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
