January 6, 2017

The second Bay Area Microbiome Meetup, urban finches have more feather-damaging bacteria than rural birdies, metagenomic analysis of children with IBD, airborne fungi in a hospital.

Second San Francisco Bay Area Microbiome Meetup @Illumina. January 31, 2017, San Francisco. Theme: Tools & Techniques. Sign up for this free event.

Pregnancy and early life microbiome

Letter: Alterations in human milk leptin and insulin are associated with early changes in the infant intestinal microbiome – Martin Gotteland – The American Journal of Clinical Nutrition

Human eye microbiome

Review: Gut microbiota as a source of a surrogate antigen that triggers autoimmunity in an immune privileged site – Carlos R Zárate-Bladés – Gut Microbes

Human respiratory microbiome

Eosinophilic airway inflammation in asthma is associated with an altered airway microbiome – Asger Sverrild- Journal of Allergy and Clinical Immunology

Anaerobic Bacteriological Microbiota in Surface and Core of Tonsils in Chronic Tonsillitis – Meera Niranjan Khadilkar – Journal of Clinical and Diagnostic Research

Human urinary tract microbiome

Review: Microbiota in 2016: Associating infection and incontinence with the female urinary microbiota – Linda Brubaker – Nature Reviews Urology

Human gut microbiome

Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition – a metagenomic analysis – Rebecca Luise Knoll – American Journal of Physiology – Gastrointestinal and Liver Physiology

Irritable Bowel Syndrome-Like Symptoms Following Fecal Microbiota Transplantation: A Possible Donor-Dependent Complication – Bianca W Chang – American Journal of Gastroenterology

Review: The potential impact of gut microbiota on your health: Current status and future challenges – Stitaya Sirisinha – Asian Pacific Journal of Allergy and Immunology

Review: Gut microbiome, surgical complications and probiotics – George Stavrou – Annals of Gastroenterology

Review: Perceptions of fecal microbiota transplantation for Clostridium difficile infection: factors that predict acceptance – Leslie Park – Annals of Gastroenterology

Review: Analysis of Gut Microbiota – an ever changing landscape – Michael J. Sadowsky – Gut Microbes

Animal experiments

GAS6 is a key homeostatic immunological regulator of host–commensal interactions in the oral mucosa – Maria Nassar – PNAS

Bacteria isolated from lung modulate asthma susceptibility in mice – Aude Remot – The ISME Journal

Epimural bacterial community structure in the rumen of Holstein cows with different responses to a long-term subacute ruminal acidosis diet challenge – S.U. Wetzels – Journal of Dairy Science

Effect of faecal microbiota transplantation on mouse gut colonization with carbapenemase-producing Escherichia coli – R. Mahieu – Journal of Antimicrobial Chemotherapy

Changes in Intestinal Motility and Gut Microbiota Composition in a Rat Stress Model
Murakami T – Digestion

Animal microbiome

* House finches: Plumage micro-organisms and preen gland size in an urbanizing context – Mathieu Giraudeau – Science of The Total Environment

Impacts of canine distemper virus infection on the giant panda population from the perspective of gut microbiota – Na Zhao – Scientific Reports

From Seoul Zoo: Comparison of fecal microbiota of three captive carnivore species inhabiting Korea – Choa AN – Journal of Veterinary Medical Science

Yeast: An Overlooked Component of Bactrocera tryoni (Diptera: Tephritidae) Larval Gut Microbiota – Ania T. Deutscher – Journal of Economic Entomology

Symbiotic bacterial communities in ants are modified by invasion pathway bottlenecks and alter host behavior – Philip J. Lester – Ecology

Plant, root, and soil microbiome

Microbial Response to Soil Liming of Damaged Ecosystems Revealed by Pyrosequencing and Phospholipid Fatty Acid Analyses – Ramya Narendrula-Kotha – PLOS ONE

Microbial taxa and functional genes shift in degraded soil with bacterial wilt – Hongchun Zhang – Scientific Reports

Review: Can plant microbiome studies lead to effective biocontrol of plant diseases? – Jeffrey Ellis – Molecular Plant-Microbe Interactions

Water and extremophile microbiome

Endemicity of the cosmopolitan mesophilic chemolithoautotroph Sulfurimonas at deep-sea hydrothermal vents – Sayaka Mino – ISME Journal

Earth analogues for past and future life on Mars: isolation of perchlorate resistant halophiles from Big Soda Lake – Toshitaka Matsubara – International Journal of Astrobiology

Bacterial growth tolerance to concentrations of chlorate and perchlorate salts relevant to Mars – Amer F. Al Soudi – International Journal of Astrobiology

Built environment microbiome

High diversity of airborne fungi in the hospital environment as revealed by meta-sequencing-based microbiome analysis – Xunliang Tong – Scientific Reports

Food microbiology

Effect of postharvest practices including degreening on citrus carpoplane microbial biomes – A Gomba – Journal of Applied Microbiology

Waste and pollution microbiology

Heavy metal bioleaching and sludge stabilization in a single stage reactor using indigenous acidophilic heterotrophs – Akanksha Mehrotra – Environmental Technology

Integrated Anaerobic-Aerobic Biodegradation of Multiple Contaminants Including Chlorinated Ethylenes, Benzene, Toluene, and Dichloromethane – Miho Yoshikawa – Water, Air, & Soil Pollution

Arsenic resistance genes of As-resistant purple nonsulfur bacteria isolated from As-contaminated sites for bioremediation application – Phitthaya Nookongbut – Journal of Basic Microbiology

Metagenomics and bioinformatics

Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics – Léa Siegwald – PLOS ONE

Negative binomial mixed models for analyzing microbiome count data – Xinyan Zhang – BMC Bioinformatics


Impact of Glycosidic Bond Configuration on Short Chain Fatty Acid Production from Model Fermentable Carbohydrates by the Human Gut Microbiota – Hannah C. Harris – Nutrients

The Fumarate Reductase of Bacteroides thetaiotaomicron, unlike That of Escherichia coli, Is Configured so that It Does Not Generate Reactive Oxygen Species – Zheng Lu – mBio

Microbial ecology

The impact of resource dependence of the mechanisms of life on the spatial population dynamics of an in silico microbial community – Aisling J. Daly – Chaos

Review: Multispecies Swarms of Social Microorganisms as Moving Ecosystems – Eshel Ben-Jacob – Trends in Microbiology

Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems – Sergei Maslov – Scientific Reports

Prebiotics and probiotics

Extensively hydrolysed casein formula containing L. rhamnosus GG reduces the occurrence of other allergic manifestations in children with cow’s milk allergy: 3-year randomized controlled trial – Roberto Berni Canani – Journal of Allergy and Clinical Immunology


Application of Stochastic Labeling with Random-Sequence Barcodes for Simultaneous Quantification and Sequencing of Environmental 16S rRNA Genes – Tatsuhiko Hoshino – PLOS ONE

Microbes in the news

Roadkill Animals Are Surprising Sources of Drug Discovery – Jamie Durrani – Scientific American

Inspecting the genomic link between Archaea and Eukaryota – Tom O. Delmont – Meren Lab

Mealworms’ gut bacteria possible plastic pollution reduction solution, specialist says – Olivier Rey – ReddirtReport

‘The Doctors’ star talks about good gut bacteria – Alyssa Harvey – BG Daily News
How the brain helps the body fight bacteria – Jesmond Dalli – The Conversation

Will the Bacteria Wear Hardhats? – Charles Osgood – The Osgood File

Indigestion pills taken by millions of Britons could triple stomach bug risk by reducing acid that help fight off the bacteria – Victoria Allen – Daily Mail

Book review: Microbe, 2nd edition (2016) – ASM Science

Bacteria Hysteria

Killer bacteria, drugs and even white rhino DNA: Researchers reveal dollar bills have up to 3,000 different types of organism on them – Daily Mail

Microbes on the market

uBiome Appoints Boston Children’s Hospital Genomics Expert, Dr. Olaf Bodamer, to its Advisory Board – Benzinga

uBiome Review: What Does Your Gut Have to Say About You? – Sally Jones – Exploring Life’s Mysteries

French Microbiome Biotech enters its First Clinical Trial – Labiotech

CosmosID Launches Metagenomic and Antibiotic Resistance Application in Thermo Fisher Cloud – Benzinga

AOBiome Partners with iCarbonX and Secures $30 Million Investment for Drug Development – PR Newswire

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