation in <span class="named-content genus-species" id="named-content-1">Escherichia coli</span>
    Research Article | Molecular Biology and Physiology
    Harnessing Machine Learning To Unravel Protein Degradation in Escherichia coli

    Bacteria use protein degradation to control proliferation, dispose of misfolded proteins, and adapt to physiological and environmental shifts, but the factors that dictate which proteins are prone to degradation are mostly unknown. In this study, we have used a combined computational-experimental approach to explore protein degradation in E. coli.

    Natan Nagar, Noa Ecker, Gil Loewenthal, Oren Avram, Daniella Ben-Meir, Dvora Biran, Eliora Ron, Tal Pupko
    2 Feb 2021
  • Systematic Analysis of the Lysine Crotonylome and Multiple Posttranslational Modification Analysis (Acetylation, Succinylation, and Crotonylation) in <span class="named-content genus-species" id="named-content-1">Candida albicans</span>
    Research Article | Molecular Biology and Physiology
    Systematic Analysis of the Lysine Crotonylome and Multiple Posttranslational Modification Analysis (Acetylation, Succinylation, and Crotonylation) in Candida albicans

    C. albicans is a kind of pathogen of fungal infections that is found worldwide. Lysine crotonylation of proteins as a recently discovered PTM (posttranslational modification) may have a critical role in regulating cells.

    Xiaowei Zhou, Nana Song, Dongmei Li, Xiaofang Li, Weida Liu
    26 Jan 2021
  • Modeling Growth Kinetics, Interspecies Cell Fusion, and Metabolism of a <span class="named-content genus-species" id="named-content-1">Clostridium acetobutylicum</span>/<span class="named-content genus-species" id="named-content-2">Clostridium ljungdahlii</span> Syntrophic Coculture
    Research Article
    Modeling Growth Kinetics, Interspecies Cell Fusion, and Metabolism of a Clostridium acetobutylicum/Clostridium ljungdahlii Syntrophic Coculture

    Widespread cell fusion and protein exchange between microbial organisms as observed in synthetic C. acetobutylicum/C. ljungdahlii culture is a novel observation that has not been explored in silico. The mechanisms responsible for the observed cell fusion events in this culture are still unknown.

    Charles Foster, Kamil Charubin, Eleftherios T. Papoutsakis, Costas D. Maranas
    23 Feb 2021
  • The <em>Azospirillum brasilense</em> Core Chemotaxis Proteins CheA1 and CheA4 Link Chemotaxis Signaling with Nitrogen Metabolism
    Research Article | Molecular Biology and Physiology
    The Azospirillum brasilense Core Chemotaxis Proteins CheA1 and CheA4 Link Chemotaxis Signaling with Nitrogen Metabolism

    Bacterial chemotaxis is widespread in bacteria, increasing competitiveness in diverse environments and mediating associations with eukaryotic hosts ranging from commensal to beneficial and pathogenic. In most bacteria, chemotaxis signaling is tightly linked to energy metabolism, with this coupling occurring through the sensory input of several energy-sensing chemoreceptors.

    Elena E. Ganusova, Lam T. Vo, Paul E. Abraham, Lindsey O’Neal Yoder, Robert L. Hettich, Gladys Alexandre
    16 Feb 2021
  • Human Milk-Fed Piglets Have a Distinct Small Intestine and Circulatory Metabolome Profile Relative to That of Milk Formula-Fed Piglets
    Research Article | Host-Microbe Biology
    Human Milk-Fed Piglets Have a Distinct Small Intestine and Circulatory Metabolome Profile Relative to That of Milk Formula-Fed Piglets

    Exclusive HM feeding for newborns is recommended at least for the first 6 months of life. However, when breastfeeding is not possible, MF is recommended as a substitute.

    Fernanda Rosa, Katelin S. Matazel, Ahmed A. Elolimy, Sean H. Adams, Anne Bowlin, Keith D. Williams, Lars Bode, Laxmi Yeruva
    9 Feb 2021
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mSystems: 6 (1)

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