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

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