Category Archives: Animal experiments

September 15, 2016

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A review on the human skin microbiome, review on therapeutic manipulation of microbiotas, and microbial enzymes around earthworm casts.

Jobs and events

Faculty Positions in Microbiology and Immunology – University of South Alabama College of Medicine

Human respiratory microbiome

Investigation of sinonasal microbiome spatial organization in chronic rhinosinusitis – Vijay R. Ramakrishnan – International Forum on Allergy & Rhinology

Respiratory pathogen colonization of dental plaque, the lower airways, and endotracheal tube biofilms during mechanical ventilation – Kirsty M. Sands – Journal of Critical Care

Human skin microbiome

Review, will be open access soon: Experimental metagenomics and ribosomal profiling of the human skin microbiome – Pamela Ferretti – Experimental Dermatology 

Human gut microbiome

Gut microbiome alterations in patients with stage 4 hepatitis C – AbdelRahman Mahmoud Aly – Gut Pathogens

Commentary: Thinking with your stomach? Gut feelings on microbiome modulation of brain structure and function (Commentary on Luczynski et al.) – Anthony J. Hannan – European Journal of Neuroscience

Review: Therapeutic Manipulation of the Microbiota: Past, Present and Considerations for the Future – Vincent B. Young – Clinical Microbiology and Infection

Animal experiments

Effects of different diets on intestinal microbiota and nonalcoholic fatty liver disease development – Jian-Ping Liu – World Journal of Gastroenterology

Sex-specific effects of docosahexaenoic acid (DHA) on the microbiome and behavior of socially-isolated mice – Daniel J. Davis – Brain, Behavior, and Immunity

Animal microbiome

Structural differences in gut bacteria communities in developmental stages of natural populations of Lutzomyia evansi from Colombia’s Caribbean coast – Rafael José Vivero – Parasites & Vectors

Plant, root, and soil microbiome

Linking Microbial Enzymatic Activities and Functional Diversity of Soil around Earthworm Burrows and Casts – Jerzy Lipiec – Frontiers in Microbiology

Air microbiome

Influence of Rain on the Abundance and Size Distribution of Bioaerosols –
Chathurika M. Rathnayake – Atmospheric Chemistry and Physics Discussions

Techniques

Preparation of a standardised faecal slurry for ex-vivo microbiota studies which reduces inter-individual donor bias – Michelle M. O’Donnell – Journal of Microbiological Methods

Application of Next Generation Sequencing Technologies in Revealing Plant-Microbe Interactions – Ramesh Kothari – Journal of Next Generation: Sequencing & Applications

Technical note: Discard the specimen collection swab directly at point of care to improve extensive automated processing in clinical microbiology laboratories – Manuela Avolio – Journal of Microbiological Methods

Comparison of a modified phenol/chloroform and commercial-kit methods for extracting DNA from horse fecal material – Ali H.D. Janabi – Journal of Microbiological Methods

Microbes in the news

Secrets of life in the soil.Diana Wall has built a career on overturning assumptions about underground ecosystems. Now she is seeking to protect this endangered world – Rachel Cernansky – Nature

Ice machine, sinks linked to Legionnaires’ cases at UW Medical Center – JoNel Aleccia – Seattle Times

Israeli product that pinpoints viruses, bacteria gets European grant – ImmunoXpert is based on the fact that viruses and bacteria stimulate different protein pathways when they infect the body – Judy Siegel-Itzkovich – Jpost.com

A spoonful of sugar helps the bacteria go down. Gel-like layers protect microbes and help them stick to your intestines – Sara Chodosh – Popsci

Bik’s non-microbiology Picks

VA Palo Alto’s spending on artwork blasted – Jacqueline Lee – The Mercury News

 

September 13, 2016

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Infant gut microbiome and allergy risk, gut microbiome in mice and susceptibility to Plasmodium, microbiome of a stranded striped dolphin, cadavers in Canada, rRNA operon copy numbers.

Events

(repeat posting) 4th Microbiome R&D Business collaboration Forum & Probiotics Congress, October 3-4, 2016, La Jolla,San Diego, USA. Use discount code: ALLONG for a special rate of $399.

Pregnancy and birth

Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation – Kei E Fujimura – Nature Medicine

Press: Infant gut microbiome appears to shape allergy risk by altering immune responses – EurekAlert
Newborn gut microbiome predicts later allergy and asthma, study finds. Microbial byproducts link particular early-life gut microbes to immune dysfunction – Science Daily
Clues in microbiome of infants point to future allergies and asthma – Yvette Brazier – Medical News Today
Neonatal Gut Bacteria Might Promote Asthma. Byproducts of gut microbes in some 1-month–old babies trigger inflammation that is linked to later asthma development, researchers find. – Anna Azvolinsky – The Scientist

Human urinary tract microbiome

Urinary microbiome of kidney transplant patients reveals dysbiosis with potential for antibiotic resistance – Asha Rani – Translational Research

Human gut microbiome

Gut bacterial microbiota in psoriasis: A case control study – Doaa Masallat – African Journal of Microbiology Research

Review: Cognitive Function and the Microbiome – M.G. Gareau – International Review of Neurobiology

Review: Advances in Gut Microbiome Research and Relevance to Pediatric Diseases – Lindsey Albenberg – The Journal of Pediatrics

Animal experiments

Monitoring perinatal gut microbiota in mouse models by mass spectrometry approaches: parental genetic background and breastfeeding effects – Stefano Levi Mortera – Frontiers in Microbiology

Functional characteristics of the gut microbiome in C57BL/6 mice differentially susceptible to Plasmodium yoelii – Joshua M. Stough – Frontiers in Microbiology

Modulation of the bifidobacterial communities of the dog microbiota by zeolite – Alberto Sabbioni – Frontiers in Microbiology

Animal microbiome

The microbiome of a striped dolphin (Stenella coeruleoalba) stranded in Portugal – Filipa Godoy-Vitorino – Research in Microbiology

Book Chapter: Microbial Interactions on Coral Surfaces and Within the Coral Holobiont – Max Teplitski – The Cnidaria, Past, Present and Future

Book Chapter: Association of Coral-Microbes, and the Ecological Roles of Microbial Symbionts in Corals – Wei Sun – The Cnidaria, Past, Present and Future

Human Lice in Paleoentomology and Paleomicrobiology – Rezak Drali – ASM Microbiology Spectrum

Plant, root, and soil microbiome

Resource partitioning between bacteria, fungi and protists in the detritusphere of an agricultural soil – Susanne Kramer – Frontiers in Microbiology

Composition and activity of soil microbial communities in different types of temperate forests – Marcin Chodak – Biology and Fertility of Soils

The effect of the Falcon 460 EC fungicide on soil microbial communities, enzyme activities and plant growth – Małgorzata Baćmaga – Ecotoxicology

Review: Plant microbe interactions in post genomic era: perspectives and applications – Jahangir Imam – Frontiers in Microbiology

Water microbiome

Quantification of viral and prokaryotic production rates in benthic ecosystems: a methods comparison – Eugenio Rastelli – Frontiers in Microbiology

Microbiome of death

Cadavers in Canada: Book Chapter: Changes in Soil Microbial Activity Following Cadaver Decomposition During Spring and Summer Months in Southern Ontario – Heloise A. Breton – Soil in Criminal and Environmental Forensics

Wastewater and pollution microbiology

Poster: MiDAS: A curated database for the microorganisms of activated sludge and anaerobic digesters – Simon Jon McIlroy – Water Engineering and Biofilm IWA Specialist Conference, 2016

Probiotics

Layer-by-Layer Encapsulation of Probiotics for Delivery to the Microbiome – Aaron C. Anselmo – Advanced Materials

Food microbiology

Book: Functional Nucleic Acids Detection in Food Safety: Theories and Applications – Wentao Xu – Springer

Microbial ecology

Aligning the Measurement of Microbial Diversity with Macroecological Theory – James C. Stegen – Frontiers in Microbiology

Editorial: Insights into microbe-microbe interactions in human microbial ecosystems: strategies to be competitive – Nuria Salazar – Frontiers in Microbiology

Bioinformatics and metagenomics

Exploiting rRNA operon copy number to investigate bacterial reproductive strategies – Benjamin R.K. Roller – Nature Microbiology

Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers – Michelle Davison – PLOS ONE

SnpFilt: A pipeline for reference-free assembly-based identification of SNPs in bacterial genomes – Carmen H.S. Chan – Computational Biology and Chemistry

Review: Advances in biodiversity: metagenomics and the unveiling of biological dark matter – Robert J. Robbins – Standards in Genomic Sciences

Microbes in the news

What we have in common with corals and their unexplored microbial world – Alejandra Hernandez – The Conversation

September 12, 2016

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Individual response of gut microbiota to diet (in mice), appendicitis, adaptive evolution of goose with its microbiome, fungi in rubber plantations.

Events

Storify of days 1-2 of the 6th ASM Beneficial Microbes Meeting, Sept 9-12, Seattle, WA.

Pregnancy and birth

Urinary Microbiota Associated with Preterm Birth: Results from the Conditions Affecting Neurocognitive Development and Learning in Early Childhood (CANDLE) Study – Nicholas J. Ollberding – PLOS ONE

Review: The role of the bacterial microbiota on reproductive and pregnancy health – Deborah B. Nelson – Anaerobe

Human skin microbiome

Skin microbiome prior to development of atopic dermatitis: early colonization with commensal staphylococci at 2 months is associated with a lower risk of atopic dermatitis at 1 year – Elizabeth A. Kennedy – Journal of Allergy and Clinical Immunology

Human respiratory microbiome (and Methods)

Note that 2 different amplification strategies were performed, so IMHO this is more reflection of primer differences than sequencing differences: Different next generation sequencing platforms produce different microbial profiles and diversity in cystic fibrosis sputum – Andrea Hahn – Journal of Microbiological Methods

Human gut microbiome

Evaluation of the microbiome in children’s appendicitis – Martin Salö – International Journal of Colorectal Disease

Review: Food: a new form of personalised (gut microbiome) medicine for chronic diseases? – Tess Pallister – Journal of the Royal Society of Medicine

Review: Linking the Microbiota, Chronic Disease, and the Immune System – Timothy W. Hand – Trends in Endocrinology & Metabolism

Animal and bioreactor experiments

From the Sonnenburg lab @Stanford: Individualized Responses of Gut Microbiota to Dietary Intervention Modeled in Humanized Mice – Samuel A. Smits – mSystems

An In Vitro Approach to Study Effects of Prebiotics and Probiotics on the Faecal Microbiota and Selected Immune Parameters Relevant to the Elderly – Yue Liu – PLOS ONE

Animal microbiome

Genome and metagenome analyses reveal adaptive evolution of the host and interaction with the gut microbiota in the goose – Guangliang Gao – Scientific Reports

Hold off on the orange oil: Characterization of Antibacterial Activities of Eastern Subterranean Termite, Reticulitermes flavipes, against Human Pathogens – Yuan Zeng – PLOS ONE

Use of MALDI-TOF MS and culturomics to identify mosquitoes and their midgut microbiota – Fatalmoudou Tandina – Parasites & Vectors

Plant, root, and soil microbiome

Drought history affects grassland plant and microbial carbon turnover during and after a subsequent drought event – Lucia Fuchslueger – Journal of Ecology

Effect of organic matter enrichment on the fungal community in limestone cave sediments – ELS Marques – Genetics and Molecular Research

Contrasting elevational diversity patterns for soil bacteria between
two ecosystems divided by the treeline – Guixiang Li – Science China Life Sciences

Review: Diversity and ecology of soil fungal communities in rubber plantations – Jutamart Monkai – Fungal Biology Reviews

Illumina sequencing reveals a rhizosphere bacterial community associated with foxtail millet smut disease suppression – Yansha Han – Plant and Soil

Water and extremophile microbiome

Viruses-to-mobile genetic elements skew in the deep Atlantis II brine pool sediments – Mustafa Adel – Scientific Reports

Built environment microbiome

Review: The Microbiome of the Built Environment and Human Behavior: Implications for Emotional Health and Well-Being in Postmodern Western Societies – C.E. Stamper – International Review of Neurobiology

Microbes in the news

The Bacteria on Your Skin Are Safer Than These Two Chemicals the FDA Just Banned From Your Soap – Jill Richardson – Truth Digg

DNA in London Grave May Help Solve Mysteries of the Great Plague – Roff Smith – National Geographic

Bik’s Non-Microbiology Picks

This paper was discussed on Twitter this weekend because of a conflict of interest of one of the authors (Deepak Chopra) and the design and interpretation of the study:

Identification of Altered Metabolomic Profiles Following a Panchakarma-based Ayurvedic Intervention in Healthy Subjects: The Self-Directed Biological Transformation Initiative (SBTI) – Christine Tara Peterson – Scientific Reports

September 10, 2016

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Bifidobacteria and ulcerative colitis, the pollen microbiome, busting the 5-second rule, resistance genes in 23,000 microbial genomes, and a cool video of evolution of bacterial resistance.

Events

Gut health, microbiota & probiotics throughout the lifespan – Metabolic & Brain function 2016 – Sept 15-16, Harvard Medical School, Boston, MA

Human oral microbiome

Deep sequencing reveals microbiota dysbiosis of tongue coat in patients with liver carcinoma – Haifeng Lu – Scientific Reports

Human respiratory microbiome

Review: The microbiome in asthma – Magali Noval Rivas – Current Opinion Pediatrics

Human gut microbiome

Elucidating the gut microbiome of ulcerative colitis: bifidobacteria as novel microbial biomarkers – Sabrina Duranti – FEMS Microbiology Ecology

Review: Gut Microbiota, Inflammation, and Colorectal Cancer – Caitlin A. Brennan – Annual Review of Microbiology

Review: Microbiota—myeloid cell crosstalk beyond the gut – Sayeh Gorjifard – Journal of Leukocyte Biology

Four reviews in Current Pharmaceutical Design in the category “Could the gut microbiota perhaps be involved in disease X?” – with 4 different X’s. 

Animal models

Antibiotic Treatment Induces Long-lasting Changes in the Fecal Microbiota that Protect Against Colitis – Naomi L. Ward – Inflammatory Bowel Diseases

Differences In CD8αα And Cecal Microbiome Community During Proliferation And Late Cytolytic Phases Of Marek’s Disease Virus (MDV) Infection Are Associated With Genetic Resistance To Marek’s Disease – Sudeep Perumbakkam – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Bacterial microbiota associated with flower pollen is influenced by pollination type, and shows a high degree of diversity and species-specificity – Binoy Ambika Manirajan – Environmental Microbiology

Land use intensification in the humid tropics increased both alpha and beta diversity of soil bacteria – Teotonio Soares de Carvalho – Ecology

Small-scale spatial heterogeneity of ecosystem properties, microbial community composition and microbial activities in a temperate mountain forest soil – Martina Štursová – FEMS Microbiology Ecology

Extremophile microbiome

Seasonal dynamics of extremely halophilic microbial communities in three Argentinian salterns – Leonardo Di Meglio – FEMS Microbiology Ecology

Built environment microbiome

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Christin Lola / Fotolia (via Science Direct)

Longer Contact Times Increase Cross-Contamination of Enterobacter aerogenes from Surfaces to Food – Robyn C. Miranda – Applied and Environmental Microbiology

Researchers debunk ‘five-second rule’: Eating food off the floor isn’t safe. Sometimes bacteria transfer in less than a second – Science Daily

Forget the ‘five-second rule’: Food dropped on the floor picks up bacteria in just ONE second – David Gardner – Daily Mail

Antimicrobial Chemicals Are Associated with Elevated Antibiotic Resistance Genes in the Indoor Dust Microbiome – Erica M. Hartmann – Environmental Science & Technology

Antibiotic Resistance Genes in Indoor Dust – Technology Networks

Metagenomics and bioinformatics

The transfer network of bacterial mobile resistome connecting animal and human microbiome – Yongfei Hu – Applied and Environmental Microbiology

Catalog of Mobile Antibiotic Resistance Genes Helps Explain Transfer to Human Pathogens – Genome Web

Chinese investigators characterize the world of resistance gene exchange among bacteria – Phys.org

Phages and viruses

Bacteriophages in clinical samples can interfere with microbiological diagnostic tools – Maryury Brown-Jaque – Scientific Reports

Techniques

Absolute quantification of microbial taxon abundances – Ruben Props – The ISME Journal

Microbes in the news

Jo Handelsman of White House Office of Science and Technology to Speak Monday – University of Tennessee

WATCH: Bacteria Invade Antibiotics And Transform Into Superbugs – Angus Chen – NPR
This might be the coolest visualization of evolution ever. Watch these bacteria evolve antibiotic resistance in just 12 days – Brian Resnick – Vox

These researchers would like you to mail them your gut bacteria – Katherine Lindemann – Research Gate Blog

Hepatitis A Outbreak Linked to Strawberries at Smoothie Chain – Daniel Victor – New York Times

Bacteria Hysteria

M&S becomes first supermarket to offer anti-bacterial shopping bags to banish bugs such as E. coli –  Katie Morley – The Telegraph

Bik’s non-microbiology Picks

Microbiome analysis, please! Giraffes aren’t just giraffes. Turns out there are four species – Rachel Feltman – Washington Post

Flatworm parasite named after Barack Obama: Is that a compliment? – Rowena Lindsay Christian Science Monitor

 

September 9, 2016

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Microbiome and tuberculosis, mangoes, lessons from amphibians, and the microbiome of buildings.

Human gut microbiome

Oral, frozen fecal microbiota transplant (FMT) capsules for recurrent Clostridium difficile infection – Ilan Youngster – BMC Medicine

Review: Microbiome Changes during Tuberculosis and Antituberculous Therapy – Bo-Young Hong – Clinical Microbiology Reviews

No consensus on how the microbiome affects tuberculosis, review finds – Science Daily

Animal models

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Mango, “hedgehog” style – Wikipedia

Mango Supplementation Modulates Gut Microbial Dysbiosis and Short-Chain Fatty Acid Production Independent of Body Weight Reduction in C57BL/6 Mice Fed a High-Fat Diet – Babajide Ojo – Journal of Nutrition

Mango and the Microbiota: New Research Reveals Potential Role of this Superfruit in Maintaining Gut Health – National Mango Board – PR Newswire

Antibiotics Suppress Activation of Intestinal Mucosal Mast Cells and Reduce Dietary Lipid Absorption in Sprague-Dawley Rats – Hirokazu Sato – Gastroenterology

Press (with ugly title): The influence of fat when gut bacteria is reduced by antibioticsm – Science Daily

Animal microbiome

Harnessing the Microbiome to Prevent Fungal Infections: Lessons from Amphibians – Jenifer B. Walke – PLOS Pathogens

Built environment microbiome

Ten questions concerning the microbiomes of buildings – Rachel I. Adams – Building and Environment

The hot new 10 questions concerning the microbiomes of buildings will surprise you – Jonathan Eisen – MicroBEnet

Microbes in the news

“I’ll never let go, Jack I promise”
Titanic expected to disappear by 2030 thanks to hungry bacteria – Matthew Humphries – Geek.com
Video: Will Bacteria Completely Destroy The Titanic’s Remains? – MSN Video

Scientists find deadly scrub typhus bacteria in South America – Reuters

Mount Sinai Beth Israel Says Legionella Bacteria Found in Several Areas of Hospital – NY1.com

Mood, mind and memory: can gut bacteria meddle with the brain? – Dyani Lewis – Cosmos Magazine
Bugs as drugs – medicine’s next frontier – Dyani Lewis – Cosmos Magazine

Driving Microbiome Science: PKU and Probiotics – Raredr

Experts urge a defensive stance in efforts against antimicrobial resistance – EurekAlert

Microbes and money

Microban Opens Microbiology Testing Services to Non-Partners – Genevieve Scarano – Sourcing Journal

Science, publishing, and career

Your toughest experiment: taking the lead in the lab. Eight scientists share the secrets of being a successful PI – Times Higher Education

September 8, 2016

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Geese in wintering areas, Hirschsprung’s disease, and extreme metagenomics.

Jobs and Events

Assistant Professor in Microbiome Research – University of Maryland Baltimore County

Virtual Conference: Microbiology & Immunology 2016 interactive online conference, latest Research on Microscopic Organisms and How They Impact the Human Body – September 7-8, 2016

EPA Webinar and Discussion: What Have We Learned about the Microbiomes of Indoor Environments? – Brent Stephens – September 22, 2016

SMi’s 6th annual Pharmaceutical Microbiology conference – January 18-19, London, UK

Human gut microbiome

screen-shot-2016-09-08-at-7-35-07-amCharacterization of Intestinal Microbiomes of Hirschsprung’s Disease Patients with or without Enterocolitis Using Illumina-MiSeq High-Throughput Sequencing – Yuqing Li – PLOS ONE

Preview: Harnessing Genes and Diet to Fine-Tune the Gut Microbial Fitness – Patrice D. Cani – Cell Metabolism

Animal microbiome

Geese: Characterising the interspecific variations and convergence of gut microbiota in Anseriformes herbivores at wintering areas – Yuzhan Yang – Scientific Report

Water and extremophile microbiome

Extreme metagenomics using nanopore DNA sequencing: a field report from Svalbard, 78 N – Arwyn Edwards – bioRxiv

Bacterial community succession in a high altitude sub-arctic glacier foreland is a three-stage process – Sina Kazemi – Molecular Ecology

Communities that thrive in extreme conditions captured from a freshwater lake – Etienne Low-Décarie – Biology Letters

Review: Substratum-Associated Microbiota – Paula C. Furey – Water Environment Research

Food microbiology

Mungo bean sprout microbiome and changes associated with culture based enrichment protocols used in detection of Gram-negative foodborne pathogens – Heike Margot – Microbiome

Bioinformatics and metagenomes

De novo extraction of microbial strains from metagenomes reveals intra-species niche partitioning – Christopher Quince – bioRxiv

Microbes in the news

Captive Komodo Dragons Share Their Teeming Microbiome with Their Environment, Just Like Us – Naomi Shavin – Smithsonian Magazine

OSTP call to action on saving soil – Jonathan Eisen – MicroBEnet

IIT-Bombay team finds bacteria responsible for neonatal deaths – Priyanka Sahoo – The Indian Express

Scientists discover link between bacteria and supposedly non-infectious diseases – BBSRC

Life on Mars? Martian Meteorites, Martian Microbes – Julie Taylor – uBiome blog

New website (with a link to my blog, so it’s all good): The Microbiome, sponsored by Era7 Bioinformatics Inc.

Science integrity

Macchiarini scandal is a valuable lesson for the Karolinska Institute – Nature

September 6, 2016

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Tongue diagnostics and bacterial communities, microbiome and ALS, flowers and bees sharing microbes, and CRISPR assembly.

Events

4th World Congress on Targeting Microbiota is organized at Institut Pasteur, Paris, France – October 17-19, 2016

How the Indoor Microbiome Influence Health, with Jack A. Gilbert – October 27, 2016 at British International School of Chicago – Lincoln Park in Chicago

Human oral microbiome

Bacillus as a potential diagnostic marker for yellow tongue coating – Juan Ye – Scientific Reports

Human skin microbiome

Redefining the Chronic-Wound Microbiome: Fungal Communities Are Prevalent, Dynamic, and Associated with Delayed Healing – Lindsay Kalan – mBio

Human respiratory tract microbiome

Review: Development of the respiratory tract microbiota in cystic fibrosis – Emma M. de Koff – Current Opinion in Pulmonary Medicine

Human urinary tract microbiome

Commentary: “Urinary tract infection” and the microbiome – Thomas E. Finucane – The American Journal of Medicine

Human gut microbiome

Pitfalls in Inferring Human Microbial Dynamics from Temporal Metagenomics Data – Hong-Tai Cao – bioRxiv

Evaluation of the microbial diversity in amyotrophic lateral sclerosis using high-throughput sequencing – Xin Fang – Frontiers in Microbiology

Review: Beyond 16S rRNA community profiling: intra-species diversity in the gut microbiota – Kirsten M. Ellegaard – Frontiers in Microbiology

Review: Epigenetic mechanisms in microbial members of the human microbiota: current knowledge and perspectives – Natacha Cureau – Future Medicine

Microbiology and immunology

Perspective: Autoimmunity and the microbiome: T-cell receptor mimicry of “self” and microbial antigens mediates self tolerance in holobionts – Robert Root-Bernstein – BioEssays

Animal models of microbiome research

Ketogenic diet modifies the gut microbiota in a murine model of autism spectrum disorder – Christopher Newell – Molecular Autism

Animal microbiome

Disentangling a holobiont – recent advances and perspectives in Nasonia wasps – Jessica Dittmer – Frontiers in Microbiology

Review: The terrestrial isopod microbiome: An all-in-one toolbox for animal-microbe interactions of ecological relevance – Didier Bouchon – Frontiers in Microbiology

Plant, root, and soil microbiome

Microbial communities in passive remediation systems at three abandoned coal mine sites in the United Kingdom – Carmen Falagán – Proceedings IMWA 2016, Freiberg

Primary Succession of Nitrogen Cycling Microbial Communities Along the Deglaciated Forelands of Tianshan Mountain, China – Jun Zeng – Frontiers in Microbiology

Flowers and Wild Megachilid Bees Share Microbes – Quinn S. McFrederick – Microbial Ecology

Triclosan Resistome from Metagenome Reveals Diverse Enoyl Acyl Carrier Protein Reductases and Selective Enrichment of Triclosan Resistance Genes – Raees Khan – Scientific Reports

Water and extremophile microbiome

Oligotrophic Lagoons of the South Pacific Ocean Are Home to a Surprising Number of Novel Eukaryotic Microorganisms – Eunsoo Kim – Environmental Microbiology

Upstream freshwater and terrestrial sources are differentially reflected in the bacterial community structure along a small Arctic river and its estuary – Aviaja L. Hauptmann – Frontiers in Microbiology

Built environment microbiology

Review: Emerging Investigators Series: Sewer surveillance for monitoring antibiotic use and prevalence of antibiotic resistance: urban sewer epidemiology – Nicole Fahrenfeld – Environmental Science: Water Research & Technology

Food microbiology

High-throughput identification of the microbial biodiversity of cocoa bean fermentation by MALDI-TOF MS – S. Miescher Schwenninger – Letters in Applied Microbiology

Bioinformatics and metagenomics

Assemble CRISPRs from metagenomic sequencing data – Jikai Lei – Bioinformatics

Contig annotation tool CAT robustly classifies assembled metagenomic contigs and long sequences – Diego D. Cambuy – bioRxiv

Techniques

High throughput sequencing of multiple amplicons for barcoding and integrative taxonomy – Perrine Cruaud – bioRxiv

Microbes in the news

Podcast (12 min) with Stephen Pointing: Protecting the Earth’s Microbiome – Jesse Mulligan – Radio NZ

Biochemists’ discovery could lead to vaccine against ‘flesh-eating’ bacteria – Science Daily

Enzyme from oral bacteria could be potential therapy for celiac disease – News Medical

Bik’s Non-Microbiology Picks

Bizarre ant colony discovered in an abandoned Polish nuclear weapons bunker – Annalee Newitz – ArsTechnica

September 2, 2016

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Correlation between oligosaccharides and gut microbes in infants, metabolic pathways in 10 infant twin pairs, an Open-Source alternative for USEARCH, and an important new FDA rule.

Events

Unfortunately, all of the confirmed speakers are men. Nature Conference on Environmental and Human Microbiomes: Drivers of Future Sustainability, February 12-15, 2017, Singapore

Pregnancy and birth

Identification of Oligosaccharides in Feces of Breast-fed Infants and Their Correlation with the Gut Microbial Community – Jasmine C. C. Davis – Molecular & Cellular Proteomics

Membrane Vesicles of Group B Streptococcus Disrupt Feto-Maternal Barrier Leading to Preterm Birth – Manalee Vishnu Surve – PLOS Pathogens

Press: Bacteria linked to stillbirth: mouse study – Sarah Wiedersehn – Australian Associated Press

Diversity of Gut Microbiota Metabolic Pathways in 10 Pairs of Chinese Infant Twins – Shaoming Zhou – PLOS ONE

A preliminary investigation on the relationship between gut microbiota and gene expressions in peripheral mononuclear cells of infants with autism spectrum disorders – Ryo Inoue – Bioscience, Biotechnology, and Biochemistry

Human gut microbiome

Commentary: Gut microbiota: Changes in gut microbes and host metabolism: squaring the circle? – Patrice D. Cani – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

Bacterial diversity of the American sand fly Lutzomyia intermedia using high-throughput metagenomic sequencing – Carolina Cunha Monteiro – Parasites & Vectors

Deep COI sequencing of standardized benthic samples unveils overlooked diversity of Jordanian coral reefs in the northern Red Sea – Mamoon M.D. Al-Rshaidat – Genome

Plant, root, and soil microbiome

Metagenomic Analysis of Some Potential Nitrogen-Fixing Bacteria in Arable Soils at Different Formation Processes – Agnieszka Wolińska – Microbial Ecology

Water microbiome

Microbial diversity within the Trichodesmium holobiont – Mónica Rouco – Environmental Microbiology

Bioinformatics and metagenomics

MetaProb: accurate metagenomic reads binning based on probabilistic sequence signatures – Samuele Girotto – Bioinformatics

A heritability-based comparison of methods used to cluster 16S rRNA gene sequences into operational taxonomic units – Matthew A. Jackson – PeerJ

An Open Source alternative for USEARCH: VSEARCH: a versatile open source tool for metagenomics – Torbjørn Rognes- PeerJ Preprint

Using viromes to predict novel immune proteins in non-model organisms – Steven D. Quistad – Proceedings of the Royal Society B

Microbes in the news

FDA issues final rule on safety and effectiveness of antibacterial soaps. Rule removes triclosan and triclocarban from over-the-counter antibacterial hand and body washes – FDA

FDA bans antibacterial soaps; “No scientific evidence” they’re safe, effective
Ban includes soaps with any of 19 chemicals, including triclosan – Beth Mole – ArsTechnica

Living Russian Dolls.They have bacteria in their cells, and smaller bacteria in those bacteria—and that’s not even the weirdest bit – Ed Yong – The Atlantic

Sydney scientists accidentally discover antibiotic to treat koalas with chlamydia – Matt Wordsworth – ABC Australia

High Demand For Antibiotics Leads To Growth In Microbiology Culture Industry In United States – MedGadget

August 31, 2016

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ICU, Rudlavibizon, Flickr

Gut microbiota changes in the ICU, air microbiome of the Gobi desert, host response of human cells to gut microbiota.

Event

Synbiobeta SF2016, October 4-6, South San Francisco, CA

Human gut microbiome

Extreme Dysbiosis of the Microbiome in Critical Illness – Daniel McDonald – mSphere

Press: ICU patients lose helpful gut bacteria within days of hospital admission – Science Daily
Tracking Bacterial Imbalance in the ICU – Stephen Ornes -mBiosphere

Review: The human gut microbiome, diet, and health: “post hoc non ergo propter hoc” – Guus Roeselers – Trends in Food Science & Technology

Review: Interplay between gut microbiota, its metabolites and human metabolism: dissecting cause from consequence – A.V. Hartstra – Trends in Food Science & Technology

Animal and other model experiments

Bidirectional communication between the Aryl hydrocarbon Receptor (AhR) and the microbiome tunes host metabolism – Agata Korecka – NPJ Biofilms and Microbiomes

Temporal dynamics of bacterial microbiota in the human oral cavity determined using an in situ model of dental biofilms – Nanako Wake – NPJ Biofilms and Microbiomes

Normalizing Microbiota-Induced Retinoic Acid Deficiency Stimulates Protective CD8+ T Cell-Mediated Immunity in Colorectal Cancer – Nupur Bhattacharya – Immunity

Genetic and Transcriptional Analysis of Human Host Response to Healthy Gut Microbiota – Allison L. Richards – mSystems

Animal microbiome

Whole gut microbiome composition of damselfish and cardinalfish before and after reef settlement – Darren J Parris – PeerJ

Plant, root, and soil microbiome

Specialized Microbiome of a Halophyte and its Role in Helping Non-Host Plants to Withstand Salinity – Zhilin Yuan – Scientific Reports

A native and an invasive dune grass share similar, patchily distributed, root-associated fungal communities – Renee B. Johansen – Fungal Ecology

Bacterial community structure and function shift across a northern boreal forest fire chronosequence – Hui Sun – Scientific Reports

Water microbiome

Complex bacterial communities in the deep-sea sediments of the Bay of Bengal and volcanic Barren Island in the Andaman Sea – Pankaj Verma – Marine Genomics

Neutral processes and species sorting in benthic microalgal community assembly: effects of tidal resuspension – Craig J. Plante – Journal of Phycology

Air microbiome

Variations in the structure of airborne bacterial communities in Tsogt-Ovoo of Gobi desert area during dust events – Teruya Maki – Air Quality, Atmosphere & Health

Bioinformatics and metagenomics

A phylogenetic transform enhances analysis of compositional microbiota data – Justin D Silverman – bioRxiv

Higher classification sensitivity of short metagenomic reads with CLARK-S – Rachid Ounit – Bioinformatics

GRASPx: efficient homolog-search of short peptide metagenome database through simultaneous alignment and assembly – Cuncong Zhong – BMC Bioinformatics

Microbial ecology

Quantifying human impact on Earth’s microbiome – Stephen B. Pointing – Nature Microbiology

Synthetic microbial ecology and the dynamic interplay between microbial genotypes –
Jan Dolinšek – FEMS Microbiology Reviews

Microbes in the news

Engineered gut bacteria protect mice against obesity, improve liver function – Oliver Worsley – Fierce Biotech

You’re probably not doing metagenomics – Mick Watson – Opiniomics

Mayo Adds To Its List Of Gut Microbiome Startup Collaborators – Don Jacobson – Twin Cities Business

Nice analysis of Tweets from #ISME16 by Keith Turner – Jonathan Eisen – MicroBEnet

Peer review and science misconduct

Recognizing Peer Reviewers: a Webinar to Celebrate Editors and Researchers – September 19, 2016 – Elsevier Publishing Campus

Stop ignoring misconduct – Donald S. Kornfeld & Sandra L. Titus – Nature

Bik’s Non-Microbiology Picks

Paperfuge: An ultra-low cost, hand-powered centrifuge inspired by the mechanics of a whirligig toy – M. Saad Bhamla – bioRxiv

August 30, 2016

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Red-shanked douc, Wikipedia

The human gut phageome, monkey microbiome humanizes in captivity, and a Yersinia genome from the 6th century (OK, that’s not microbiome, but just cool).

Human gut microbiome

Healthy human gut phageome – Pilar Manrique – PNAS

Press: Your Gut’s Gone Viral, And That Might Be Good For Your Health – Michaeleen Doucleff – NPR

Animal experiments

Standardizing Mouse Models to Account for Host–Microbial Interactions – Maria-Luisa Alegre – American Journal of Transplantation

Note: no mention of blanks/extraction controls: Consumption of a high-fat diet alters the seminal fluid and gut microbiomes in male mice – Angela B. Javurek – Reproduction , Fertility and Development

Animal microbiome

Captivity humanizes the primate microbiome – Jonathan B. Clayton – PNAS

Press (also see yesterday’s post): Gut biome of monkeys found to change when they are kept in captivity – Bob Yirka – Phys.org
Monkeys in zoos have human gut bacteria – Science Daily

Water microbiome

Coastal connectivity and spatial subsidy from a microbial perspective – Christin Säwström – Ecology and Evolution

Taxonomic profiling of bacterial community structure from coastal sediment of Alang–Sosiya shipbreaking yard near Bhavnagar, India – Vilas Patel – Marine Pollution Bulletin

Proteobacteria become predominant during regrowth after water disinfection – Cristina Becerra-Castro – Science of the Total Environment

Microbial Ecology

Understanding How Microbiomes Influence the Systems they Inhabit: Insight from Ecosystem Ecology – Ed Hall – bioRxiv

More microbes

A high-coverage Yersinia pestis Genome from a 6th-century Justinianic Plague Victim – Michal Feldman – Molecular Biology and Evolution

Press: World’s 1st Plague Pandemic Bacteria Gets New Genetic Analysis – Greg Uyeno – Live Science
Why scientists reconstructed an ancient plague – Nikki Ferlaino – KFOR
Reconstructing the sixth century plague from a victim – Phys.org
The Same Microbe That Led to Black Death Also Caused a Huge Plague Centuries Before – Jennifer Ouellette – Gizmodo
Medieval victim reveals secrets of the Plague of Justinian – Gretchen Vogel – Science

Microbes in the news

Hand dryers spread bacteria, affect health on campus – Shane Olney – The Volante

Science, publishing, and career

A Framework for Improving the Quality of Research in the Biological Sciences – Arturo Casadevall – mBio

Bik’s Non-Microbiology Picks

Dental calculus reveals Mesolithic foragers in the Balkans consumed domesticated plant foods – Emanuela Cristiani – PNAS

Surprisingly Little Evidence for the Accepted Wisdom About Teeth – Aaron E. Carroll – New York Times