Microbiome of pregnancy and birth
Metagenomic Analysis of Milk of Healthy and Mastitis-Suffering Women – Esther Jiménez – Journal of Human Lactation
Human oral microbiome
Abstract: Changes In The Oral Microbiome Of HIV-Infected Individuals May Alter Nitrogen Metabolism And The Enterosalivary Circulation Of Nitrate – Carl D. Koch – Am J Respir Crit Care Med
Human respiratory microbiome
Conference abstracts in Am J Respir Crit Care Med:
- Pulmonary Microbiome: Analysis Of Microbial Diversity In Lung Cancer – C. Ascoli
- A Lung Microbiome Enriched In Anaerobes Is Associated With A Blunted Tlr Response – E. Friedman – Am J Respir Crit Care Med
- Influence Of Corticosteroid Therapy And Airflow Obstruction In The Endobronchial And Peripheral Microbiomes Of Asthmatic Airways – D. R. Denner
- Contamination Of Reagents Can Critically Impact Sequence-Based Microbiome Studies – M. J. Cox
Human gut microbiome
Metabolism Links Bacterial Biofilms and Colon Carcinogenesis – Caroline H. Johnson – Cell Metabolism
Review: The gut microbiome: What do we know? – Francisco Guarner – Clinical Liver Disease
Review: A model for the role of gut bacteria in the development of autoimmunity for type 1 diabetes – Austin G. Davis-Richardson – Diabetologia
Functional foods
Review: A breakthrough in probiotics: Clostridium butyricum regulates gut homeostasis and anti-inflammatory response in inflammatory bowel disease – Takanori Kanai – Journal of Gastroenterology
Animal models of microbiome research
Phylum Level Change in the Cecal and Fecal Gut Communities of Rats Fed Diets Containing Different Fermentable Substrates Supports a Role for Nitrogen as a Factor Contributing to Community Structure – Martin Kalmokoff – Nutrients
Animal microbiome
Variation in koala microbiomes within and between individuals: effect of body region and captivity status – Niccoló Alfano – Scientific Reports
Plants and soil microbiome
Minimal genomes of mycoplasma-related endobacteria are plastic and contain host-derived genes for sustained life within Glomeromycota – Mizue Naito – PNAS
Transcriptome diversity among rice root types during asymbiosis and interaction with arbuscular mycorrhizal fungi – Caroline Gutjahr – PNAS
Reintroduction of locally extinct vertebrates impacts arid soil fungal communities –
Laurence J. Clarke – Molecular Ecology
Compartmentalized and contrasted response of ectomycorrhizal and soil fungal communities of Scots pine forests along elevation gradients in France and Spain
Ana Rincón – Environmental Microbiology
Impact of tropical lowland rainforest conversion into rubber and oil palm plantations on soil microbial communities – Valentyna Krashevska – Biology and Fertility of Soils
Masters Thesis: The establishment of apple orchards as temperate forest garden systems and their impact on indigenous bacterial and fungal population abundance in Southern Ontario, Canada – Paul Wartman – University of Guelph, Canada
Review: Plant growth promoting rhizobacteria and sustainable agriculture: A review –
Muhammad Arslan Ashraf – African Journal of Microbiology Research
Water microbiome
Organic and inorganic composition and microbiology of produced waters from Pennsylvania shale gas wells – Denise M. Akob – Applied Geochemistry
Perspective: Using dispersants after oil spills: impacts on the composition and activity of microbial communities – Sara Kleindienst – Nature Reviews Microbiology
Not sure if these are small enough (20-500 um) to be classified as microbes: Metagenetic tools for the census of marine meiofaunal biodiversity: An overview – Laura Carugati – Marine Genomics
Extremophile microbiome
Arsenic rich Himalayan hot spring metagenomics reveal genetically novel predator-prey genotypes – Naseer Sangwan – Environmental Microbiology Reports
Comparison of Archaeal and Bacterial Diversity in Methane Seep Carbonate Nodules and Host Sediments, Eel River Basin and Hydrate Ridge, USA – Olivia U. Mason – Microbial Ecology
Deep-sea hydrothermal vent bacteria related to human pathogenic Vibrio species – Nur A. Hasan – PNAS
Microbial communities of the Lemon Creek Glacier show subtle structural variation yet stable phylogenetic composition over space and time – Cody S. Sheik – Frontiers in Microbiology
Built environment microbiome
Forensic analysis of the microbiome of phones and shoes – Simon Lax – Microbiome
The Actinobacterial Colonization of Etruscan Paintings – Marta Diaz-Herraiz – Scientific Reports
Food microbiology
Molecular Analysis of Skin Bacterial Assemblages from Codfish and Pollock after Dry-Salted Fish Production – Natalia Pegoraro
Viruses and phages
Infection of phytoplankton by aerosolized marine viruses – Shlomit Sharoni – PNAS
Archaea
The two-domain tree of life is linked to a new root for the Archaea – Kasie Raymann – PNAS
Review: Archaeal Lineages within the Human Microbiome: Absent, Rare or Elusive?
Hans-Peter Horz – Life
Review: The interplay between nucleoid organization and transcription in archaeal genomes – Eveline Peeters – Nature Reviews Microbiology
Metagenomics and bioinformatics
Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data – Kathrin P. Aßhauer – Bioinformatics
ProtPhylo: identification of protein–phenotype and protein–protein functional associations via phylogenetic profiling – Yiming Cheng – Nucleic Acids Research
IonGAP: integrative bacterial genome analysis for Ion Torrent sequence data – Adrian Baez-Ortega – Bioinformatics
Natural Bacterial Communities Serve as Quantitative Geochemical Biosensors – Mark B. Smith – mBio
Manuscript: Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant – Andreas Bremges
Review: The integration of sequencing and bioinformatics in metagenomics – Firouz Abbasian – Reviews in Environmental Science and Bio/Technology
Book Chapter: Protocols and Methods for the in Silico Reconstruction of the Origin and Evolution of Metabolic Pathways – Luana Presta – Briefs in Molecular Science 2015
Book Chapter: Molecular Screening of Azurin-Like Anticancer Bacteriocins from Human Gut Microflora Using Bioinformatics – Van Duy Nguyen – Advanced Computational Methods for Knowledge Engineering
Other microbial papers of interest
Bacterial Swarms Recruit Cargo Bacteria To Pave the Way in Toxic Environments – Alin Finkelshtein – mBio
Mosaic genome of endobacteria in arbuscular mycorrhizal fungi: Transkingdom gene transfer in an ancient mycoplasma-fungus association – Gloria Torres-Cortés – PNAS
Perspective: Resilience vs. historical contingency in microbial responses to environmental change – Christine V. Hawkes – Ecology Letters
A tortoise–hare pattern seen in adapting structured and unstructured populations suggests a rugged fitness landscape in bacteria – Joshua R. Nahum – PNAS
Microbes in the news
Can The Microbes You Leave Behind Be Used to Identify You? – Ed Yong – National Geographic
UGSG looks at microbiology, chemistry of Pa. fracked wells – Bob Downing – Ohio.com
Chinese breast milk discovery strengthens case for probiotics in infant formula: Chr Hansen – By Mark Astley – Dairy Reporter
Researchers find metabolic link between bacterial ‘biofilms’, colon cancer – Medical Xpress
Accessing the Hidden Kingdom: Fungal ITS Reference Sequences – NCBI Insights
#BacteriaHysteria
Tests found bacteria on popular single-serve coffeemakers – Your Central Valley
Bik’s Picks
De novo synthesis of a sunscreen compound in vertebrates – Andrew R Osborn – eLIFE
Chemical messages in 170-year-old champagne bottles from the Baltic Sea: Revealing tastes from the past – Philippe Jeandet – PNAS
Unraveling ancient Egypt’s animal mummy mystery: Roughly a third of the animal mummies examined were completely empty – Michael E. Miller – Washington Post
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