Category Archives: Extremophiles

July 2, 2016

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Colonic transit time, innovations in artificial gut systems, and how the majority of the human gut microbiome members can be cultured.

Human respiratory microbiome

Nasopharyngeal microbiota composition of children is related to the frequency of upper respiratory infection and acute sinusitis – Clark A. Santee – Microbiome

Metagenomics Study of Viral Pathogens in Undiagnosed Respiratory Specimens
and Identification of Human Enteroviruses at a Thailand Hospital – Yanfei Zhou – American Journal of Tropical Medicine and Hygiene

Review: The respiratory microbiome of HIV-infected individuals – MB Lawani – Expert Review of Anti-infective Therapy

Review: A tale of two sites: how inflammation can reshape the microbiomes of the gut and lungs – Brittan S. Scales – Journal of Leukocyte Biology

Human gut microbiome

Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut – Henrik M. Roager – Nature Microbiology

Behind the paper: How we got captivated by colonic transit time – Henrik Munch Roager – Nature Microbiology Community

Datafying microbes: Malnutrition at the intersection of genomics and global health – Amber Benezra – BioSocieties

Several reviews in the July issue of Therapeutic Advances in Gastroenterology:
The interplay between the microbiome and the adaptive immune response in cancer development – Edda Russo
The intestinal microbiome, barrier function, and immune system in inflammatory bowel disease: a tripartite pathophysiological circuit with implications for new therapeutic directions – Stephen M. Vindigni
Role of the gut microbiota in health and chronic gastrointestinal disease: understanding a hidden metabolic organ – Caitriona M. Guinane
Novel perspectives on therapeutic modulation of the gut microbiota – Justin L. McCarville

Review: The Brain-Body-Microbial Communities: A Crosstalk and Stress Exchange
Beyond the “Gut hypothesis” – Afifi Ma – Abnormal and Behavioural Psychology

Review: The Role of the Microbial Metabolites Including Tryptophan Catabolites and Short Chain Fatty Acids in the Pathophysiology of Immune-Inflammatory and Neuroimmune Disease – Gerwyn Morris – Molecular Neurobiology

Animal experiments

Relationship between the microbiota in different sections of the gastrointestinal tract, and the body weight of broiler chickens – Geon Goo Han – Springer Plus

The upper respiratory tract microbiome and its potential role in bovine respiratory disease and otitis media – Svetlana F. Lima – Scientific Reports

Review: Farewell to Animal Testing: Innovations on Human Intestinal Microphysiological Systems – Tae Hyun Kang – Micromachines

Plant, root, and soil microbiome

Effects of Short-Term Warming and Altered Precipitation on Soil Microbial Communities in Alpine Grassland of the Tibetan Plateau – Kaoping Zhang – Frontiers in Microbiology

Bacterial diversity in the rhizosphere of two phylogenetically closely related plant species across environmental gradients – Xiaofan Na – Journal of Soils and Sediments

Soil microbial communities of three major Chinese truffles in Southwest China – Yu Fu – Canadian Journal of Microbiology

Review: Ecology of nitrogen fixing, nitrifying and denitrifying microorganisms in tropical forest soils – Silvia Pajares – Frontiers in Microbiology

Water and extremophile microbiome

Metagenomic analysis of microbial community of an Amazonian geothermal spring in Peru – Sujay Paul – Genomics Data

Characterization of microbial mat microbiomes in the modern thrombolite ecosystem of Lake Clifton, Western Australia using shotgun metagenomics – John G. Warden – Frontiers in Microbiology

Built environment microbiome

Microbes in the Water Infrastructure: Underpinning Our Society – Takashi Narihiro – Microbes and Environments

Techniques / Metabolomics

Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling – Jennifer T. Lau – Genome Medicine

A Microbiome DNA Enrichment Method for Next-Generation Sequencing Sample Preparation – Erbay Yigit – Current Protocols in Molecular Biology

Sample preparation optimization in fecal metabolic profiling – Olga Deda – Journal of Chromatography B

Viruses and phages

Survival studies of a temperate and lytic bacteriophage in bovine faeces and slurry – Sepo Nyambe – Journal of Applied Microbiology

Microbes in the news

Conference report: Machine Learning Method Differentiates Between Healthy Male, Female Microbiomes: Topological Data Analysis – UC San Diego

A New Role for Marine Archaea. Researchers discover acetogenesis in archaea, suggesting an important role for these little-studied organisms in generating organic carbon below the seafloor – Catherine Offord – The Scientist

Stop worrying about GMOs; it’s that organic granola bar that could make you sick: Listeria – Henry I. Miller – LA Times

USM marine microbiologist Jay Grimes weighs in on vibrio vulnificus – WDAM

Chesterfield Royal scientists send ripples around the NHS – Andy Done-Johnson – Derbyshire Times

Efficiency in the pathology lab: Friend or Foe; the probiotic power of helminths can prevent Crohn’s Disease – Anouk Gouvras – BioMedCentral blog

Supplement may switch off cravings for high-calorie foods – Stephen Feller – UPI
Cravings for high-calorie foods may be switched off by new food supplement – Kate Wighton – Imperial College London

Science, publishing, and career

“He Thinks He’s Untouchable”: Michael Katze, famous for his studies of Ebola and the flu, ran a lab at the University of Washington where intoxication and sexual harassment went unchecked – Azeen Ghorayshi – Buzzfeed

June 30, 2016

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Mycorrhizal fungi and CO2, pathogen defense in the gut, Mississippi River plume.

Animal experiments

Defensive Mutualism Rescues NADPH Oxidase Inactivation in Gut Infection – Gratiela Pircalabioru – Cell Host & Microbe

Press: Good gut relationships key in defence against pathogens – Medical Xpress

Plant, root, and soil microbiome

Mycorrhizal association as a primary control of the CO2 fertilization effect – César Terrer – Science

Press: Study finds that plant growth responses to high carbon dioxide depend on symbiotic fungi – EurekAlert

Grassland to woodland transitions: Dynamic response of microbial community structure and carbon use patterns – Courtney A. Creamer – Journal of Geophysical Research

The interaction between arbuscular mycorrhizal fungi and endophytic bacteria enhances plant growth of Acacia gerrardii under salt stress – Abeer Hashem – Frontiers in Microbiology

Water and extremophile microbiome

Mississippi River plume enriches microbial diversity in the northern Gulf of Mexico – Olivia U. Mason – Frontiers in Microbiology

Editorial: Anthropogenic impacts on the microbial ecology and function of aquatic environments – Maurizio Labbate – Frontiers in Microbiology

Unanticipated geochemical and microbial community structure under seasonal ice cover in a dilute, dimictic Arctic lake – Ursel Schuette – Frontiers in Microbiology

Comparative activity and functional ecology of permafrost soils and lithic niches in a hyper-arid polar desert – Jacqueline Goordial – Environmental Microbiology

Metagenomics and bioinformatics

Bioinformatic Characterization of Mosquito Viromes within the Eastern United States and Puerto Rico: Discovery of Novel Viruses – Kenneth G. Frey – Evolutionary Bioinformatics

Review: Reconstructing single genomes from complex microbial communities – Dongwan D. Kang – it-Information Technology

Review: A history of DNA sequence assembly – Eugene W. Myers Jr – it-Information Technology

Review: Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes – Miklós Bálint – FEMS Microbiology Reviews

Microbes in the news

Stanford undergrads cook up a biotech startup to develop new antibiotics for drug-resistant superbugs – Rosemary Mena-Werth – Stanford News

From the Evolution Conference, talk by Danielle Whittaker: Bacteria give bird its sexy smells – Patrick Monahan – Science

Australia’s Melbourne takes selfie of its microbiome – i4U News

The Microbiome and Bronchiolitis: An Unusual Pairing or Is It? – Lewis First – AAP Gateway

An Ounce of (Water) Prevention: microbial fuel degradation – Katherine Vanover – Fuel Market News

New study shows chronic fatigue isn’t just in your head. It may have to do with your gut – Ariana Eunjung Cha – Washington Post

Resistance to antibiotics and to immune system are interconnected in bacteria – EurekAlert

In times of great famine, microalgae digest themselves. AWI researchers decipher the connection between nutrient availability and algae growth – EurekAlert

Researchers develop effective strategy for disrupting bacterial biofilms – EurekAlert

How a germ catches a virus – Phys.org

Coming Soon: Gut Bacteria That Actually Cure Your Disease: The $34 billion probiotics market includes some dubious products. This crop looks different – Deena Shanker – Bloomberg

TV weatherman retracts story about toxic bacteria at Northwest Florida beaches – The Destin Log

Bik’s non-microbiology Picks

Former Relman lab member: NASA Astronaut Kate Rubins Prepares for First Trip to Space – Alison Thoet – ABC News

107 Nobel laureates sign letter blasting Greenpeace over GMOs – Joel Achenbach – Washington Post

The Academic Hermit – What are you going to do with your tool?: installation as the Frederick G. Novy Collegiate Professor of Microbiome Research at the University of Michigan – Pat Schloss

June 29, 2016

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Two new papers on multiple sclerosis and breast tissue, cross-respiration, the Boston urban transit microbiome, and plastic debris.

Human respiratory microbiome

Review: The respiratory microbiome of HIV-infected individuals – MB Lawawni – Expert Review of Anti-infective Therapy

Human skin microbiome

The microbiota of breast tissue and its association with tumours – Camilla Urbaniak – Applied and Environmental Microbiology

Human gut microbiome

Alterations of the human gut microbiome in multiple sclerosis – Sushrut Jangi – Nature Communications

Review: Gut microbiota and hematopoietic stem cell transplantation: where do we stand? – D Zama – Bone Marrow Transplantation

Review: The neuropharmacology of butyrate: The bread and butter of the microbiota-gut-brain axis? – Roman M. Stilling – Neurochemistry International

Animal and in vitro experiments

A Commensal Bacterium Promotes Virulence of an Opportunistic Pathogen via Cross-Respiration – Apollo Stacy – mBio

Press: Cross-respiration between oral bacteria leads to worse infections – EurekAlert

Microbiota-Regulated IL-25 Increases Eosinophil Number to Provide Protection during Clostridium difficile Infection – Erica L. Buonomo – Cell Reports

Animal microbiome

Genome-wide survey of gut fungi (Harpellales) reveals the first horizontally transferred ubiquitin gene from a mosquito host – Yan Wang – Molecular Biology and Evolution

In barn swallows: Stress response, gut microbial diversity and sexual signals correlate with social interactions – Iris I. Levin – Biology Letters

Plant, root, and soil microbiome

Plant Host and Geographic Location Drive Endophyte Community Composition in the Face of Perturbation – Natalie Christian – Microbial Ecology

Perspective: Soil immune responses – Jos M. Raaijmakers – Science

Water and extremophile microbiome

Microbes in mercury-enriched geothermal springs in western North America – Gill G. Geese – Science of The Total Environment

Environmental Disturbances Decrease the Variability of Microbial Populations within Periphyton – Cristina M. Herren – mSystems

Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments – Marina N. Mato – Environmental Microbiology

Built environment microbiome

Commentary: Avoiding Pandemic Fears in the Subway and Conquering the Platypus – A. Gonzalez – mSystems

Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment – Tiffany Hsu – mSystems

Press: ‘Bugs’ on the subway: Monitoring the microbial environment to improve public health – EurekAlert

Diversity and Activity of Communities Inhabiting Plastic Debris in the North Pacific Gyre – Jessica A. Bryant – mSystems

Food microbiology

Culture-independent bacterial community profiling of carbon dioxide treated raw milk – Raquel Lo – International Journal of Food Microbiology

Metagenomics and bioinformatics

MetaPalette: a k-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation – David Koslicki – mSystems

Bayesian identification of bacterial strains from sequencing data – Aravind Sankar – Microbial Genomics

MetaTreeMap: An Alternative Visualization Method for Displaying Metagenomic Phylogenic Trees – Maxime Hebrard – PLOS ONE

Proteomics and metabolomics

MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses – Ernesto S. Nakayasu – mSystems

An Integrated Metabolomic and Genomic Mining Workflow To Uncover the Biosynthetic Potential of Bacteria – Maria Maansson – mSystems

Techniques

16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform – Fiona Fouhy – BMC Microbiology

Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies – Se Jin Song – mSystems

Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes – Richard Allen White III – mSystems

A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses – Lindsey A. Moser- mSystems

Fungal identification biases in microbiome projects – Leho Tedersoo – Environmental Microbiology Reports

Microbes in the news

Germs in the Subway Are the Harmless Kind – Nicholas Bakalar – New York Times

An Industrial Microbiologist Who Adds Biofuel to the Fire – Nandita Jayaraj – The Wire India

Interview of Faculty of Clinical Microbiology, Prof. Generalov Igor Ivanovich, at VSMU, Belarus – LinkedIn

 

June 28, 2016

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A fundraiser to study the turtle microbiome, multiple sclerosis, generalists inside specialist, and visualizing translational activity.

Events

IndieGoGo campaign: TurtleTracts: Study Microbes to Save Sea Turtles – Aubrey Tauer

Also see this blog post: Sneak Peak at our Sea Turtle Microbiome Initiative – Aubrey Tauer

Pregnancy and birth

Gut bacteria and late-onset neonatal bloodstream infections in preterm infants – Phillip I. Tarr – Seminars in Fetal and Neonatal Medicine

Human respiratory microbiome

Commentary: Mode of delivery to the brave new (microbial) world: a defining moment for the respiratory microbiome? – Georgios D. Kitsios – EBioMedicine

Human gut microbiome

Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls – Jun Chen – Scientific Reports

Press: Link between gut bacteria, MS discovered. MS patients show lower levels of good bacteria – Science Daily

Review: Microbiota as Therapeutic Targets – Xavier R.J. – Digestive Diseases

Animal microbiome
The Generalist Inside the Specialist: Gut Bacterial Communities of Two Insect Species Feeding on Toxic Plants Are Dominated by Enterococcus sp. – Cristina Vilanova – Frontiers in Microbiology

Review: The gut microbiome as a virtual endocrine organ with implications for farm and domestic animal endocrinology – T.F. O’Callaghan – Domestic Animal Endocrinology

Plant, root, and soil microbiome
Systemic enrichment of antifungal traits in the rhizosphere microbiome after pathogen attack – Jan-Hendrik Dudenhöffer – Journal of Ecology

A multi-biological assay approach to assess microbial diversity in arsenic (As) contaminated soils – S.R. Stazi – Geomicrobiology Journal

Effects of two fungicide formulations on microbial and macroinvertebrate leaf decomposition under laboratory conditions – Adria A. Elskus – Environmental Toxicology and Chemistry

Book: Plant, Soil and Microbes – Editors: Khalid Rehman Hakeem, Mohd Sayeed Akhtar – Springer

Water and extremophile microbiome

Metagenomics-Guided Mining of Commercially Useful Biocatalysts from Marine Microorganisms – A.R. Uria – Advances in Food and Nutrition Research

Lessons learned from thirty years of geomicrobiological studies of Río Tinto – Ricardo Amils – Research in Microbiology

Metabolic diversity and adaptive mechanisms of iron- and/or sulfur-oxidizing autotrophic acidophiles in extremely acidic environments – Xian Zhang – Environmental Microbiology Reports

Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill – Nina Dombrowski – Nature Microbiology

News and views: Marine microbiology: Community clean up – Rachel Mackelprang – Nature Microbiology

Assessing viral taxonomic composition in benthic marine ecosystems: reliability and efficiency of different bioinformatic tools for viral metagenomic analyses – M. Tangherlini – Scientific Reports

Marine phage genomics: the tip of the iceberg – Blanca Perez Sepulveda – Microbiology Letters

Metabolic networks and proteomics

MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota – Xu Zhang – Microbiome

The use of propidium monoazide in conjunction with qPCR and Illumina sequencing to identify and quantify live yeasts and bacteria – Mansak Tantikachornkiata – International Journal of Food Microbiology

Protocol: Constructing and Analyzing Metabolic Flux Models of Microbial Communities – José P. Faria – Springer Protocols

Viruses and phages

Opinion: The Janus-Face of Bacteriophages across Human Body Habitats – Adam Wahida – PLOS Pathogens

Review: Research on the human virome: where are we and what is next – Shimian Zou – Microbiome

Microbial ecology and techniques

Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia – Roland Hatzenpichler – PNAS

Press: See and sort: Developing novel techniques to visualize uncultured microbial cell activity – Science Daily

High functional diversity stimulates diversification in experimental microbial communities – Alexandre Jousset – Science Advances

Measuring the biodiversity of microbial communities by flow cytometry – Ruben Props – Methods in Ecology and Evolution

Highlight: A timely reminder of technical limitations – James I. Prosser – Microbial Biotechnology

Species-sorting and mass-transfer paradigms control managed natural metacommunities – Susanne Günther – Environmental Microbiology

Microbes in the news

Slimy clumps of bacteria kill thousands. Scientists are fighting back – Usha Lee McFarling – STAT News

Why everyone’s suddenly talking about gut bacteria – Laura Entis – Fortune

Scientists find link between makeup of individual’s microbiome and head and neck cancer – News Medical

June 27, 2016

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A short Monday post. Bronchiolitis and virome milestones in infants, and playing drums.

Pregnancy and birth

The Fecal Microbiota Profile and Bronchiolitis in Infants – Kohei Hasegawa – Pediatrics

Editorial: Do Bacteria in the Gut Set the Stage for Who Gets Viral Bronchiolitis and Its Severity? – Patrick C. Seed – Pediatrics

Research Highlight: Distinct Fecal Microbiota Pattern Associated with Infant Bronchiolitis – Christine Judge – NEJM Journal Watch

The Bacterial Microbiome and Virome Milestones of Infant Development – Efrem S. Lim – Trends in MIcrobiology

More microbiology

Is there an Infection Risk when Playing Drums Contaminated with Bacillus anthracis? –
A M Bennett – Journal of Applied Microbiology

Microbes in the news

UI researcher finds link between gut bacteria and MS. MS patients show lower levels of good bacteria – EurekAlert

Microbes in extreme heat and cold hold lessons about life on Earth, and beyond – Don Cowan – The Conversation

Olympic rowers unveil special suits to combat bacteria in Rio – WHEC

Pineapples Can Stop Harmful Bacteria In The Gut – Diane Palmer – Parent Herald

June 24, 2016

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Placenta samples not distinguishable from controls, gut microbiome in ME/CFS and PKU patients, childhood undernutrition, corals’ microbial sentinels, and plant root traps.

Pregnancy and birth

I was hoping for this study to be done: Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota – Abigail P. Lauder – Microbiome

Systematic review: Treatment of bacterial vaginosis in pregnancy in order to reduce the risk of spontaneous preterm delivery – a clinical recommendation – Thor Haahr – Acta Obstetricia et Gynecologica Scandinavica

Human ear microbiome

The microbiome of otitis media with effusion – Chun Ling Chan – The Laryngoscope

Human gut microbiome

Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome – Ludovic Giloteaux – Microbiome

Phenylketonuria and Gut Microbiota: A Controlled Study Based on Next-Generation Sequencing – Felipe Pinheiro de Oliveira – PLOS ONE

Review: Childhood undernutrition, the gut microbiota, and microbiota-directed therapeutics – Laura V. Blanton – Science

Editorial: Gut microbiota and undernutrition – Caroline Ash – Science

Infection and microbiology

Role of Clinicogenomics in Infectious Disease Diagnostics and Public Health Microbiology – Lars F. Westblade – Journal of Clinical Microbiology

Novel Taxa Associated with Human Fungal Black-Grain Mycetomas: Emarellia grisea gen. nov., sp. nov., and Emarellia paragrisea sp. nov. – Andrew M. Borman – Journal of Clinical Microbiology

Sociomicrobiology and Pathogenic Bacteria – Joao B. Xavier – Microbiology Spectrum

Paleomicrobiology Data: Authentification and Interpretation – Michel Drancourt – Microbiology Spectrum

Animal experiments

Dietary fucoidan modulates the gut microbiota in mice by increasing the abundance of Lactobacillus and Ruminococcaceae – Qingsen Shang – Food & Function

Animal microbiome

Perspective: Corals’ microbial sentinels – Tracy D. Ainsworth – Science

Plant, root, and soil microbiome

Escaping Underground Nets: Extracellular DNases Degrade Plant Extracellular Traps and Contribute to Virulence of the Plant Pathogenic Bacterium Ralstonia solanacearum – Tuan Minh Tran – PLOS Pathogens

Press: An ‘arms race’ raging beneath our plants: A crop’s DNA-laden root trap manages to hold on to only a quarter of its bacterial prisoners. – Amy Middleton – Cosmos Magazine

Responsiveness of soil nitrogen fractions and bacterial communities to afforestation in the Loess Hilly Region (LHR) of China – Chengjie Ren – Scientific Reports

Spatial Shifts in Soil Microbial Activity and Degradation of Pasture Cover Caused by Prolonged Exposure to Cement Dust – Fuensanta Caravaca – Land Degradation & Development

Water and extremophile microbiome

Biogeochemical and 16S rRNA gene sequence evidence supports a novel mode of anaerobic methanotrophy in permanently ice-covered Lake Fryxell, Antarctica – Matthew A. Saxton – Limnology and Oceanography

Food microbiology

The Microbiome and Metabolites in Fermented Pu-erh Tea as Revealed by High-Throughput Sequencing and Quantitative Multiplex Metabolite Analysis – Yongjie Zhang – PLOS ONE

More microbiology

Sugar Synthesis from CO2 in Escherichia coli – Niv Antonovsky – Cell

Press: Eating air, making fuel. Scientists engineer bacteria to create sugar from the greenhouse gas carbon dioxide – Science Daily

Not a scientific paper, just a list of links: Web Alert: Synthetic microbial communities: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology – Lawrence P. Wackett – Environmental Microbiology

Techniques

High stability of faecal microbiome composition in guanidine thiocyanate solution at room temperature and robustness during colonoscopy – Yuichiro Nishimoto – Gut

Microbes in the news

New life form discovered in saliva is linked to human disease – Andy Coghlan – New Scientist

Seagulls Are Carrying a Dangerous Superbug Through the Skies – Maryn McKenna – National Geographic
Beware of Seagulls Carrying This Dangerous Superbug – Laura Lorenzetti – Fortune

Microbes In The Body Affect Success Of Organ Transplants: Study – Katrina Pascual -Tech Times

Scientists just found a compound that kills 98% of a drug-resistant bacteria – Fiona MacDonald – Science Alert

Milken Institute School of Public Health researchers awarded $7 million to study microbiome – Sera Royal – The GW Hatchet

Mycobacterium in olive oil for cancer treatment – EurekAlert

Scientists discover unsuspected bacterial link to bile duct cancer – MedicalXpress

Bik’s completely-not-microbiology Picks

The social dilemma of autonomous vehicles – Jean-François Bonnefon – Science

June 23, 2016

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Red snow microbiomes and melting glaciers, effect of earthworms on microbes, microbiome in COPD.

Pregnancy and birth

Early Gut Microbiota Perturbations Following Intrapartum Antibiotic Prophylaxis to Prevent Group B Streptococcal Disease – Giuseppe Mazzola – PLOS ONE

Human respiratory microbiome

Editorial: Early life nasal microbiota in infants with cystic fibrosis – Fiona J Whelan – The Lancet Respiratory Medicine

Review: Understanding the role of the microbiome in COPD: Principles, Challenges and Future Directions – Yvonne J. Huang – Translational Research

Human gut microbiome

Anaerococcus rubiinfantis sp. nov., isolated from the gut microbiota of a Senegalese infant with severe acute malnutrition – Maryam Tidjani Alou – Anaerobe

Review: Understanding the mechanisms of faecal microbiota transplantation – Alexander Khoruts – Nature Reviews Gastroenterology & Hepatology

Review: Microbe-host interactions: Influence of the gut microbiota on the enteric nervous system – Niall P. Hyland – Developmental Biology

Systematic review: Probiotic supplementation can positively affect anxiety and depressive symptoms: a systematic review of randomized controlled trials – Meysam Pirbaglou – Nutrition Research

Animal experiments

Maternal gut and fetal brain connection: Increased anxiety and reduced social interactions in Wistar rat offspring following peri-conceptional antibiotic exposure – Stéphanie Degroote – Progress in Neuro-Psychopharmacology and Biological Psychiatry

A human gut ecosystem protects against C. difficile disease by targeting TcdA – Sarah Lynn Martz – Journal of Gastroenterology

Animal microbiome

Species-specific effects of earthworms on microbial communities and the fate of litter-derived carbon – Chih-Han Chang – Soil Biology and Biochemistry

Diversity of natural product biosynthetic genes in the microbiome of the deep sea sponges Inflatella pellicula, Poecillastra compressa and Stelletta normani – Alan D. Dobson – Frontiers in Microbiology

Plant, root, and soil microbiome

Tree species select diverse soil fungal communities expressing different sets of lignocellulolytic enzyme-encoding genes – Florian Barbi – Soil Biology and Biochemistry

Repeated annual glyphosate applications may impair beneficial soil microorganisms in temperate grassland – M. Druille – Agriculture, Ecosystems & Environment

Water and extremophile microbiome

 The biogeography of red snow microbiomes and their role in melting arctic glaciers – Stefanie Lutz – Nature Communications

Press: The Arctic’s pretty but alarming strawberry-pink snow – Ben Guarino – Washington Post
This Pink Snow Does Not Bode Well For Our Future – Maddie Stone – Gizmodo

Effects of heap-bioleaching plant on microbial community of the nearby river – Mingjiang Zhang – International Biodeterioration & Biodegradation

Molecular Characterization of Aquatic Bacterial Communities in Dinaric Range Caves – Pleše, Bruna – Water Environment Research

Air microbiome

High-throughput sequencing reveals unprecedented diversities of Aspergillus species in outdoor air – Seungeun Lee – Letters in Applied Microbiology

Food microbiology

Changes in the microbiota of lamb packaged in a vacuum and in modified atmospheres during chilled storage analysed by high-throughput sequencing – Taojun Wang – Meat Science

Microbial Diversity of Type I Sourdoughs Prepared and Back-Slopped with Wholemeal and Refined Soft (Triticum aestivum) Wheat Flours – Manuela Taccari – Journal of Food Science

Added ingredients affect the microbiota and biochemical characteristics of durum wheat type-I sourdough – Fabio Minervini – Food Microbiology

Fungal diversity and ecosystem function data from wine fermentation vats and microcosms – Primrose J. Boynton – Data in Brief

The phenotypic characterization of yeast strains to stresses inherent to wine fermentation in warm climates – M. García – Journal of Applied Microbiology

Built environment microbiology

Contamination of healthcare workers’ mobile phones by epidemic viruses – S. Pillet – Clinical Microbiology and Infection

Press: Mobile devices of healthcare workers often contaminated by viral RNA – News Medical

No access for me, but intriguing title: Show research into the human microbiome can be used to solve crimes – Kyle Nothern – Southern California Interdisciplinary Law Journal

Microbes in the news
Video: Citizen Science and Mapping the Microbiome – Eric J. Topol interviews Jessica Richman – Medscape

Mapping the subway’s microbiome. Barcelona takes part in the international research project Metasub, which aims to map the microbiome of public transit systems in 54 cities worldwide – EurekAlert

Biology professor helps author free textbook, saving students hundreds: OpenStax Microbiology – Lainie Mazzullo – Wichita State University

Science, publishing, and career

At 31, she runs one of the hottest biotech companies in the country, with Rachel Haurwitz, CEO of Caribou Biosciences – Andrew Joseph – STAT news

Stem cell scientist Paolo Macchiarini suspected of involuntary manslaughter – STAT news

June 22, 2016

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Nipple aspirate, CNS infections, fiber and food allergies, horses and honeybee bacteria, and a report from the subway citizen science project.

General human microbiome

Commentary: Lessons Learned from Probing for Impacts of Triclosan and Triclocarban on Human Microbiomes – Rolf U. Halden – mSphere

Human nipple microbiome

Characterization of the microbiome of nipple aspirate fluid of breast cancer survivors – Alfred A. Chan – Scientific Reports

Human vaginal microbiome

Impact of Probiotic SYNBIO® Administered by Vaginal Suppositories in Promoting Vaginal Health of Apparently Healthy Women – Maria Cristina Verdenelli – Current Microbiology

Human gut microbiome

Alterations of Intestinal Microbiome by Antibiotic Therapy in Hospitalized Children – Miriam R. Fernandes – Microbial Drug Resistance

Could gut microbiota serve as prognostic biomarker associated with colorectal cancer patients’ survival? A pilot study on relevant mechanism – Zhiliang Wei – Oncotarget

ASM Microbe 2016 abstract: Increased Akkermansia muciniphila and Bacteroides fragilis Group Abundance After Islamic Fasting – C. Erdogdu – ASM Microbe 2016

Press: Happy Ramadan From Your Microbiome! – Gastroenterology & Endoscopy News

Review: Inflammation and the microbiome: implications for depressive disorders – Shawn Hayley – Current Opinion in Pharmacology

Review: Role of the microbiome, probiotics, and ‘dysbiosis therapy’ in critical illness.– Wischmeyer, Paul E. – Current Opinion in Critical Care

Infection and microbiology

Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system – Steven L. Salzberg – Neurology Neuroimmunology & Neuroinflammation

Press: Diagnosing brain infections using metagenomics – Julian Harris – PHG Foundation

Animal experiments

Dietary Fiber and Bacterial SCFA Enhance Oral Tolerance and Protect against Food Allergy through Diverse Cellular Pathways – Jian Tan – Cell Reports

Press: Diet high in fiber and vitamin A key to preventing allergies to peanuts and other triggers – EurekAlert

Gut microbiota translocation to the pancreatic lymph nodes triggers NOD2 activation and contributes to T1D onset – Frederico R.C. Costa – Journal of Experimental Medicine

Cutting Edge: Commensal Microbiota Has Disparate Effects on Manifestations of Polyglandular Autoimmune Inflammation – Camilla H. F. Hansen – The Journal of Immunology

Fighting Off Wound Pathogens in Horses with Honeybee Lactic Acid Bacteria – Tobias C. Olofsson – Current Microbiology

Plant, root, and soil microbiome

Local diversity of heathland Cercozoa explored by in-depth sequencing – Christoffer Bugge Harder – the ISME Journal

Press: Immense species richness of bacterial-eating microorganisms discovered in soil – Phys.org

Characterization of cadmium-resistant bacteria and their potential for reducing accumulation of cadmium in rice grains – Xiaoyan Lin – Science of The Total Environment
Editorial special issue: Soil, plants and endophytes – Stéphane Compant – Plant and Soil

Water and extremophile microbiome

Diverse Sulfur Metabolisms from Two Subterranean Sulfidic Spring Systems – Karen Rossmassler – FEMS Microbiology Letters

Metabolic potential of microbial mats and microbialites: autotrophic capabilities described by an in silico stoichiometric approach from shared genomic resources – Daniel Cerqueda-García – Journal of Bioinformatics and Computational Biology

Waste and pollution microbiology

Microbial contamination along the main open wastewater and storm water channel of Hanoi, Vietnam, and potential health risks for urban farmers – Samuel Fuhrimann – Science of The Total Environment

Isolation of Bdellovibrio bacteriovorus from a tropical wastewater treatment plant and predation of mixed species biofilms assembled by the native community members – Shugeng Feng – Environmental Microbiology

Microbial forensics

Microbial forensics: next‐generation sequencing as catalyst – Irene Kuiper – EMBO Reports

Bioinformatics and metagenomics

MEGAN Community Edition – Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data – Daniel H. Huson – PLOS Computational Biology

Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses – François Enault – The ISME Journal

More microbiology

Rates and mechanisms of bacterial mutagenesis from maximum-depth sequencing – Justin Jee – Nature

Press: Sequencing method precise enough to reveal mechanisms by which bacteria resist antibiotics – Phys.org

Darwinolide, a New Diterpene Scaffold That Inhibits Methicillin-Resistant Staphylococcus aureus Biofilm from the Antarctic Sponge Dendrilla membranosa – Jacqueline L. von Salm – Organic Letters

Press: Antibiotics from a Sponge. Could a new compound from Antarctic sea sponges be the key to breaching MRSA’s impregnable barricades? – Michael Lucibella – Antarctic Sun

Microbes in the news

MetaSUB Citizen Science Project:
With video of researchers swabbing away: Biologists Study What Kind Of Bacteria Is On New York City Subways – CBS Local
Qiagen, CosmosID Join International Urban Microbiome Project – Genome Web

New Life Found That Lives Off Electricity. Scientists have figured out how microbes can suck energy from rocks. Such life-forms might be more widespread than anyone anticipated – Emily Singer – Quanta Magazine

High-tech program on microbiome-based research launched in Qingdao – Hu Qing – China Daily

Explained: flesh eating bacteria in the Gulf of Mexico – Dylan Baddour – Houston Chronicle

Science, publishing, and career

Your Science Conference Should Have a Code of Conduct – Brett Favaro – Frontiers in Marine Science

Science in China – A special issue looks at the country’s astonishing scientific trajectory as it seeks to secure its spot among the leaders in innovation – Nature
China by the numbers. Research capacity has grown rapidly, and now quality is on the rise – Richard Van Noorden – Nature

Global Research Council: Commit to equity for women researchers – France A. Córdova – Nature

June 21, 2016

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An invertebrate gets its amino acids from microbial symbionts, microbiota and allograft rejection, high-altitude Andes lakes, and determining absolute microbiota abundances by spiking-in bacteria.

Jobs and events

Postdoctoral Researcher Microbial Ecology & Bioinformatics – NIOO-KNAW, WUR, Wageningen, The Netherlands

Report from the Microbiome R&D and Business Collaboration Forum, April 11–12, 2016, London, UK – Duc H. Le – EBioMedicine

General microbiome

Review: Diversity at low abundance: The phenomenon of the rare bacterial biosphere – M. Yu. Skopina – Microbiology

Workshop report: Culture-Independent Diagnostics for Health Security – Doggett Norman A.- Health Security

Viewpoint: Addressing Infectious Disease Challenges by Investigating Microbiomes – Emily P. Balskus – ACS Infectious Diseases

Human oral microbiome

Molecular analysis of fungal populations in patients with oral candidiasis using next-generation sequencing – Yumi Imabayashi – Scientific Reports

Human reproductive tract microbiome

Review: Chlamydia trachomatis Genital Tract Infections: When Host Immune Response and the Microbiome Collide – Noa Ziklo – Trends in Microbiology

Human gut microbiome

Review: Microbes, Immunity and Behaviour: Psychoneuroimmunology Meets the Microbiome – Timothy G Dinan – Neuropsychopharmacology

Review: Emerging roles for antigen presentation in establishing host–microbiome symbiosis – Nicholas J. Bessman – Immunological Reviews

Book Chapter: The Effect of H. pylori Infection on the Gastric Microbiota – Hyun Jin Jo – Helicobacter Pylori (Springer book)

Animal and in vitro experiments

The composition of the microbiota modulates allograft rejection – Yuk Man Lei – The Journal of Clinical Investigation

Press: Microbiota affect the rate of transplant acceptance and rejection – MedicalXpress

Maternal Metabolic Syndrome Programs Mitochondrial Dysfunction via Germline Changes across Three Generations – Jessica L. Saben – Cell Reports

Press, extrapolated conclusion: Obese Pregnant Women With Poor Diets May Worsen The Childhood Obesity Epidemic: Study – Samantha Olson – Medical Daily

Diet-dependent, microbiota-independent regulation of IL-10-producing lamina propria macrophages in the small intestine – Takanori Ochi – Scientific Reports

Characterization of Cimex lectularius (bedbug) defensin peptide and its antimicrobial activity against human skin microflora – Akanksha Kaushal – Biochemical and Biophysical Research Communications

Variability of arsenic bioaccessibility and metabolism in soils by human gut microbiota using different in vitro methods combined with SHIME – Naiyi Yin – Science of The Total Environment

Transient activation of mucosal effector immune responses by resident intestinal bacteria in normal hosts is regulated by interleukin-10 signalling – Cong Wu – Immunology

Mining of hemicellulose and lignin degrading genes from differentially enriched methane producing microbial community – Prabhakar D. Pandit – Bioresource Technology

Review: Strategies to modulate the intestinal microbiota of Tilapia (Oreochromis sp.) in aquaculture: a review – Alyssa M. Haygood – Reviews in Aquaculture

Animal microbiome

Seasonality and Locality Affect the Diversity of Anopheles gambiae and Anopheles coluzzii Midgut Microbiota from Ghana – Jewelna Akorli – PLOS ONE

A Nightmare for Males? A Maternally Transmitted Male-Killing Bacterium and Strong Female Bias in a Green Lacewing Population – Masayuki Hayashi – PLOS ONE
http://journals.plos.org/plosone/article?

Testosterone levels are positively correlated with cloacal bacterial diversity and the relative abundance of Chlamydiae in breeding male rufous-collared sparrows
– Camilo Escallón – Functional Ecology

The dominant detritus-feeding invertebrate in arctic peat soils derives its essential amino acids from gut symbionts – Thomas Larsen – Journal of Animal Ecology

Genomic characterization of symbiotic mycoplasmas from the stomach of deep-sea isopod Bathynomus sp – Yong Wang – Environmental Microbiology

Review: Is gastrointestinal microbiota relevant for endogenous mercury methylation in terrestrial animals? – R.C. Rodríguez Martín-Doimeadios – Environmental Research

Plant, root, and soil microbiome

Multi-targeted metagenetic analysis of the influence of climate and environmental parameters on soil microbial communities along an elevational gradient – Anders Lanzén – Scientific Reports

Integrated analysis of root microbiomes of soybean and wheat from agricultural fields – Nicolás Rascovan – Scientific Reports

Dark stains on rock surfaces in Driny Cave (Little Carpathian Mountains, Slovakia)
Rafał Ogórek – Extremophiles

Water and extremophile microbiome

Diversity of extremophilic bacteria in the sediment of high-altitude lakes located in the mountain desert of Ojos del Salado volcano, Dry-Andes – Júlia Margit Aszalós – Extremophiles

Microbial interactions lead to rapid micro-scale successions on model marine particles –
Manoshi S. Datta – Nature Communications

Bacteriophages in Arctic and Antarctic low-temperature systems – S. N. Filippova – Microbiology

Diversity of methanogenic archaea from the 2012 terrestrial hot spring (Valley of Geysers, Kamchatka) – A. Y. Merkel – Microbiology

Comparative analysis of prokaryotic diversity in solar salterns in eastern Anatolia (Turkey) – Seval Çınar – Extremophiles

Techniques

Adjusting microbiome profiles for differences in microbial load by spike-in bacteria – 
Frank Stämmler – Microbiome

Metagenomics and bioinformatics

Data Labours: How the Sequence Databases GenBank and EMBL-Bank Make Data – Tahani Nadima – Science as Culture

Principle, analysis, application and challenges of next-generation sequencing: a review – Khalid Raza – arXIv

Microbes in the news

Does a pipette work in space? with NASA Astronaut Dr Kate Rubins – Microbe Talk – Microbe Post

An Antarctic sponge offers new hope against deadly MRSA infection – Matt Windsor – UAB

Dental Microbes Not All in the Family. Kids often acquire cavity-causing bacteria from non-family members, researchers report at the American Society for Microbiology annual meeting – Tanya Lewis – The Scientist

Never-Before Human-Detected, Potentially Pathogenic Bacterium Found in Children With Acute Leukemia Human Microbiology Institute investigates potential role of previously unknown bacteria – PR Newswire

Geisinger’s Donna Wolk recognized for work in microbiology – Daily Item

Microbial mass extinctions were kicked off by human evolution – Andy Coghlan – New Scientist

Global Microbiome Initiative Explores Subways for Drug-Resistance Markers:
MetaSUB Consortium will collect DNA and RNA samples from high-traffic areas in subway systems, buses, and parks in 54 cities worldwide – GenEngNews

June 20, 2016

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The temperate tree phyllosphere, Qaanaaq Glacier, effect of human activities on Hong Kong coast microbes, and genome assembly from read clouds.

Events

Microbiome R&D and Business Collaboration Forum: USA, October 3-4, San Diego

Pregnancy and birth

Putative periodontopathic bacteria and herpesviruses in pregnant women: a case-control study – Haixia Lu – Scientific Reports

Human gut microbiome

Letter to Editor: Reduction of antibiotic resistance genes in intestinal microbiota of recurrent Clostridium difficile patients after fecal microbiota transplantation – Hanne Jouhten – Clinical Infectious Diseases Advance Access

Review: The Gut Microbiota and Inflammatory Bowel Diseases – Jun Miyoshi – Translational Research

Review: Links Between the Microbiome and Bone – C.J. Hernandez – Journal of Bone and Mineral Research

Animal models

Interactions between the colonic transcriptome, metabolome and microbiome in mouse models of obesity-induced intestinal cancer – Anna C. Pfalzer – Physiological Genomics

Plant, root, and soil microbiome

Host species identity, site and time drive temperate tree phyllosphere bacterial community structure – Isabelle Laforest-Lapointe – Microbiome

Nitrogen deposition and management practices increase soil microbial biomass carbon but decrease diversity in Moso bamboo plantations – Quan Li – Scientific Reports

A comparative analysis of microbiomes in natural and anthropogenically disturbed soils of northwestern Kazakhstan – E. V. Pershina – Eurasian Soil Science

A novel isolate and widespread abundance of the candidate alphaproteobacterial order (Ellin 329), in southern Appalachian peatlands – Austin B. Harbison – FEMS Microbiology Letters

Water and extremophile microbiome

Microbial community variation in cryoconite granules on Qaanaaq Glacier, NW Greenland – Jun Uetake – FEMS Microbiology Ecology

Mechanisms driving Antarctic microbial community responses to ocean acidification: a network modelling approach – Roshni C. Subramaniam – Polar Biology

Video article: Simultaneous DNA-RNA Extraction from Coastal Sediments and Quantification of 16S rRNA Genes and Transcripts by Real-time PCR – Enrico Tatti – Journal of Visualized Experiments

Waste and pollution microbiology

Microorganisms in heavy metal bioremediation: strategies for applying microbial-community engineering to remediate soils – Jennifer L. Wood – AIMS Bioengineering

Impacts of Human Activities on Distribution of Sulfate Reducing Prokaryotes and Antibiotic Resistance Genes in Marine Coastal Sediments of Hong Kong – Feng Guo – FEMS Microbiology Ecology

Shotgun metagenomic profiles have a high capacity to discriminate activated sludge according to wastewater type – Federico M. Ibarbalz – Applied and Environmental Microbiology

Characteristics of Sediment Bacterial Community in Response to Environmental Impacts in a Sewage Polluted River – Jialin Li – Journal of Coastal Research

Plants rather than mineral fertilization shape microbial community structure and functional potential in legacy contaminated soil – Jakub Ridl – Frontiers in Microbiology

Food microbiology

Viable bacterial population and persistence of foodborne pathogens on the pear carpoplane – Francois J. Duvenage – Journal of the Science of Food and Agriculture

Book: Acetic Acid Bacteria: Ecology and Physiology – Springer

Metagenomics and bioinformatics

Genome assembly from synthetic long read clouds – Volodymyr Kuleshov – Bioinformatics

Unsupervised Binning of Metagenomic Assembled Contigs Using Improved Fuzzy C-Means Method – Yun Liu – IEEE/ACM Transactions on Computational Biology and Bioinformatics

Bioreactor microbiology

Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion – Inka Vanwonterghem – Environmental Microbiology

Microbes in the news

From ASM Microbe 2016: Bacteria Can Persist on Gloves, Transfer to Surfaces – Neil Osterweil – Medscape

Ischemic stroke therapy – does the gut microbiota hold the key? – Sara Adães – PLOS Neuro Community

French microbiologist hopes CRISPR/Cas9 can be used medically, with Emmanuelle Charpentier – Focus Taiwan

Chipotle Bosses Accused Of Insider Trading During Bacteria Scandals – Scott Heins – Gothamist

Bik’s Not-Microbiology Picks

Why Did Scientists Release Dead Sea Turtles into Chesapeake Bay? – Erica Tennenhouse – The Science Explorer