April 19, 2016

A review about breastmilk with a great name, skin microbiome in different populations, a mouse model for Sjögren’s, the office microbiome, Guam reef sponges, the Alaska tundra ecosystem, and taxonomic classification. Note that I will be traveling internationally in the next couple of days due to (another) tragic family situation, so posting will be irregular. But I will try my best!

Pregnancy and birth

Review: Breastfed at Tiffany’s – Thierry Hennet – Trends in Biochemical Sciences

Human skin microbiome

Body Site Is a More Determinant Factor than Human Population Diversity in the Healthy Skin Microbiome – Guillermo I. Perez Perez – PLOS ONE

Pathogenic bacteria profile and antimicrobial susceptibility patterns of ear infection at Bahir Dar Regional Health Research Laboratory Center, Ethiopia – Derese Hailu – SpringerPlus

Human oral microbiome (also see Animal models, below)

Comparison of the Oral Microbiome of Siblings Using Next-generation Sequencing: a Pilot Study – Hyo-Seol Lee – Oral Diseases

Human gastric microbiome

Characterisation of the gastrointestinal mucosa-associated microbiota: a novel technique to prevent cross-contamination during endoscopic procedures – E. R. Shanahan – Alimentary Pharmacology & Therapeutics

Human gut microbiome

Conference Abstract: Walnut Consumption Influences the Human Gut Microbiome – Heather M Guetterman – The FASEB Journal

Conference Abstract: Anemia and Iron Status are Predictors of Gut Microbiome Composition and Metabolites in Infants and Children in Rural Kenya – Daniela Paganini – The FASEB Journal

Recurrent Clostridium difficile infection associates with distinct bile acid and microbiome profiles – J. R. Allegretti – Alimentary Pharmacology & Therapeutics

Effects of sardine-enriched diet on metabolic control, inflammation and gut microbiota in drug-naïve patients with type 2 diabetes: a pilot randomized trial – Mariona Balfegó – Lipids in Health and Disease

Review: From gut dysbiosis to altered brain function and mental illness: mechanisms and pathways – G B Rogers – Molecular Psychiatry

Review: Reshaping the gut microbiota: Impact of low calorie sweeteners and the link to insulin resistance? – Jodi E. Nettleton – Physiology & Behavior

Book chapter, some plagiarism: Impact of Probiotics and Gut Microbiota on Host Behavior – Sarabjit Singh Kanwar – Microbes in Food and Health

Animal models of microbiome research

Mouse model: Altered Mucosal Microbiome Diversity and Disease Severity in Sjögren Syndrome – Cintia S. de Paiva – Scientific Reports

Systemic Characterization of an Obese Phenotype in the Zucker Rat Model Defining Metabolic Axes of Energy Metabolism and Host-Microbial Interactions – Jutarop Phetcharaburanin – Journal of Proteome Research

Metagenomic analysis of antibiotic-induced changes in gut microbiota in a pregnant rat model – Imran Khan – Frontiers in Pharmacology

Inflammasome signaling affects anxiety- and depressive-like behavior and gut microbiome composition – M-L Wong – Molecular Psychiatry

Animal microbiome

The reproductive tracts of two malaria vectors are populated by a core microbiome and by gender- and swarm-enriched microbial biomarkers – Nicola Segata – Scientific Reports

In four shallow and mesophotic tropical reef sponges from Guam the microbial community largely depends on host identity – Georg Steinert – PeerJ

Microbiome analysis and detection of pathogenic bacteria of Penaeus monodon from Jakarta Bay and Bali – Vincensius S.P. Oetama – Marine Pollution Bulletin

Diversity of endosymbiont bacteria associated with a non-filarial nematode group – Stela S. Lazarova – Nematology

Master thesis: Effects of Roundup (glyphosate) on gut microorganisms of farm animals – Charlotte Lynggaard Katholm – Aarhus University

Plant, root, and soil microbiome

Functional composition of plant communities determines the spatial and temporal stability of soil microbial properties in a long-term plant diversity experiment – Tanja Strecker – Oikos

Bacterial communities of the cotton aphid Aphis gossypii associated with Bt cotton in northern China – Yao Zhao – Scientific Reports

Soil microbial community composition and respiration along an experimental precipitation gradient in a semiarid steppe – Cancan Zhao – Scientific Reports

Bioaerosol Deposition to Food Crops near Manure Application: Quantitative Microbial Risk Assessment – Michael A. Jahne – Journal of Environmental Quality

Effects of biofumigation using Brassica juncea and Raphanus sativus in comparison to disinfection using Basamid on apple plant growth and soil microbial communities at three field sites with replant disease – Bunlong Yim – Plant and Soil

Bacterial and eukaryal diversity in soils forming from acid mine drainage precipitates under reclaimed vegetation and biological crusts – Claudia Rojas – Applied Soil Ecology

Assessment of Bacterial Communities and Predictive Functional Profiling in Soils Subjected to Short-Term Fumigation-Incubation – Lin Chen – Microbial Ecology

Archaeal communities in the sediments of different mangrove stands at Dongzhaigang, China – Wei Li – Journal of Soils and Sediments

Metagenomics reveals pervasive bacterial populations and reduced community diversity across the Alaska tundra ecosystem – Eric R. Johnston – Frontiers in Microbiology

Water microbiome

Bacterioplankton biogeography in the Atlantic Ocean: a case study of the distance-decay relationship – Mathias Milici – Frontiers in Microbiology

Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities – Jeffrey Marlow – Frontiers in Microbiology

Metagenomic analysis of sediments under seaports influence in the Equatorial Atlantic Ocean – Tallita Cruz Lopes Tavares – Science of The Total Environment

Dissolution Tests and Microbial Community Analysis Using the Bottom Sediment before and after a Heavy Storm – Ikuo Tsushima – Journal of Water and Environment Technology

Carbohydrate production by microbial mats communities in tidal flat from Bahía Blanca Estuary (Argentina) – E. M. Fernández – Environmental Earth Sciences

Built environment microbiome

Geography and Location Are the Primary Drivers of Office Microbiome Composition – John Chase – mSystems

Waste and pollution microbiology

Population Dynamics of Bulking and Foaming Bacteria in a Full-scale Wastewater Treatment Plant over Five Years – Xiao-Tao Jiang – Scientific Reports

Quantification of microbial load in diesel storage tanks using culture- and qPCR-based approaches – Pedro M. Martin-Sanchez – International Biodeterioration & Biodegradation

Bacterial communities in oil contaminated soils: Biogeography and co-occurrence patterns – Shuo Jiao – Soil Biology and Biochemistry

Methanogen Population of an Oil Production Skimmer Pit and the Effects of Environmental Factors and Substrate Availability on Methanogenesis and Corrosion Rates – Okoro Chuma Conlette – Microbial Ecology

Phages and viruses

Parasite diversity drives rapid host dynamics and evolution of resistance in a bacteria-phage system – Alex Betts – Evolution

Research highlight: More of the world’s a phage – Naomi Attar – Nature Reviews Microbiology

Bioinformatics and metagenomics

Fast and sensitive taxonomic classification for metagenomics with Kaiju – Peter Menzel – Nature Communications

META-pipe – Pipeline Annotation, Analysis and Visualization of Marine Metagenomic Sequence Data – Espen Mikal Robertsen – ArXiv

Fast and sensitive mapping of nanopore sequencing reads with GraphMap – Ivan Sović – Nature Communications

Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity – Beverly E. Flood – Frontiers in Microbiology

Editorial: A tale of two tardigrades – Thomas A. Richards – PNAS

Review: A guide through a family of phylogenetic dissimilarity measures among sites – Sandrine Pavoine – Oikos

Review: Compositional analysis: a valid approach to analyze microbiome high throughput sequencing data – Gregory B Gloor – Canadian Journal of Microbiology

More microbiology

Accessing Nature’s diversity through metabolic engineering and synthetic biology – Jason R. King – F1000 Research

Utilization and control of ecological interactions in polymicrobial infections and community-based microbial cell factories – Vinoth Wigneswaran – F1000 Research

Microbes in the news

Your Invisible Neighbors: Each City Has Unique Microbes – Katherine Du – NPR

Can the bacteria on your skin reveal where you are from? Floors, walls and people in different cities have distinct microbial ‘signatures’ – Abigail Beall – Daily Mail

6 surprising facts about sugar-laden, virus-fighting breast milk – Megan Thielking – STAT News

Gut microbiota development driven by specific enzyme in breast milk – Yvette Brazier – Medical News Today

Mothers’ milk and the infant gut microbiota: An ancient symbiosis – Science Daily

Microbiome-Brain Research to Get $2.8M Boost from NIDA, NCCIH – Genome Web

Earth Day: New insights into coral health hidden in reefs’ microbiomes – National Science Foundation

Downwind safety on the farm. Manure application research aims to improve food safety – American Society of Agronomy

Heartburn Meds Alter the Gut. Acid blockers reduce the diversity of bacteria in the intestines—and that could lead to trouble – Melinda Wenner Moyer – Scientific American

Bacteria that ‘breathes’ iron: Microbes that might change our search for life in space – Dawn Papple – Inquisitr

Microbes and art
This artist uses bacteria as paint: Paint by Microbes – Steph Yin – PopSci

Science, publishing, and career

From #realtimechem to #whywedoresearch: Who are the Tweeting scientists? – Andrew Marsh – Piirus

Tips for Using Social Media to Promote Your Research – Emma Hedington – NPJ Biofilms and Microbiomes

About Joseph MercolaKnown Quack Forced to Refund Customers for Lying About Effects of Tanning Beds – Bryan Menegus – Gizmodo

Bik’s Picks

Meet the woman who makes fake fingers for Japan’s reformed gangsters – Justin McCurry – The Guardian

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