June 19, 2018

In today’s digest you can read about: the field of CRISPR-CAS antimicrobials by E. Pursey, “microbiota influencers” by G. Rizzatti, bioplastic producing bacterial communities by V. Kumar, mixotrophic behavior of the harmful benthic dinoflagellate by B. Lee and many many diverse and interesting articles. Enjoy!

General microbiome

CRISPR-Cas antimicrobials: Challenges and future prospects Elizabeth Pursey – PLOS Pathogens

Considering Microbial CO2 during Microbe-Plant Cocultivation – Birgit Piechulla – Plant Physiology

Metabolic model-based analysis of the emergence of bacterial cross-feeding via extensive gene loss – Colin P. McNally  – BMC Systems Biology

Pregnancy and early life

Prevalence of antibiotic resistance in commensal Escherichia coli among the children in rural hill communities of Northeast India – Ashish Kumar Singh – PLOS One

Shared and Distinct Features of Human Milk and Infant Stool Viromes – Pia S. Pannaraj – Frontiers in Microbiology

Preterm infant gut microbial patterns related to the development of necrotizing enterocolitis – Tristan P. Lindberg – The Journal of Maternal-Fetal & Neonatal Medicine

Human respiratory microbiome

Multi-omic profiling to assess the effect of iron starvation in Streptococcus pneumoniae TIGR4 – Irene Jiménez-Munguía – PeerJ

Human gut microbiome

Addendum: “I will survive”: A tale of bacteriophage-bacteria coevolution in the gut – Luisa De Sordi – Gut Microbes

The Gut-Associated Microbiome of the Eastern Spruce Budworm Does Not Influence Larval Growth or Survival – Melbert T Schwarz – bioRxiv

Prioritizing and modelling of putative drug target proteins of Candida albicans by systems biology approach – Tariq Ismail – Acta Biochimica Polonica

Antibiotic and Modulation of Microbiota: A New Paradigm? – Gianenrico Rizzatti – Journal of Clinical Gastroenterology

Streptomyces, shared microbiome member of soil and gut, as “old friends” against colon cancer – Alireza Bolourian – FEMS Microbiology Ecology

Gut Microbial-related Choline Metabolite Trimethylamine-N-oxide is Associated with Progression of Carotid Artery Atherosclerosis in HIV Infection – Zhilei Shan – The Journal of Infectious Diseases

Role of Microbiota in Sexually Dimorphic Immunity – Marlies Elderman – Frontiers in Immunology

Early results of fecal microbial transplantation protocol implementation at a community-based university hospital – Rodrigo Duarte-Chavez – Journal of Global Infectious Diseases

Gut microbiota modulate neurobehavior through changes in brain insulin sensitivity and metabolism – Marion Soto – Molecular Psychiatry

The Rise and Rise of Eosinophilic Gut Diseases Including Eosinophilic Esophagitis Is Probably Not Explained by the Disappearance of Helicobacter pylori, so Who or What’s to Blame? – Nicholas J. Talley – The American Journal of Gastroenterology

Effect of administration of a probiotic preparation on gut microbiota and immune response in healthy women in India: an open-label, single-arm pilot study – Ankita Singh – BMC Gastroenterology

Animal experiments

Toxin-positive Clostridium difficile latently infect mouse colonies and protect against highly pathogenic C. difficile – Lucie Etienne-Mesmin – Gut microbiome

Animal microbiome

A comparative analysis of microbial profile of Guinea fowl and chicken using metagenomic approach – Sarayu Bhogoju – PLOS One

Tracking sources of Clostridium botulinum type E contamination in seal meat – Daniel Leclair – International Journal of Circumpolar Health

Plant, root, and soil microbiome

Applying predictive models to decipher rhizobacterial modifications in common reed die-back affected populations – Giovanni Bacci – Science of The Total Environment

Bioplastic reservoir of diverse bacterial communities revealed along altitude gradient of Pangi-Chamba trans-Himalayan region – Vijay Kumar – FEMS Microbiology Letters

Antagonism and antibiotic resistance drive a species-specific plant microbiota differentiation in Echinacea spp – Valentina Maggini – FEMS Microbiology Ecology

Divergent Responses of the Diazotrophic Microbiome to Elevated CO2 in Two Rice Cultivars – Yongjie Yu – Frontiers in Microbiology

Synthesis and detoxification of nitric oxide in the plant beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 and its effect on biofilm formation – Xiaoyan Dong – Biochemical and Biophysical Research Communications

Understanding the Strategies to Overcome Phosphorus–Deficiency and Aluminum–Toxicity by Ryegrass Endophytic and Rhizosphere Phosphobacteria – Patricio J. Barra – Frontiers in Microbiology

Soil viruses are underexplored players in ecosystem carbon processing – Gareth Trubl – bioRxiv

Dispersal limitation and thermodynamic constraints govern spatial structure of permafrost microbial communities –  Eric M Bottos – FEMS Microbiology Ecology

Changes of soil microbial and enzyme activities are linked to soil C, N and P stoichiometry in afforested ecosystems – F.Z. Zhao – Forest Ecology and Management

Responses of soil microbial communities to nutrient limitation in the desert-grassland ecological transition zone – Cui Y – The Science of the Total Environment

Observed metabolic asymmetry within soybean root nodules reflects unexpected complexity in rhizobacteria-legume metabolite exchange – Dušan Veličković – The ISME Journal

Antibacterial activity of soil bacteria isolated from Kochi, India and their molecular identification – Davis Gislin – Journal of Genetic Engineering and Biotechnology

Brassica napus Growth in Lead-Polluted Soil: Bioaccumulation in Plant Organs at Different Ontogenetic Stages and Lead Fractionation in Soil – Gisele V. Ferreyroa – Water, Air, & Soil Pollution

Editorial: “Plant-Microbe-Insect Interaction: Source for Bio-fertilizers, Bio-medicines and Agent Research” – Gero Benckiser – Frontiers in Plant Science

Broad-spectrum antimicrobial activity by Burkholderia cenocepacia TAtl-371, a strain isolated from the tomato rhizosphere – Fernando Uriel Rojas-Rojas – Microbiology

Improvement of Ni phytoextraction by Alyssum murale and its rhizosphere microbial activities by applying nitrogen fertilizer – Ali Kanso – Ecological Research

Water and extremophile microbiome

Abundance determines the functional role of bacterial phylotypes in complex communities – Damian W. Rivett  – Nature Microbiology

Metabolic Diversity within the Globally Abundant Marine Group II Euryarchaea Drives Ecological Patterns – Benjamin J Tully – bioRxiv

Diversity of bacterial communities and dissolved organic matter in a temperate estuary – Helena Osterholz – FEMS Microbiology Ecology

Clean Low-Biomass Procedures and Their Application to Ancient Ice Core Microorganisms – Zhi-Ping Zhong – Frontiers in Microbiology

Genetic diversity and co-occurrence patterns of marine cyanopodoviruses and picocyanobacteria – Yingting Sun – Applied and Environmental Microbiology

Proteome response of a metabolically flexible anoxygenic phototroph to Fe(II) oxidation – Casey Bryce – Applied and Environmental Microbiology

Genome rearrangement shapes Prochlorococcus ecological adaptation – Wei Yan – Applied and Environmental Microbiology

High CO2 Under Nutrient Fertilization Increases Primary Production and Biomass in Subtropical Phytoplankton Communities: A Mesocosm Approach – Nauzet Hernández-Hernández – Frontiers in Microbiology

Genetic Analyses of the rbcL and psaA Genes From Single Cells Demonstrate a Rhodophyte Origin of the Prey in the Toxic Benthic Dinoflagellate Ostreopsis – Bora Lee – Frontiers in Marine Science

Ubiquitous abundance distribution of non-dominant plankton across the global ocean – Enrico Ser-Giacomi – Nature Ecology & Evolution

Copiotrophic marine bacteria are associated with strong iron‐binding ligand production during phytoplankton blooms – Shane L. Hogle – Limnology and Oceanography

Dynamics and interactions of highly resolved marine plankton via automated high-frequency sampling – David M. Needham – The ISME Journal

Distinct patterns and processes of abundant and rare eukaryotic plankton communities following a reservoir cyanobacterial bloom – Yuanyuan Xue – The ISME Journal

Coral Microbiomes as Bioindicators of Reef Health – Sofia Roitman – Population Genomics

Microbial community structure and functional potential along a hypersaline gradient – Jeffrey A. Kimbrel – Frontiers in Microbiology

Comparative genomics of Pseudomonas sp. strain SI-3 associated with macroalga Ulva prolifera, the causative species for green tide in the Yellow Sea – Huihui Fu – Frontiers in Microbiology

Probiotics / prebiotics

Pilot assessment of probiotics for pregnant women in Rwanda – Amy McMillan – PLOS One

Phages and viruses

Low spatial structure and selection against secreted virulence factors attenuates pathogenicity in Pseudomonas aeruginosa – Elisa T Granato – bioRxiv

Identification of anti-norovirus genes in mouse and human cells using genome-wide CRISPR activation screening –  Robert Orchard – bioRxiv

Biotechnology

Simultaneous autotrophic removal of sulphate and nitrate at different voltages in a bioelectrochemical reactor (BER): Evaluation of degradation efficiency and characterization of microbial communities – Hao Xua – Bioresource Technology

Evaluation of A Novel Split-Feeding Anaerobic/Oxic Baffled Reactor (A/OBR) For Foodwaste Anaerobic Digestate: Performance, Modeling and Bacterial Community – Shaojie Wang – Scientific Reports

Viewpoint: Synthetic Biology for Natural Compounds – Xinrui Zhao – Biochemistry

Bioinformatics

iMetaLab 1.0: A web platform for metaproteomics data analysis – Bo Liao – Bioinformatics

Taxonomy annotation and guide tree errors in 16S rRNA databases – Robert Edgar​ – PeerJ

The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level – Luis M Rodriguez-R – Nucleic Acids Research

Techniques

Whole-Cell MALDI-TOF MS Versus 16S rRNA Gene Analysis for Identification and Dereplication of Recurrent Bacterial Isolates – Michal Strejcek – Frontiers in Microbiology

Low-power portable devices for metagenomics analysis: Fog computing makes bioinformatics ready for the Internet of Things –  Ivan Merelli – Future Generation Computer Systems

Microbes in the news 

Unique microbe could thrive on Mars, help future manned missions

In a Warming World, Deadly Bacteria Are More Resistant to Antibiotics

Microbes on the market

Startup aims to make allies of human gut’s microbes

Department of Energy Announces $40 Million for Bio-Based Research

Tina’s non-microbiology picks

Towards an Evolutionary Perspective in Teaching and Popularizing Microbiology – Fernando Bueno Ferreira Fonseca de Fraga – Journal of  Microbiology & Biology Education

 

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