Human respiratory microbiome
Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencing – Bittinger K – Genome Biology
Human gut microbiome
* Prolonged use of a proton pump inhibitor reduces microbial diversity: implications for Clostridium difficile susceptibility – Charlie T Seto – Microbiome
Intestinal dysbiosis in ankylosing spondylitis – Mary-Ellen Costello – Arthritis & Rheumatology
Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota – Dmitry A. Ravcheev and Ines Thiele – Frontiers in Microbiology
* Bacteroides dorei dominates gut microbiome prior to autoimmunity in Finnish children at high risk for type 1 diabetes – Austin G. Davis-Richardson – Frontiers in Microbiology
* Children Living near a Sanitary Landfill Have Increased Breath Methane and Methanobrevibacter smithii in Their Intestinal Microbiota – Humberto Bezerra de Araujo Filho – Archaea
Gut microbiota and metabolic syndrome – Davide Festi – World Journal of Gastroenterology
Animal and other models of microbiome research
Simulating distal gut mucosal and luminal communities using packed-column biofilm reactors and an in vitro chemostat model – Julie A.K. McDonald – Journal of Microbiological Methods
Infant formula supplemented with low protein and high carbohydrate alters the intestinal microbiota in neonatal SD rats – Wenguang Fan – BMC Microbiology
Comparing the effects of acute alcohol consumption in germ-free and conventional mice: the role of the gut microbiota – Canesso MCC – BMC Microbiology
The presence of nitrate dramatically changed the predominant microbial community in perchlorate degrading cultures under saline conditions – Victor G Stepanov – BMC microbiology
Intestinal Epithelial Cell Toll-like Receptor 5 Regulates the Intestinal Microbiota to Prevent Low-Grade Inflammation and Metabolic Syndrome in Mice – Benoit Chassaing – Gastroenterology
Model systems to analyze the role of miRNAs and commensal microflora in bovine mucosal immune system development – Guanxiang Liang – Molecular Immunology
Animal microbiome
* Gorilla gorilla gorilla gut: a potential reservoir of pathogenic bacteria as revealed using culturomics and molecular tools – Fadi Bittar – Scientific Reports
* Influence of dietary feathers on the fecal microbiota in captive Arctic fox: Do dietary hair or feathers play a role in the evolution of carnivorous mammals? – Liang Zhang – Integrative Zoology
An Antimethanogenic Nutritional Intervention in Early Life of Ruminants Modifies Ruminal Colonization by Archaea – Leticia Abecia – Archaea
The microbiome of New World vultures – Michael Roggenbuck – Nature Communications
* Uncovering the Cultivable Microbial Diversity of Costa Rican Beetles and Its Ability to Break Down Plant Cell Wall Components – Gabriel Vargas-Asensio – PLOS ONE
The effect of anthropogenic arsenic contamination on the earthworm microbiome – Pass D. A – Environmental Microbiology
Plant microbiome
Brassica seed meal soil amendments transform the rhizosphere microbiome and improve apple production though resistance to pathogen re-infestation – Mark Mazzola – Phytopathology
Water microbiome
* Deciphering Diversity and Ecological Function From Marine Metagenomes – Holly M. Bik – The Biological Bulletin
Ciliate Diversity, Community Structure, and Novel Taxa in Lakes of the McMurdo Dry Valleys, Antarctica – Yuan Xu – The Biological Bulletin
Impact of ocean phytoplankton diversity on phosphate uptake – Michael W. Lomas – PNAS USA
Metagenomes of Microbial Communities in Arsenic-and Pathogen-Contaminated Well and Surface Water from Bangladesh – AC Layton – Genome Announcements
Comparisons of the composition and biogeographic distribution of the bacterial communities occupying South African thermal springs with those inhabiting deep subsurface fracture water – Cara Magnabosco – Frontiers in Microbiology
Soil microbiome
Fluazifop-P-butyl (herbicide) affects richness and structure of soil bacterial communities
Trabelsi Darine – Soil Biology and Biochemistry
Prolonged irrigation with municipal wastewater promotes a persistent and active soil microbial community in a semiarid agroecosystem – F. García-Orenes – Agricultural Water Management
Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soil – Jian-Qiang Su – Molecular Ecology
Different bulk and active bacterial communities in cryoconite from the margin and interior of the Greenland ice sheet – Marek Stibal – Environmental Microbiology Reports
Soil bacterial community structure remains stable over a five-year chronosequence of insect-induced tree mortality – Scott Ferrenberg – Frontiers in Microbiology
Metagenomics and genome organization
Rapid Core-Genome Alignment and Visualization for Thousands of Intraspecific Microbial Genomes – Treangen TJ – Genome Biology
Flexibility and Symmetry of Prokaryotic Genome Rearrangement Reveal Lineage-Associated Core-Gene-Defined Genome Organizational Frameworks – Yu Kang – mBio
Antibacterial gene transfer across the tree of life – Jason A Metcalf – eLife
Transcriptomics
Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation – Celaj A – Microbiome
Metabolomics
* Metabolomics reveals differential metabolic adjustments of normal and overweight subjects during overfeeding – Beatrice Morio – Metabolomics
Microbes in the news
* Healthy gut microbiota can prevent metabolic syndrome, researchers say – Science Daily
Microbiome Study Reveals Typically Pathogenic Bugs in Vulture Guts – GenomeWeb
The Excrement Experiment – Treating disease with fecal transplants – Emily Eakin – The New Yorker
Science and art
Maria Merian’s Butterflies: The Illustrated Story of How a 17th-Century Woman Forever Changed the Course of Science Through Art – Maria Popova – Brain Pickings
Bik’s Picks
Genome of the house fly, Musca domestica L., a global vector of diseases with adaptations to a septic environment – Jeffrey G Scott – Genome Biology
Museum specimens reveal loss of pollen host plants as key factor driving wild bee decline in The Netherlands – Jeroen Scheper – PNAS USA
* We don’t read about dinosaurs – Pat Schloss – Mothur blog
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Microbiome Digest - Bik's Picks 