July 11, 2017

Welcome to your Tuesday Digest. Today, some interesting pieces from Science mag about scientific career. A few pre-prints in the Plant & Soil section, including a paper by Hubbard et al. that presents an interesting concept on plant’s diel cycle and rhizosphere community. Enjoy!

Events and jobs
Director, Sterile and Microbiology Quality Assurance Job
Merck – West Point – PA, US

Multi-site human microbiome
The influence of the commensal microbiota on distal tumor-promoting inflammation.
Buchta Rosean CM, Rutkowski MR – Seminars in Immunology

Human gut microbiome
Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life
Weili Xiong et al. – Microbiome

Genome-scale model and omics analysis of metabolic capacities of Akkermansia muciniphila reveal a preferential mucin-degrading lifestyle
Ottman N et al. – Applied Environmental Microbiology

Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy
Sivaranjani Namasivayam et al. – Microbiome

Animal experiments
Host specificity of Segmented Filamentous Bacteria (SFB) flagellins affects their interaction patterns with mouse ileal mucosal proteins.
Chen H et al. – Applied Environmental Microbiology

Plant, root, and soil microbiome
Pre-print: The plant circadian clock influences rhizosphere community structure and function
Charley Hubbard et al. – bioRxiv

Microbial functional diversity responses to 2 years since biochar application in silt-loam soils on the Loess Plateau
Zhu LX et al. – Ecotoxicology and Environmental Safety

Review: Microbes from mined sites: Harnessing their potential for reclamation of derelict mine sites
Thavamani P. et al – Environmental Pollution

Review: Microbial activity and the dynamics of ecosystem processes in forest soils
Baldrian P. – Current Opinion in Microbiology

Pre-print: Maize Phyllosphere Microbial Community Niche Development Across Stages of Host Leaf Growth
Heather C. Manching et al. – bioRxiv

Water, estuarine and sediment microbiome
Distinct Aeromonas Populations in Water Column and Associated with Copepods from Estuarine Environment (Seine, France)
Gautier Chaix et al. – Frontiers in Microbiology

Vertical and horizontal assemblage patterns of bacterial communities in a eutrophic river receiving domestic wastewater in southeast China.
Gao Y et al. – Environmental Pollution

Extremophile and space microbiome
Human presence impacts fungal diversity of inflated lunar/Mars analog habitat
A. Blachowicz et al. – Microbiome

Built environment
Metagenomic analysis reveals wastewater treatment plants as hotspots of antibiotic resistance genes and mobile genetic elements
Guo J et al. – Water Research

Review: The potential implications of reclaimed wastewater reuse for irrigation on the agricultural environment: The knowns and unknowns of the fate of antibiotics and antibiotic resistant bacteria and resistance genes – A review.
Christou A et al – Water Research

New insights into the spatial variability of biofilm communities and potentially negative bacterial groups in hydraulic concrete structures.
Cai W. et al – Water Reseach

Pre-print: Cyanobacterial Growth on Municipal Wastewater Requires Low Temperatures
Travis C. Korosh et al. – bioRxiv

Microbial biotechnology
Expanding landscapes of the diversified mcr-1-bearing plasmid reservoirs
Qingjing Wang & Jian Sun et al. – Microbiome

General microbiology and evolution
Effect of a Pseudomonas fluorescens tailocin against phytopathogenic Xanthomonas observed by atomic force microscopy
M. Fernandez et al. – Journal of Biotechnology

Natural-Product Antibiotics: Cues for Modulating Bacterial Biofilm Formation
Townsley L. & Shank EA – Trends in Microbiology

Bioinformatics and statistics
VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data
Jie Ren & Nathan A. Algren et al. – Microbiome

Pre-print: A supervised statistical learning approach for accurate Legionella pneumophila source attribution during outbreaks
Andrew H. Buultjens et al. – bioRxiv

Review: Mining Metagenomic Data Sets for Ancient DNA: Recommended Protocols for Authentication
Key FM et al – Trends in Genetics

Techniques and methods
Formulation, stabilisation and encapsulation of bacteriophage for phage therapy
Malik DJ et al. – Advances in Colloid and Interface Science

A novel ultra high-throughput 16S rRNA gene amplicon sequencing library preparation method for the Illumina HiSeq platform
Eric J. de Muinck et al. – Microbiome

Microbes in the news
I gave my cat a poop transplant—here’s what happened next
Jonathan Gitlin – arstechnica

Gonorrhea is getting even harder to treat
Ashley Welch – CBS News

Science, publishing, and career
Reprogramming my career
Charmaine Tam – Science

The cyberscientist
John Bohannon – Science

The scientists’ apprentice
Tim Appenzeller – Science

Food and microbiota in the FDA regulatory framework
Jonathan M. Green et al. – Science

June 12, 2017

An unusually quiet Monday to start your week of microbiome literature. In the methods section, some new protocols from Springer’s “Diagnostic Bacteriology” volume. Enjoy!

General microbiome

Review: Influences of environmental bacteria and their metabolites on allergies, asthma and host microbiota
G Jatzlauk et al. – Allergy

Human gut microbiome

Microbiome and NAFLD: Potential Influence of Aerobic Fitness and Lifestyle Modification
Matthew R. Panasevich – Physiological Genomics

Mucosa-associated microbiota signature in colorectal cancer
R. Gao et al. – European Journal of Clinical Microbiology & Infectious Diseases

Microbial diseases

Pre-print: Epistasis mediated alleviation of the cost of antibiotic resistance for MRSA
Maho Yokoyama et al. – bioRxiv

Animal experiments

Alteration of gut microbiota in association with cholesterol gallstone formation in mice
Qihan Wang et al – BMC Gastroenterology

Improved detection of gene-microbe interactions in the mouse skin microbiota using high-resolution QTL mapping of 16S rRNA transcripts
Meriem Belheouane et al. – Microbiome

Animal microbiome

Symbionts in waiting: the dynamics of incipient endosymbiont complementation and replacement in minimal bacterial communities of psyllids
Jennifer L. Morrow et al – Microbiome

Diet shifts provoke complex and variable changes in the metabolic networks of the ruminal microbiome
Sara M. Wolff et al – Microbiome

Plant, root, and soil microbiome

Novel microbial assemblages dominate weathered sulfide-bearing rock from copper-nickel deposits in the Duluth Complex, Minnesota, USA
DS Jones et al. – Applied and Environmental Microbiology

Water, estuarine and sediment microbiome

Colonization habitat controls biomass, composition, and metabolic activity of attached microbial communities in the Columbia River hyporheic corridor
N Stern et al. – Applied and Environmental Microbiology

Microbial biotechnology

Efficacy of Bacillus amyloliquefaciens as biocontrol agent to fight fungal diseases of maize under tropical climates: from lab to field assays in south Kivu
Parent Zihalirwa Kulimushi et al. – Environmental Science and Pollution Research

Food microbiology

RNA-based amplicon sequencing highlights the impact of the processing technology on microbiota composition of artisanal and industrial PDO Lard d’Arnad
I Ferrocino et al. – Applied and Environmental Microbiology

General microbiology and evolution

Nitrogen-source stabilization of quorum sensing in the Pseudomonas aeruginosa bioaugmentation strain SD-1
M Wang et al – Applied and Environmental Microbiology

Phages and viruses

Pre-print: Gene networks provide a high-resolution view of bacteriophage ecology
Jason Shapiro & Catherine Putonti – bioRxiv

Bioinformatics and statistics

MetabolitePredict: a de-novo human metabolomics prediction system and its applications in rheumatoid arthritis
Quan Qiu Wang & Rong Xu – Journal of Biomedical Informatics

Techniques and methods

Protocol: Detection of Helicobacter pylori in the Gastric Mucosa by Fluorescence In Vivo Hybridization
Silvia Fontenete et al. – Diagnostic Bacteriology

Protocol: Detection of Helicobacter pylori DNA in Formalin-Fixed Paraffin-Embedded Gastric Biopsies Using Laser Microdissection and qPCR
María Fernanda Loayza Villa et al. – Diagnostic Bacteriology

Protocol: Characterization of Sinus Microbiota by 16S Sequencing from Swabs
Thad W. Vickery et al. – Diagnostic Bacteriology

Protocol: Whole-Genome Enrichment Using RNA Probes and Sequencing of Chlamydia trachomatis Directly from Clinical Samples
Amanda Claire Brown & Mette T. Christiansen

Microbes in the news

Bacteria Behind Legionnaires’ Disease Found at New York Police Station
Ashley Southall – The New York Times

Science, publishing, and career

Microbiology Graduate Program – University of California

May 30, 2017.

A bit of a late night Digest today! Still here though, quite a few articles about rhizosphere, a hot topic at the moment; some genome sequences from ASM Genome Announcements, and a few methods & bioinformatics papers. Enjoy!

Multi-site human microbiome

Bacterial Composition and Diversity in Breast Milk Samples from Mothers Living in Taiwan and Mainland China
Shiao-Wen Li et al. – Frontiers in Microbiology

Review: Recent advances in dental biofilm: impacts of microbial interactions on the biofilm ecology and pathogenesis
Yung-Hua Li et al. – AIMS Bioengineering

The Evolving Cystic Fibrosis Microbiome: A Comparative Cohort Study Spanning Sixteen Years
Nicole Acosta et al. – Annals of the American Thoracic Society

Human epitelial microbiome

A tale of two risks: smoking, diabetes and the subgingival microbiome
Sukirth M. Ganesan et al. – The ISME Journal

Quantitative proteomic analysis of host epithelial cells infected by Salmonella enterica serovar Typhimurium
Linlu Qi et al. – Proteomics

Human gut microbiome

Distinctive microbiomes and metabolites linked with weight loss after gastric bypass, but not gastric banding
Zehra Esra Ilhan et al. – The ISME Journal

Microbe Profile: Akkermansia muciniphila: a conserved intestinal symbiont that acts as the gatekeeper of our mucosa
Willem M de Vos – Microbiology

Fecal Microbiota Transplantation: From Clostridium difficile to Inflammatory Bowel Disease
Robert J. Gianotti & Alan C. Moss – Gastroenterology & Hepatology

Bacteriophage transfer during faecal microbiota transplantation in Clostridium difficile infection is associated with treatment outcome
Tao Zuo et al. – Gut

Microbial diseases

Review: ‘Omic’ Approaches to Study Uropathogenic Escherichia coli Virulence
Alvin W. Lo et al. – Trends in Microbiology

Case report: Ecthyma Gangrenosum: Escherichia coli or Pseudomonas aeruginosa?
Mohamed Abbas et al. – Frontiers in Microbiology

General environmental microbiology

Successive range expansion promotes diversity and accelerates evolution in spatially structured microbial populations
Felix Goldschmidt et al. – The ISME Journal

Animal microbiome

Thesis: Biotic and Abiotic Factors Influence Formation and Ontogenic Dynamics of Molecularly Defined Gastro-Intestinal Microbial Communities in Lake Sturgeon (Acipenser Fulvescens) and Channel Catfish (Ictalurus Punctatus)
Abdul Razak – Michigan State University

Plant, root, and soil microbiome

Interactive effects of seasonal drought and elevated atmospheric carbon dioxide concentration on prokaryotic rhizosphere communities
Barbara Drigo et al. – Environmental Microbiology

The biogeographic pattern of microbial functional genes along an altitudinal gradient of the Tibetan pasture
Qi Qi et al. – Frontiers in Microbiology

Communication: Microbial functionality as affected by experimental warming of a temperate mountain forest soil—A metaproteomics survey
Dong Liu et al. – Applied Soil Ecology

Letter: Leaf bacterial diversity mediates plant diversity and ecosystem function relationships
Isabelle Laforest-Lapointe et al. – Nature

Soil amendments influence Pratylenchus penetrans populations, beneficial rhizosphere microorganisms, and growth of newly planted sweet cherry
Tristan T. Watson et al. – Applied Soil Ecology

Comparative analysis of bacterial community structure in the rhizosphere of maize by high-throughput pyrosequencing
Yi Yang et al. – PLoS One

Soil Warming Increases Arsenic Availability in the Rice Rhizosphere
Rebecca B. Neumann et al. – Agricultural & Environmental Letters

Secondary metabolite genes encoded by potato rhizosphere microbiomes in the Andean highlands are diverse and vary with sampling site and vegetation stage
Gajender Aleti et al. – Scientific Reports

Metagenomic-based impact study of transgenic grapevine rootstock on its associated virome and soil bacteriome
Jean-Michel Hilly et al. – Plant Biotechnology Journal

A Small Number of Low-abundance Bacteria Dominate Plant Species-specific Responses during Rhizosphere Colonization
Wayne Dawson et al. – Frontiers in Microbiology

Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling
Linwei Wu et al. – The ISME Journal

Book chapter: Cannabis Endophytes and Their Application in Breeding and Physiological Fitness
Parijat Kusari et al. – Cannabis sativa L. – Botany and Biotechnology

Water, estuarine and sediment microbiome

Nutrient Stoichiometry Shapes Microbial Community Structure in an Evaporitic Shallow Pond
Zarraz M.-P. Lee et al. – Frontiers in Microbiology

Microbes influence the biogeochemical and optical properties of maritime Antarctic snow
Hodson, AJ et al. – Journal of Geophysical Research

Bacterial diversity in Shahu lake, northwest China is significantly affected by nutrient composition rather than location
Jing-Yu Li et al. – Annals of Microbiology

Built environment

Effects of triclosan on bacterial community composition and Vibrio populations in natural seawater microcosms
Keri Ann Lydon et al. – Elementa Science

Thesis: Characterization of Microbial Contaminants Associated with Floor Material Types
Mridula Gupta – The Ohio State University

Microbial biotechnology

Magnetotactic Coccus Strain SHHC-1 Affiliated to Alphaproteobacteria Forms Octahedral Magnetite Magnetosomes
Heng Zhang et al. – Frontiers in Microbiology

Abundance and diversity of ammonia-oxidizing archaea in a biological aerated filter process
Hongyi Chen et al. – Annals of Microbiology

Biochemical Mechanisms and Catabolic Enzymes Involved in Bacterial Estrogen Degradation Pathways
Yi-Lung Chen et al. – Cell Chemical Biology

An environment friendly engineered Azotobacter can replace substantial amount of urea fertilizer and yet sustain same wheat yield
Umesh K. Bageshwar et al. – Applied and Environmental Microbiology

Biofertilizers and sustainable agriculture: exploring arbuscular mycorrhizal fungi
Nicholas O. Igiehon & Olubukola O. Babalola – Applied Microbiology and Biotechnology

Food microbiology

Removal of foodborne pathogen biofilms by acidic electrolyzed water
Qiao Han et al. – Frontiers in Microbiology

General microbiology and evolution

Systematics of haloarchaea and biotechnological potential of their hydrolytic enzymes
Amoozegar MA et al. – Microbiology

Surface sensing for flagellar gene expression on solid media in Paenibacillus sp. NAIST15-1
Kazuo Kobayashi et al. – Applied and Environmental Microbiology

Complete genome sequence of a denitrifying bacterium, Pseudomonas sp. CC6-YY-74, isolated from Arctic Ocean sediment
Xuenzheng Lin et al. – Marine Genomics

Draft Genome Sequence of Acidihalobacter ferrooxidans DSM 14175 (Strain V8), a New Iron- and Sulfur-Oxidizing, Halotolerant, Acidophilic Species
Himel N. Khaleque et al. – Genome Announcements

Draft Genome Sequence of Saccharomonospora sp. Strain LRS4.154, a Moderately Halophilic Actinobacterium with the Biotechnologically Relevant Polyketide Synthase and Nonribosomal Peptide Synthetase Systems
Scarlett Alonso-Carmona et al. – Genome Announcements

Genome-Wide Analyses Reveal Genes Subject to Positive Selection in Pasteurella multocida
Peili Cao et al. – Frontiers in Microbiology

Phages and viruses

Review: Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches
Stephen Hayes et al. – Viruses

Bioinformatics and statistics

Predicting microbial interactions from time series data with network information
Yan Wang et al. – International Journal of Data Mining and Bioinformatics

Commentary: Bioinformatics can boost metabolomics research
René Meier et al. – Journal of Biotechnology

Techniques and methods

Thesis: Carbon dioxide titration method for soil respiration measurements
Luis Martín Rubio – Tampere University of Applied Sciences

Protocol: Harnessing the Power of PCR Molecular Fingerprinting Methods and Next Generation Sequencing for Understanding Structure and Function in Microbial Communities
Sujal Phadke et al. – PCR

An optimized extraction method to remove humic acids interferences from soil samples prior to microbial proteome measurements
Chen Qian & Robert L. Hettich – Journal of Proteome Research

Microbes in the news

Gene Drives Could Wipe Out Insect-Borne Disease — But What’s the Price?
Shelly Fan – Ontological Design

Non-microbiology picks

Application of mass spectrometry-based metabolomics approaches for food safety, quality and traceability
María Castro-Puyana et al. – Trends in Analytical Chemistry

Hunting for Nature’s Treasures or Learning from Nature?: The Narrative Ambivalence of the Ecotechnological Turn
Sanne van der Hout & Martin Drenthen – Berghahn Journals

May 16, 2017

Our Tuesday Digest came a bit late but still it is packed with content! Lots going on, specially in the Plant & Soil Microbiome section. Good reading!

Events and jobs

Scientist for Food Microbiology and Modelling – nationale vacaturebank (Link in Dutch)

General human microbiome

The Threat of Antimicrobial Resistance on the Human Microbiome
Lauren Brinkac et al – Microbial Ecology

Human epitelial microbiome

Compositionally and functionally distinct sinus microbiota in chronic rhinosinusitis patients have immunological and clinically divergent consequences
Emily K. Cope et al – Microbiome

Review: Is the role of human female reproductive tract microbiota underestimated?
D. Kaminska & M. Gajecka – Beneficial Microbes

Human gut microbiome

Uncovering the trimethylamine-producing bacteria of the human gut microbiota
Silke Rath et al – Microbiome

Pre-print: The effect of treatment on the microbiota of patients diagnosed with colonic lesions
Marc A Sze et al – bioRxiv

Microbial diseases

Targeted Metagenome Based Analyses Show Gut Microbial Diversity of Inflammatory Bowel Disease patients
Zhibing Qiu et al – Indian Journal of Microbiology

Report: Zinc metalloproteinase ZmpC suppresses experimental pneumococcal meningitis by inhibiting bacterial invasion of central nervous systems
Masaya Yamaguchi et al – Virulence

Review: Fungal Biofilms and Polymicrobial Diseases
Caroline B. Costa-Orlandi et al – Journal of Fungi

Inflammatory bacteriome featuring Fusobacterium nucleatum and Pseudomonas aeruginosa identified in association with oral squamous cell carcinoma
Nezar Noor Al-hebshi et al – Scientific Reports

Identification of Atypical El Tor V. cholerae O1 Ogawa Hosting SXT Element in Senegal, Africa
Bissoume Sambe-Ba et al – Frontiers in Microbiology

General environmental microbiome

Following Rapoport’s Rule: The geographic range and genome size of bacterial taxa decline at warmer latitudes
Gavin Lear et al – Environmental Microbiology

Animal experiments

Examining the efficacy of intravenous administration of predatory bacteria in rats
Kenneth Shatzkes et al – Scientific Reports

Animal microbiome

Characterization of the juvenile green turtle (Chelonia mydas) microbiome throughout an ontogenetic shift from pelagic to neritic habitats
James T. Price et al – PLoS One

Temporal Variations of Microbiota Associated with the Immature Stages of Two Florida Culex Mosquito Vectors
Dagne Duguma et al – Microbial Ecology

Understanding the gut microbiome of dairy calves: Opportunities to improve early-life gut health
Nilusha Malmuthuge & Le Luo Guan – Journal of Dairy Science

Pre-print: Uncovering the drivers of animal-host microbiotas with joint distribution modeling
Johannes R. Björk – bioRxiv

Plant, root, and soil microbiome

Ecology and Genomic Insights on Plant-Pathogenic and -Nonpathogenic Endophytes
Günter Brader et al – Annual Review of Phytopathology

High-throughput sequencing reveals bacterial community composition in the rhizosphere of the invasive plant Flaveria bidentis
Z Song et al – Weed Research

Functioning grouped soil microbial communities according to ecosystem type, based on comparison of fallows and meadows in the same region
Dominika Chmolowska et al – Science of the Total Environment

Microbial Community Dynamics in Soil Depth Profiles over 120,000 Years of Ecosystem Development
Stephanie Turner et al – Frontiers in Microbiology

Functional structure of the bromeliad tank microbiome is strongly shaped by local geochemical conditions
Stilianos Louca et al – Environmental Microbiology

Thesis: Culture-Independent Analysis of Microbial Communities Associated with Hydroponically Grown “Living Lettuce”
Abby Matthews – The University of Mississippi

Effect of fumigation with chloropicrin on soil bacterial communities and genes encoding key enzymes involved in nitrogen cycling
Jun Li et al – Environmental Pollution

Review: The influence of bacteria on multi-trophic interactions among plants, psyllids, and pathogen
Cecilia Tamborindeguy et al – Insect Science

Pre-print: Yeasts dominate soil fungal communities in three lowland Neotropical rainforests
Micah Dunthorn et al – bioRxiv

Bacterial inoculants for enhanced seed germination of Spartina densiflora: Implications for restoration of metal polluted areas
Paredes-Páliz K et al – Marine Pollution Bulletin

A Phloem-Feeding Insect Transfers Bacterial Endophytic Communities between Grapevine Plants
Sebastiàn Lòpez-Fernàndez et al – Frontiers in Microbiology

Water, estuarine and sediment microbiome

Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA)
Jessica M. Morrison et al – PLoS One

Bacterioplankton assemblages in coastal ponds reflect the influence of hydrology and geomorphological setting
Megan J. Huggett et al – FEMS Microbiology Ecology

Unveiling microbial interactions in stratified mat communities from a warm saline shallow pond
Aurélien Saghaï et al – Environmental Microbiology

Extremophile and space microbiome

Thesis: Microbial Biogeography of the Arctic Cryosphere
Aviaja Zenia Edna Lyberth Hauptmann & Thomas Sicheritz-Pontén – Technical University of Denmark

Thermal adaptation strategies of the extremophile bacterium Thermus filiformis based on multi-omics analysis
F. Mandelli et al – Extremophiles

Aspergillus atacamensis and A. salisburgensis: two new halophilic species from hypersaline/arid habitats with a phialosimplex-like morphology
Livia Martinelli et al – Extremophiles

Built environment

Variation of microbial communities and functional genes during the biofilm formation in raw water distribution systems and associated effects on the transformation of nitrogen pollutants
Wei Chen et al – Environmental Science and Pollution Research

Microbiota and Particulate Matter Assessment in Portuguese Optical Shops Providing Contact Lens Services
Carla Viegas et al – Healthcare

QAC modified PVDF membranes: Antibiofouling performance, mechanisms, and effects on microbial communities in an MBR treating municipal wastewater
Mei Chen et al – Water Research

Microbial biotechnology

Green energy generation from plant microbial fuel cells (PMFC) using compost and a novel clay separator
A. Carmalin Sophia & S. Sreeja – Sustainable Energy Technologies and Assessments

Dynamics of two methanogenic microbiomes incubated in polycyclic aromatic hydrocarbons, naphthenic acids, and oil field produced water
Bohanis J. Oko et al – Biotechnology for Biofuels

Optimization of the extraction and purification of the compatible solute ectoine from Halomonas elongate in the laboratory experiment of a commercial production project
Ruifeng Chen et al – World Journal of Microbiology and Biotechnology

Review: Large scale cultivation of genetically modified microalgae: A new era for environmental risk assessment
Tracey A. Beacham et al – Algal Research

Subcellular localization based comparative study on radioresistant bacteria: A novel approach to mine proteins involve in radioresistance
Divya Vishambra et al – Computational Biology and Chemistry

Food microbiology

Meta-omics insights in the microbial community profiling and functional characterization of fermented foods
Gu Chen et al – Trends in Food Science & Technology

Sulfites and the Wine Metabolome
Chloé Roullier-Gall et al – Food Chemistry

Meta-omics insights in the microbial community profiling and functional characterization of fermented foods
Gu Chen et al – Trends in Food Science & Technology


Pre-print: Bifunctionality of a biofilm matrix protein controlled by redox state
Sofia Arnaouteli et al – bioRxiv

General microbiology and evolution

The biology and the importance of Photobacterium species
Ibrahim Musa Moi et al – Applied Microbiology and Biotechnology

Review: A Metagenomic Approach to Cyanobacterial Genomics
Danillo O. Alvarenga et al – Frontiers in Microbiology

In vitro affinity of Deinococcus radiodurans MutS towards mismatched DNA exceeds that of its orthologues from Escherichia coli and Thermus thermophilus
Michael Banasik et al – Journal of Biotechnology

Report: Single-cell genomics reveals pyrrolysine-encoding potential in members of uncultivated archaeal candidate division MSBL1
Yue Guan et al – Environmental Microbiology Reports

Phages and viruses

Characterization of prophages of Lactococcus garvieae
Giovanni Eraclio et al – Scientific Reports

Review: Viruses and miRNAs: More Friends than Foes
Patrice Bruscella et al – Frontiers in Microbiology

Bioinformatics and statistics

SteadyCom: Predicting microbial abundances while ensuring community stability
Siu Hung Joshua Chan et al – PLoS Computational Biology

Techniques and methods

Preview: An Elegan(t) Screen for Drug-Microbe Interactions
Alison Vrbanac et al – Cell Host & Microbe

Microbes in the news

Gut microbiome may predict response to biologic therapy for inflammatory bowel disease
ScienceDaily – Original Paper

Diseased Microbiome Varies From Condition to Condition
Ciara Curtin – GenomeWeb

Vini’s non-microbiology picks

Sociomics: Using Omic Approaches to Understand Social Evolution
Melanie Ghoul et al – Trends in Genetics

May 2, 2017

The MB Digest Team hopes everyone had a good Labour Day holiday (or just a good day depending on where you are). Our Tuesday digest is full of fresh articles, a few news pieces, and lots going on in the Environmental Microbiome sections. Enjoy!

Events and jobs

PhD in soil microbiology
Teagasc Johnstown Castle

General microbiome

Analysis of stability to cheaters in models of antibiotic degrading microbial communities
András Szilágyi et al. – Journal of Theoretical Biology

Revew: Human genome-microbiome interaction: metagenomics frontiers for the aetiopathology of autoimmune diseases
Aycan Gundogdu & Ufuk Nalbantoglu – Microbial Genomics

Review: Fingerprinting microbiomes towards screening for microbial antibiotic resistance
Naifu Jin et al – Integrative Biology

Comparative genomics and metabolomics analyses of the adaptation mechanism in Ketogulonicigenium vulgare-Bacillus thuringiensis consortium
Nan Jia et al – Nature Scientific Reports

Multi-site human microbiome

Review: A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: implications for research on the pioneer infant microbiome
Maria Elisa Perez-Muñoz et al – Microbiome

Review: Interaction between the gut microbiome and mucosal immune system
Na Shi et al – Military Medical Research

Human gut microbiome

Bacterial Diversity of the Gastric Content of Preterm Infants during Their First Month of Life at the Hospital
Moles L. et al. – Frontiers in Nutrition

Opinion: The shrinking human gut microbiome
Moeller AH – Current Opinion in Microbiology

Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome
Labus JS et al. – Microbiome

Gut microbial metabolites limit the frequency of autoimmune T cells and protect against type 1 diabetes
Eliana Mariño et al. – Nature Immunology

Microbial diseases

The Novel ASIC2 Locus is Associated with Severe Gingival Inflammation
Zhang S. et al. – JDR Clinical & Translational Research

In vitro Multi-Species Biofilms of Methicillin-Resistant Staphylococcus aureus and Pseudomonas aeruginosa and Their Host Interaction during In vivo Colonization of an Otitis Media Rat Model
Yadav MK et al. – Frontiers in Cellular and Infectious Microbiology

Reduction in fecal microbiota diversity and short-chain fatty acid producers in Methicillin-resistant Staphylococcus aureus infected individuals as revealed by PacBio single molecule, real-time sequencing technology
J Zhao et al – European Journal of Clinical Microbiology & Infectious Diseases

Perspective: Treatable traits and therapeutic targets: goals for systems biology in infectious disease
Clark D. Russell & J. Kenneth Baillie – Current Opinion in Systems Biology

General Environmental Microbiome

Review: Effects and mechanisms of biochar-microbe interactions in soil improvement and pollution remediation: A review
Zhu X et al – Environmental Pollution

Sulfur flows and biosolids processing: Using Material Flux Analysis (MFA) principles at wastewater treatment plants
Fisher RM et al. – Journal of Environmental Management

Exploration of the relationship between biogas production and microbial community under high salinity conditions
Shaojie Wang et al – Nature Scientific Reports

Review: Phytoremediation of Water Bodies
E. Etim et al. – Current Environmental Engineering

Review: Role of Phytochelators in Land Reclamation: Recent Progress and Perspectives
Resham Sharma et al. – Current Environmental Engineering

Environmental Metabarcoding Reveals Contrasting Belowground and Aboveground Fungal Communities from Poplar at a Hg Phytomanagement Site
Alexis Durand et al. – Microbial Ecology

Monitoring global protein thiol-oxidation and protein S-mycothiolation in Mycobacterium smegmatis under hypochlorite stress
Melanie Hillion et al – Nature Scientific Reports

A comprehensive multi-omics approach uncovers adaptations for growth and survival of Pseudomonas aeruginosa on n-alkanes
Sarah L Grady et al – BMC Genomics

Interpreting Omic Data for Microbially Influenced Corrosion: Lessons from a Case Study Involving a Seawater Injection System
Craig Bartling et al – OnePetro

Land scale biogeography of arsenic biotransformation genes in estuarine wetland
Si-Yu Zhang et al – Environmental Microbiology

Animal experiments

Effects of Saccharomyces cerevisiae fermentation products on dairy calves: Ruminal fermentation, gastrointestinal morphology, and microbial community
Xiao JX et al. – Journal of Dairy Science

Immunological effects of reduced mucosal integrity in the early life of BALB/c mice
Bendtsen KM et al – PLoS One

Dietary Supplementation with Raspberry Whole Fruit Modifies the Relative Abundance of Fecal Microbial Communities in Obese Diabetic (db/db) Mice
Giuliana Noratto et al – The FASEB Journal

Chemical and pathogen-induced inflammation disrupt the murine intestinal microbiome
Mikayla A. Borton et al – Microbiome

Animal microbiome

Diversity of culturable bacterial communities in the intestinal tracts of goldfish (Carassius auratus) and their ability to produce N-acyl homoserine lactone
Haruo Sugita et al. – Folia Microbiologica

Viral gut metagenomics of sympatric wild and domestic canids, and monitoring of viruses: Insights from an endangered wolf population
Nádia Conceição-Neto et al – Ecology and Evolution

Characterization of the fecal microbiome during neonatal and early pediatric development in puppies
Blake C. Guard et al – PLoS One

The environmental and host-associated bacterial microbiota of Arctic seawater-farmed Atlantic salmon with ulcerative disorders
C Karlsen et al – Journal of Fish Diseases

Pre-print: Caterpillars lack a resident gut microbiome
Tobin J Hammer et al – bioRxiv

Bacterial microbiome of the nose of healthy dogs and dogs with nasal disease
Barbara Tress et al – PLoS One

Plant, root, and soil microbiome

First “charosphere” view towards the transport and transformation of Cd with addition of manure derived biochar
Wang L et al. – Environmental Pollution

Competition drives the response of soil microbial diversity to increased grazing by vertebrate herbivores
Eldridge DJ et al. – Ecology

Soil aggregation and associated microbial communities modify the impact of agricultural management on carbon content
Pankaj Trivedi et al – Environmental Microbiology

Altitudinal, seasonal and interannual shifts in microbial communities and chemical composition of soil organic matter in Alpine forest soils
José A. Siles et al – Soil Biology and Biochemistry

Water, estuarine and sediment microbiome

Pre-peer review: Microbiome succession during ammonification in eelgrass bed sediments
Cassandra L Ettinger et al – PeerJ

Microbial communities in sediment from Zostera marina patches, but not the Z. marina leaf or root microbiomes, vary in relation to distance from patch edge
Cassandra L Ettinger et al – PeerJ

Extremophile and space microbiome

In-depth characterization of bacterial and archaeal communities present in the abandoned Kettara pyrrhotite mine tailings (Morocco)
Odile Bruneel et al – Extremophile
Microbial biotechnology

Impact of selectively enriched microbial communities on long-term fermentative biohydrogen production
Kanniah Goud R. et al – Bioresource Technology

Review: Cooperation in microbial communities and their biotechnological applications
Matteo Cavaliere et al – Environmental Microbiology

Metabolic engineering of Escherichia coli for higher alcohols production: An environmentally friendly alternative to fossil fuels
Ana L. Gonçalves & Manuel Simões – Renewable and Sustainable Energy Reviews

Weak magnetic field: A powerful strategy to enhance partial nitrification
Zhibin Wang et al – Water Research

General microbiology and evolution

Comparative genomics of host-symbiont and free-living Oceanobacillus species
Kumar Mondal A. et al – Genome Biology and Evolution

Draft Genome Sequence of Plantibacter flavus Strain 251 Isolated from a Plant Growing in a Chronically Hydrocarbon-Contaminated Site
Rhea Lumactud et al. – Genome Announcements

HexA is a versatile regulator involved in the control of phenotypic heterogeneity of Photorhabdus luminescens
Langer A. et al – PLoS One

Complete Genome Sequence of the Gamma-Aminobutyric Acid-Producing Strain Streptococcus thermophilus APC151
Daniel M Linares et al – Genome Announcements

Bioinformatics and statistics

MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data
Dhariwal A. et al – Nucleic Acids Research

Techniques and methods

Perspective: The Role of the Negative Control in Microbiome Analyses
Kyle Edmonds & Laura Williams – The FASEB Journal

Perspective: A Robust Framework for Microbial Archaeology
Warinner C. – Annual Review of Genomics and Human Genetics

Microbes in the news

Gut bacteria found to be linked to chronic fatigue syndrome
Victor Marchione – Belmarra Health News

Zapping bacteria with sanitizers made of paper

‘Electric’ bacteria can purify sewage water – fast

How The Gut May Influence Food Choices: Fruit Flies With More Bacteria Had Fewer Cravings
Janissa Delzo – Medical Daily

Harmless Bacteria on Teeth Can Hijack Harmful One That Causes Lung Infections, Study Finds
Magdalena Kegel – Cystic Fibrosis News

Retired US Navy Veteran Comments on Military Microbiome Study
Yahoo News

Microbes In Human Body: Connection Between Abundance Of Various Microbiota Species & Accessibility Of Its Resources
Piyali Roy – The Science Times

April 25, 2017

A bit of a late morning Digest today, as it is packed with articles! Diverse themes, such as rhizosphere microbiome, lots of biotechnology pieces, and insightful reviews on gut microbiota and herbivory, “wild” microbiomes and ecological stoichiometry.

General microbiome

Review: The microbiome in anti-cancer therapy
Stavros Bashiardes et al – Seminars in Immunology

Perspective: Gut Microbiota as a Trigger of Accelerated Directional Adaptive Evolution: Acquisition of Herbivory in the Context of Extracellular Vesicles, MicroRNAs and Inter-Kingdom Crosstalk
Marco Romano – Frontiers in Microbiology

Multi-site human microbiome

Review: Lung Homeostasis: Influence of Age, Microbes, and the Immune System
Clare M. Lloyd & Benjamin J. Marsland – Immunity

Human epitelial microbiome

The oral microbiome community variations associated with normal, potentially malignant disorders and malignant lesions of the oral cavity
Mok Shao Feng et al – Malaysian Journal of Pathology

Human gut microbiome

‘Microbes in sport’ -The potential role of the gut microbiota in athlete health and performance
Rankin A. et al – Journal of Sports Medicine

Effect of pistachio consumption on the modulation of urinary gut microbiota-related metabolites in prediabetic subjects
Hernandéz-Alonso P et al – Journal of Nutritional Biochemistry

Microbial diseases

Alteration of stomach microbiota compositions in the progression of gastritis induces nitric oxide in gastric cell
Tianyi Dong et al – Experimental and Therapeutic Medicine

General environmental microbiome

Review: Evolutionary Biology Needs Wild Microbiomes
Sarah M. Hird – Frontiers in Microbiology

Stratified Bacterial Diversity along Physico-chemical Gradients in High-Altitude Modern Stromatolites
Diego M. Toneatti et al – Frontiers in Microbiology

Origin-Dependent Variations in the Atmospheric Microbiome Community in Eastern Mediterranean Dust Storms
Daniella Gat et al – Environmental Science and Technology

Animal experiments

Urinary and Fecal Metabonomics Study of the Protective Effect of Chaihu-Shu-Gan-San on Antibiotic Induced Gut Microbiota Dysbiosis in Rats
Meng Yu et al – Nature Scientific Reports

Proteomic analysis of a mosquito host cell response to persistent Wolbachia infection
Gerald Baldridge et al – Research in Microbiology

Effect of ensiled mulberry leaves and sun-dried mulberry fruit pomace on the fecal bacterial community composition in finishing steers
Yan Li et al – BMC Microbiology

Effects of various weaning times on growth performance, rumen fermentation and microbial population of yellow cattle calves
Mao H et al – Asian-Australasian Journal of Animal Science

Effects of various levels of dietary copper supplementation with copper sulfate and copper hydroxychloride on Pacific white shrimp Litopenaeus vannamei performance and microbial communities
Yangen Zhou et al – Aquaculture

Plant, root, and soil microbiome

Soil Acidification Aggravates the Occurrence of Bacterial Wilt in South China
Shili Li et al – Frontiers in Microbiology

Interaction between DAPG and HCN producing Pseudomonas brassicacearum LBUM300 and Clavibacter michiganensis subsp. michiganensis in the rhizosphere of tomato
Mélanie M. Paulin et al – Applied and Environmental Microbiology

Distance-dependent varieties of microbial community structure and metabolic functions in the rhizosphere of Sedum alfredii Hance during phytoextraction of a cadmium-contaminated soil
Yang W et al – Environmental Science and Pollution Research

Rhizosphere Engineering: Enhancing Sustainable Plant Ecosystem Productivity in a Challenging Climate
Amirhossein Ahkami et al – Rhizosphere

Influence of red mud on soil microbial communities: Application and comprehensive evaluation of the Biolog EcoPlate approach as a tool in soil microbiological studies
Feigl V et al – Science of the Total Environment

Response of microbial community of organic-matter-impoverished arable soil to long-term application of soil conditioner derived from dynamic rapid fermentation of food waste
Jiaqi Hou et al – Plos One

Effects of adding trace elements on rice straw anaerobic mono-digestion: Focus on changes in microbial communities using high-throughput sequencing
Yafan Cai et al – Bioresource Technology

Cereal-legume intercropping modifies the dynamics of the active rhizospheric bacterial community
E. Taschen et al – Rhizosphere

Water, estuarine and sediment microbiome

Microbial Community Response on Wastewater Discharge in Boreal Lake Sediments
Jatta Saarenheimo et al – Frontiers in Microbiology

Perspective: The Hadal Biosphere: Recent insights and new directions
Rulong Liu et al – Deep Sea Research Part II: Topical Studies in Oceanography

Bacterial community dynamics and functional variation during the long-term decomposition of cyanobacterial blooms in-vitro
Limei Shi et al – Science of the Total Environment

Mixing of water masses caused by a drifting iceberg affects bacterial activity, community composition and substrate utilization capability in the Southern Ocean
Julie Dinasquet et al – Environmental Microbiology

DNA metabarcoding of unfractionated water samples relates phyto-, zoo- and bacterioplankton dynamics and reveals a single-taxon bacterial bloom
Christian Wurzbacher et al – Environmental Microbiology Reports

Shifts in soil microbial metabolic activities and community structures along a salinity gradient of irrigation water in a typical arid region of China
Lijuan Chen et al – Science of the Total Environment

Large-scale seaweed cultivation diverges water and sediment microbial communities in the coast of Nan’ao Island, South China Sea
Xinfei Xie et al – Science of The Total Environment

Extremophile and space microbiome

Review: Toward biotechnology in space: High-throughput instruments for in situ biological research beyond Earth
Fathi Karouia – Biotechnology Advances

Built environment

Diversity changes of microbial communities into hospital surface environments
Rika Yano et al – Journal of Infection and Chemotherapy

Microbial communities in the functional areas of a biofilm reactor with anaerobic-aerobic process for oily wastewater treatment
Li J et al – Bioresource Technology

Dominance of candidate Saccharibacteria in a membrane bioreactor treating medium age landfill leachate: Effects of organic load on microbial communities, hydrolytic potential and extracellular polymeric substances
Remmas N. et al – Bioresource Technology

Microbial biotechnology

Review: Uncovering Potential Applications of Cyanobacteria and Algal Metabolites in Biology, Agriculture and Medicine: Current Status and Future Prospects
Rachana Singh et al – Frontiers in Microbiology

The Ability of Typha angustifolia L. for Degradation of BOD and COD in Wastewater of Tofu Industry Using Phytoremediation
Pertiwi Andarani et al – Advanced Science Letters

Reversible Anaerob-Evapotranspiration Process for Removal of High Strength Ammonium in Leachate from Tropical Landfill
Badrus Zaman et al – Advanced Science Letters

Strain specific variation in plant growth promoting volatile organic compound production by five different Pseudomonas spp. as confirmed by response of Vigna radiata seedlings
Jishma P et al – Journal of Applied Microbiology

Microbial reductive dehalogenation of trihalomethanes by a Dehalobacter-containing co-culture
Zhao S. et al – Applied Microbiology and Biotechnology

Inhibitory effect of coumarin on syntrophic fatty acid oxidizing and methanogenic cultures and biogas reactor microbiomes
Denny Popp et al – Applied and Environmental Microbiology

Food microbiology

Impact of solar radiation exposure on phyllosphere bacterial community of red-pigmented baby leaf lettuce
Pilar Truchado et al – Food Microbiology

Effect of abattoir and cut on variations in microbial communities of vacuum-packaged beef
Mandeep Kaur et al – Meat Science

Smokeless tobacco products harbor diverse bacterial microbiota that differ across products and brands
Smyth EM et al – Applied Microbiology and Biotechnology
General Microbiology

Protein Acetylation and Its Role in Bacterial Virulence
Jie Ren et al – Trends in Microbiology

Perspective: Ecological Stoichiometry beyond Redfield: An Ionomic Perspective on Elemental Homeostasis
Punidan D. Jeyasingh et al – Frontiers in Microbiology


Complete Genome Sequence of Pseudomonas protegens H78, a Plant Growth–Promoting Rhizobacterium
Xianqing Huang et al – Genome Announcements

Draft Genome Sequences of Two Hydrogenogenic Carboxydotrophic Bacteria, Carboxydocella sp. Strains JDF658 and ULO1, Isolated from Two Distinct Volcanic Fronts in Japan
Yuto Fukuyama et al – Genome Announcements

The genomic sequence of Exiguobacterium chiriqhucha str. N139 reveals a species that thrives in cold waters and extreme environmental conditions
Ana Gutiérrez-Preciado et al – PeerJ

Phages and viruses

A novel type of polyhedral viruses infecting hyperthermophilic archaea
Ying Liu et al – Journal of Virology

Phage therapy: an alternative or adjunct to antibiotics?
Shawna McCallin & Harald Brüssow – Emerging Topics in Life Sciences

Highlights from the HIV Research for Prevention Conference (R4P)
Sandhya Vasan et al – Journal of Virus Eradication

Bioinformatics and statistics

A powerful microbiome-based association test and a microbial taxa discovery framework for comprehensive association mapping
Hyunwook Koh et al – Microbiome

The BRENDA Enzyme Information System–From a Database to an Expert System
I. Schomburg et al – Journal of Biotechnology

HirBin: high-resolution identification of differentially abundant functions in metagenomes
Tobias Österlund et al – BMC Genomics

A novel genome signature based on inter-nucleotide distances profiles for visualization of metagenomic data
Xian-Hua Xie et al – Physica A: Statistical Mechanics and its Applications

Data Intensive Genome Level Analysis for Identifying Novel,Non-Toxic Drug Targets for Multi Drug Resistant Mycobacterium tuberculosis
Divneet Kaur et al – Nature Scientific Reports

Techniques and methods

Building a Translational Microbiome Toolbox
Payal Joglekar & Julia Segre – Cell

April 10, 2017

A busy Monday digest to start your week well. Quite a few pieces from the Journal of Biological Chemistry today, as it released a special issue on host-microbiome metabolic interplay. A lot of review pieces on microbes and human health, specially in the Microbial Diseases section.

General microbiome

Introduction to the Thematic Minireview Series: Host-Microbiome Metabolic Interplay.
Banerjee R – Journal of Biological Chemistry

Human epitelial microbiome

Review: Microbiota in Exhaled Breath Condensate and the Lung
Glendinning L – Applied Environmental Microbiology

Review: The microbiota of the respiratory tract: gatekeeper to respiratory health
Wing Ho Man – Nature Reviews Microbiology

Human gut microbiome

Review: Influence of diet on the gut microbiome and implications for human health
Singh RK – Journal of Trans. Medicine

Review: Glucuronides in the Gut: Sugar-Driven Symbioses Between Microbe and Host
Pellock SJ – Journal of Biological Chemistry

Review: Chemical signaling between gut microbiota and host chromatin: What is your gut really saying?
Krautkramer KA – Jorunal of Biological Chemistry

Exposure to household furry pets influences the gut microbiota of infant at 3–4 months following various birth scenarios
Hein M. Tun – Microbiome

Review: Microbial Metabolites in Health and Disease: Navigating the Unknown in Search of Function
Martinez KB – Journal of Biological Chemistry

Review: Understanding the role of the gut ecosystem in Diabetes Mellitus
Aw W & Fukuda S – Journal of Diabetes Investigation

Microbial diseases

Review: Colonization Resistance: The Deconvolution of a Complex Trait
Olsan EE – Journal of Biological Chemistry

Helicobacter pullorum: An Emerging Zoonotic Pathogen
Sundus Javed – Frontiers in Microbiology

Bacterial virulence phenotypes of Escherichia coli and host susceptibility determine risk for urinary tract infections
Henry L. Schreiber IV – Science Trans. Medicine

Distribution of Integrons and Phylogenetic Groups among Enteropathogenic Escherichia coli Isolates from Children
Taru Singh – Frontiers in Microbiology

Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from the Gram-Positive Bacterial Pathogen A. vaginae, an Immunoevasive Factor that Interacts with the Human C5a Anaphylatoxin
Javier Querol-García – Frontiers in Microbiology

Gene Expression Profiling of Transcription Factors of Helicobacter pylori under Different Environmental Conditions
Miguel A. De la Cruz – Frontiers in Microbiology

The gut-kidney axis in IgA nephropathy: role of microbiota and diet on genetic predisposition
Coppo R. – Pediatrical Nephrology

Animal experiments

Characterization of the Fecal Bacterial Microbiota of Healthy and Diarrheic Dairy Calves
Gomez DE – Journal of Veterinary Internal Medicine

High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice
Liang Xiao – Microbiome

Plant, root, and soil microbiome

Leaf Litter Chemistry Drives the Structure and Composition of Soil Testate Amoeba Communities in a Tropical Montane Rainforest of the Ecuadorian Andes
Krashevska V – Microbial Ecology

Water, estuarine and sediment microbiome

Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment
Wurzbacher C – Microbiome

Built environment

Deciphering conjugative plasmid permissiveness dynamics in wastewater microbiomes
Jacquiod S – Molecular Ecology

Microbial biotechnology

Targeting of Microbe-Derived Metabolites to Improve Human Health: The Next Frontier for Drug Discovery
Brown JM & Hazen SL – Journal of Biological Chemistry

Genome Sequencing Reveals the Complex Polysaccharide-Degrading Ability of Novel Deep-Sea Bacterium Flammeovirga pacifica WPAGA1
Boliang Gao – Frontiers in Microbiology

Phytochemical Characterization of Terminalia catappa Linn. Extracts and Their antifungal Activities against Candida spp.
Analucia G. Terças – Frontiers in Microbiology

Natural Product Discovery from the Human Microbiome
Wilson MR – Journal of Biological Chemistry

Enhanced methane production by semi-continuous mesophilic co-digestion of potato waste and cabbage waste: Performance and microbial characteristics analysis
Mu H – Bioresource Technology

General microbiology and evolution

Evidence for early life in Earth’s oldest hydrothermal vent precipitates
Matthew S. Dodd – Nature

Determining the bacterial cell biology of Planctomycetes
Christian Boedeker – Nature Communications

Phages and viruses

Letter: CRISPR–Cas systems exploit viral DNA injection to establish and maintain adaptive immunity
Joshua W. Modell – Nature

Multiple origins of viral capsid proteins from cellular ancestors
Mart Krupovic & Eugene V. Koonin – PNAS

Molecular Dynamics Simulation of the Influenza A(H3N2) Hemagglutinin Trimer Reveals the Structural Basis for Adaptive Evolution of the Recent Epidemic Clade 3C.2a
Masaru Yokoyama – Frontiers in Microbiology

Techniques and methods

The Use of Degenerate Primers in qPCR Analysis of Functional Genes Can Cause Dramatic Quantification Bias as Revealed by Investigation of nifH Primer Performance
Gaby JC & Buckley DH – Microbial Ecology

Review: The impact of culturomics on taxonomy in clinical microbiology
Rita Abou Abdallah – Antonie van Leeuwenhoek

Review: Methodological approaches for monitoring opportunistic pathogens in premise plumbing: A review
Wang H – Water Research

Microbes in the news

One in three pints served in pubs use ‘bad’ bacteria-filled beer because landlords aren’t cleaning the pumps properly
Sara Kamouni – The Sun UK

Melioidosis: More cases of potentially fatal bacterium from NT dirt emerge
Eleni Roussos – ABC News

Vini’s non-microbiology picks

Novel soil-inhabiting clades fill gaps in the fungal tree of life.
Tedersoo L – Microbiome

Pre-print: Looking into Pandora’s Box: The Content of Sci-Hub and its Usage
Bastian Greshake – F1000 Research

March 25, 2017

A short Saturday digest for this weekend, featuring a review on dry habitat bacteria published on Nature Reviews Microbiology and an interesting piece on how knowledge of Systems Biology can aid in biochemical production challenges.

General microbiome

Review: Xerotolerant bacteria: surviving through a dry spell
Pedro H. Lebre – Nature Reviews Microbiology

Human gut microbiome

Review: Targeting the Microbiome in Heart Failure
Allyson Zabell, W.H. Wilson Tang – Current Treatment Options in Cardiovascular Medicine

Review: Gut microbiota: Neonatal gut microbiota induces lung immunity against pneumonia
Sabrina Tamburini & Jose C. Clemente – Nature Reviews Gastroenterology & Hepatology

Temporal dynamics of the gut microbiota in people sharing a confined environment, a 520-day ground-based space simulation, MARS500
Silvia Turroni – Microbiome

Review: Role of the small intestine, colon and microbiota in determining the metabolic fate of polyphenols
Gary Williamson & Michael N. Clifford – Biochemical Pharmacology

Microbial diseases

Review: Pathogenic Mechanisms of Cryptosporidium and Giardia
Gabriela Certad – Trends in Parasitology

Animal microbiome

Genome Reduction and Microbe-Host Interactions Drive Adaptation of a Sulfur-Oxidizing Bacterium Associated with a Cold Seep Sponge
Ren-Mao Tian – mSystems

Plant, root, and soil microbiome

Intercropping maize and common bean enhances microbial carbon and nitrogen availability in low phosphorus soil under Mediterranean conditions
Mourad Latati – European Journal of Soil Biology

Antibiotic and Heavy Metal Tolerance of Some Indigenous Bacteria Isolated From Petroleum Contaminated Soil
Jai Godheja – International Journal of Current Microbiology and Applied Sciences

Water, estuarine and marine microbiome

Sediment depth and habitat as predictors of the diversity and composition of sediment bacterial communities in an inter-tidal estuarine environment
Daniel F. R. Cleary – Marine Ecology

Metagenomic and Culture-Dependent Analysis of the Bacterial Diversity of a Hot Spring Reservoir as a Function of the Seasonal Variation
B. A. Kikani – International Journal of Environmental Research

Space and extremophile microbiome

Stratosphere Conditions Inactivate Bacterial Endospores from a Mars Spacecraft Assembly Facility
Christina L. Khodadad – Astrobiology

Built environment

Short-term Effects of Great Cormorant Droppings on Water Quality and Microbial Community of an Artificial Agricultural Reservoir
Il Han – Journal of Environmental Quality

Microbial biotechnology

Effect of bioaugmentation by cellulolytic bacteria enriched from sheep rumen on methane production from wheat straw
E. Gozde Ozbayram – Anaerobe

Systems biology solutions for biochemical production challenges
Anne Sofie Lærke Hansen – Current Opinion in Biotechnology

General microbiology

The Pangenome of the genus Clostridium
Zulema Udaondo – Environmental Microbiology

March 16, 2017.

A long review today, lots of environmental microbiome, a few papers on the methods, virus and microbial biotechnology sections and at the end a Nature announcement for transparency policy updates, aiming for better research reproducibility.

Oral Microbiome

Targeting of Streptococcus mutans Biofilms by a Novel Small Molecule Prevents Dental Caries and Preserves the Oral Microbiome
S. S. Garcia – Journal of Dental Research

Human nearly-sterile sites

Review: Microbiome effects on immunity, health and disease in the lung
Shakti D. Shukla – Clinical & Translational Immunology

Animal Microbiome

The Relative Abundance and Transcriptional Activity of Marine Sponge-Associated Microorganisms Emphasizing Groups Involved in Sulfur Cycle
Sigmund Jensen – Marine Ecology

Animal experiments

Influence of dairy by-product waste milk on the microbiomes of different gastrointestinal tract components in pre-weaned dairy calves
Y. F. Deng – Scientific Reports

Antiprotozoal Effect of Saponins in the Rumen Can Be Enhanced by Chemical Modifications in Their Structure
Eva Ramos-Morales – Frontiers in Microbiology

Plant, root, and soil microbiome

Habitat-specific patterns and drivers of bacterial β-diversity in China’s drylands
Xiao-Bo Wang – The ISME Journal

Phosphate solubilizing microbes: an effective and alternative approach as
Kumar Anand – International Journal of Pharmacy and Pharmaceutical Sciences

Master’s thesis: An Investigation Of The Tri-Trophic Interactions In
The Rhizosphere Of Medicago Truncatula Using A
Functional Microbiome Approach
Amanda Anne Rosier – University of Delaware

Water and extremophile microbiome

Archaea Dominate the Ammonia-Oxidizing Community in Deep-Sea Sediments of the Eastern Indian Ocean—from the Equator to the Bay of Bengal
Jing Wang – Frontiers in Microbiology

Characterization of bacterial community associated with phytoplankton bloom in a eutrophic lake in South Norway using 16S rRNA gene amplicon sequence analysis
Niranjan Nitin Parulekar – PlOS One

Sediment depth and habitat as predictors of the diversity and composition of sediment bacterial communities in an inter-tidal estuarine environment
Daniel F. R. Cleary – Marine Ecology

Built environment

Impact of water heater temperature setting and water use frequency on the building plumbing microbiome
Pan Ji – The ISME Journal

Food microbiology

Effects of cellulase-producing bacteria on bacterial community structure and diversity during fermentation of Chinese liquor grains
J. H. Guo – The Journal of The Institute of Brewing

Microbial Biotechnology

The role of inoculum and reactor configuration for microbial community composition and dynamics in mainstream partial nitritation anammox reactors
Shelesh Agrawal – Microbiology Open

Diversity of Cultivable Protease-Producing Bacteria in Laizhou Bay Sediments, Bohai Sea, China
Yan Li – Frontiers in Microbiology

General Microbiology

Global metabolic rewiring for improved CO2 fixation and chemical production in cyanobacteria
Masahiro Kanno – Nature Communications

Short communication: Membrane vesicle-mediated bacterial communication
Masanori Toyofuku – The ISME Journal

Brief Report: Influence of the alginate production on cell-to-cell communication in Pseudomonas aeruginosa PAO1
Jiayue Yang – Environmental Microbiology Reports

Genomic diversity within the haloalkaliphilic genus Thioalkalivibrio
Anne-Catherine Ahn – PlOS One

Review article: The Potential of Systems Biology to Discover Antibacterial Mechanisms of Plant Phenolics
Caroline S. Rempe – Frontiers in Microbiology

Phages and viruses

Mini-Review: Driving HIV-1 into a Vulnerable Corner by Taking Advantage of Viral Adaptation and Evolution
Shigeyoshi Harada – Frontiers in Microbiology

Infection with diverse immune-modulating poxviruses elicits different compositional shifts in the mouse gut microbiome
Daniel Aguirre de Cárcer – PlOS One

Review: The concept of commensal viruses almost 20 years later: redefining borders in clinical virology
Diem-Lan Vu & Laurent Kaiser – Clinical Microbiology and Infection

Statistics / Bioinformatics

A fast small-sample kernel independence test for microbiome community-level association analysis
Xiang Zhan – Biometrics

Revealing large metagenomic regions through long DNA fragment hybridization capture
Cyrielle Gasc & Pierre Peyret – Microbiome

Enlightening discriminative network functional modules behind Principal Component Analysis separation in differential-omic science studies
Sara Ciucci – Scientific Reports

Microbes in the news

Snow Bacteria, A Pandora’s Box? – GlacierHub

Phage therapy shown to kill drug-resistant superbug (link to original paper included) – HealthCanal

A Microbe Hunter Plies Her Trade In Space – NPR

Science, publishing, and career

Announcement: Transparency upgrade for Nature journals – Nature

March 13, 2017.

Quite a few picks from Nature Reviews Microbiology as a fresh issue was released today. We also see some nice papers on microbial diseases. The post author’s highlight today goes to the interesting review from Thurber et al. on the virus section: Virus–host interactions and their roles in coral reef health and disease. Have a great week!

General microbiome

Review: Timing the day: what makes bacterial clocks tick?
Carl Hirschie Johnson – Nature Reviews Microbiology

Microbial diseases

Evolutionary Constraints on the Norovirus Pandemic Variant GII.4_2006b over the Five-Year Persistence in Japan.
Hironori Sato – Frontiers in Microbiology

Review: Anti-trypanosomatid drug discovery: an ongoing challenge and a continuing need Mark C. Field – Nature Reviews Microbiology

Commentary: The chicken or the egg? Changes in oral microbiota as cause or consequence of mucositis during radiation therapy
Stephen T. Sonis – EBioMedicine

Commentary: From bugs to brains: The microbiome in neurological health
Kyla A. McKay – Multiple Sclerosis and Related Disorders

Commentary: A Microbiome Foundation for the Study of Crohn’s Disease
Dirk Gevers – Cell Host & Microbe

Human gut microbiome

European consensus conference on faecal microbiota transplantation in clinical practice
Giovanni Cammarota – Gut

Commentary: Microbe Hunting Hits Home
Ivaylo I. Ivanov – Cell Host & Microbe

Commentary: Microbes and Diet-Induced Obesity: Fast, Cheap, and Out of Control
Peter J. Turnbaugh – Cell Host & Microbe

Review: The gut microbiome and microbial translocation in multiple sclerosis
Ali Mirza – Clinical Immunology

Plant, root, and soil microbiome

COREXIT 9500 enhances oil biodegradation and changes microbial community structure of oil-enriched microcosms
Techtmann SM – Applied Environmental Microbiology

Soil formation and initial microbiological activity on a foreland of an Arctic glacier (SW Svalbard)
Dorota Górniak – Applied Soil Ecology

The response of soil microbial diversity and abundance to long-term application of biosolids
Abdul-Wahab Mossa – Environmental Pollution

Comparative analysis of metagenomes of Italian top soil improvers
Federica Gigliucci – Environmental Research

Water and extremophile microbiome

Legal immigrants: invasion of alien microbial communities during winter occurring desert dust storms
Weil T. – Microbiome

Built environment

Bacterial diversity on rock surface of the ruined part of a French historic monument: The Chaalis abbey
Agnes Mihajlovski – International Biodeterioration & Biodegradation

Food microbiology

Diversity of the dominant bacterial species on sliced cooked pork products at expiration date in the Belgian retail
Wim Geeraerts – Food Microbiology


Agar-degrading bacteria isolated from Antarctic macroalgae – Folia Microbiologica
Roxana Alvarado & Sergio Leiva

Exploring the Antimicrobial and Antitumor Potentials of Streptomyces sp. AGM12-1 Isolated from Egyptian Soil
Maged S. Ahmad – Frontiers in Microbiology

Phages and viruses

Review: Virus–host interactions and their roles in coral reef health and disease
Rebecca Vega Thurber – Nature Reviews Microbiology

Review: Mimivirus: leading the way in the discovery of giant viruses of amoebae
Phillippe Colson – Nature Reviews Microbiology

Change in Emiliania huxleyi Virus Assemblage Diversity but Not in Host Genetic Composition during an Ocean Acidification Mesocosm Experiment
Highfield A. – Viruses

Techniques and methods

Review: Current state and applications of microbial genome‐scale metabolic models
Won Jun Kim – Current Opinion in Systems Biology

A Comparative Analysis of the Lyve-SET Phylogenomics Pipeline for Genomic Epidemiology of Foodborne Pathogens
Lee S. Katz – Frontiers in Microbiology

FurIOS: A Web-Based Tool for Identification of Vibrionaceae Species Using the fur Gene
Henrique Machado – Frontiers in Microbiology

Research Highlights (a few from today’s issue of Nature Reviews Microbiology):

Bacterial Physiology: Treadmilling runs bacterial division – Ashley York

Symbiosis: Wolbachia’s matchmaking secret revealed – Ursula Hofer

Bacterial Physiology: Persisters running out of energy – Andrea Du Toit

Bacterial pathogenesis: Hitching a ride with DCs – Yvonne Bordon

Microbes in the news

Light rain can spread soil bacteria far and wide, study finds
Science Daily – Paper by Young Soo Joung available here.

Novel antibiotic combination therapy overcomes deadly drug-resistant bacteria
Case Western Reserve University – EurekAlert!

Researchers track spread of multidrug-resistant bacteria in hospital sinks
University of Virginia – Paper by Kotay S. available here.

Microbes on the market

CRISPR patent results
Shimona Starling – Nature Reviews Microbiology

Global Microbiology Testing Market Present Scenario and Growth Prospects 2016-2021