Category Archives: Plant Root Soil microbiome

May 11, 2015

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General microbiome / Microbial ecology

Microbiomes raise privacy concerns: DNA from microbes living on the human body can be used to identify individuals – Ewen Callaway – Nature

Identifying personal microbiomes using metagenomic codes – Eric A. Franzosa – PNAS USA

Unraveling interactions in microbial communities – from co-cultures to microbiomes – Justin Tan – Journal of Microbiology

Antagonistic interactions are sufficient to explain self-assemblage of bacterial communities in a homogeneous environment: a computational modeling approach – Román Zapién-Campos – Frontiers in Microbiology

Human oral microbiome

Hospitalisation impacts on oral hygiene: an audit of oral hygiene in a metropolitan health service – Rachael Danckert – Scandinavian Journal of Caring Sciences

DGGE: Dynamic Shifts in the Oral Microbiome during Radiotherapy – Tine De Ryck – Clinical Research in Infectious Diseases

Effects of Source- versus Household Contamination of Tubewell Water on Child Diarrhea in Rural Bangladesh: A Randomized Controlled Trial – Ayse Ercumen – PLOS ONE

Human vaginal microbiome

Review: Biofilms: An Underappreciated Mechanism of Treatment Failure and Recurrence in Vaginal Infections – Christina A. Muzny – Clinical Infectious Diseases

Human gut microbiome

Editorial: The Gut Microbiota Strikes Again – Debra D. Poutsiaka – Clinical Infectious Diseases
Belongs to:
Acute Gastrointestinal Graft-vs-Host Disease Is Associated With Increased Enteric Bacterial Bloodstream Infection Density in Pediatric Allogeneic Hematopoietic Cell Transplant Recipients – Anya Levinson – Clinical Infectious Diseases

Review: Exploring the role of environmental enteropathy in malnutrition, infant development and oral vaccine response – Allissia A. Gilmartin , William A. Petri – Philosophical Transactions B

Review: Role of the gastrointestinal ecosystem in the development of type 1 diabetes – Joseph G Daft – Pediatric Diabetes

Plant and soil microbiome

Ectomycorrhizal fungal communities coinvading with Pinaceae host plants in Argentina: Gringos bajo el bosque – Jeremy Hayward – New Phytologist

Atmospheric N Deposition Alters Connectance, but not Functional Potential Among Saprotrophic Bacterial Communities – Zachary B. Freedman – Molecular Ecology

Rhizospheric changes of fungal and bacterial communities in relation to soil health of multi-generation apple orchards – F. Caputo – Biological Control

Permafrost microbial community traits and functional diversity indicate low activity at in situ thaw temperatures – Jessica G. Ernakovich – Soil Biology and Biochemistry

Switchgrass Biochar Effects on Plant Biomass and Microbial Dynamics in Two Soils from Different Regions – Charlene N. Kelly – Pedosphere

Water microbiome

Melting glacier impacts community structure of Bacteria, Archaea and Fungi in a Chilean Patagonia fjord – Marcelo H. Gutiérrez – Environmental Microbiology

Evaluation of water sampling methodologies for amplicon-based characterization of bacterial community structure – Christopher Staley – Journal of Microbiological Methods

Thesis: Bacterial Community Structure and Petroleum Hydrocarbon Degradation in the Baltic Sea – Anna Reunamo – University of Turku

Phages and viruses

Editorial: A CRISPR sense of self – Naomi Attar – Nature Reviews Microbiology

Bioinformatics and metagenomes

Nucleotide 9-mers Characterize the Type II Diabetic Gut Metagenome – Balazs Szalkai – ArXiv

CS-SCORE: Rapid identification and removal of human genome contaminants from metagenomic datasets – Mohammed Monzoorul Haque – Genomics

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters – Tilmann Weber – Nucleic Acids Research

Review: Alignment of Next-Generation Sequencing Reads – Knut Reinert – Annual Review of Genomics and Human Genetics

Metabolic dependencies drive species co-occurrence in diverse microbial communities – Aleksej Zelezniak – PNAS USA

Functional Foods

Probiotics can improve the clinical outcomes of hepatic encephalopathy: An update meta-analysis – Li-Na Zhao – Clinics and Research in Hepatology and Gastroenterology

Microbes in the news

How Germs Might Shape the Future of Architecture – Vicky Gan – City Lab

FDA digging into hand cleaners in hospitals – Jonathan Eisen – MicroBEnet

Essay: The Fight Against the Fight Against the Fight Against Bacteria – Daniel Yin – University of Oxford

Freshman Biology, Creativity, and Extra Credit… – Mark O. Martin – MicrobesRule

You Asked: Should I Use Antibacterial Soap? – Markham Heid – Time
About Tim Spector book “The Diet Myth”: Fast food kills gut bacteria that can keep you slim, study finds – Daniel Costa-Roberts

About the Sonnenburgs’ book “The Good Gut”: To be healthy, take care of your microbiome – Kate Allen – The Start

Should you put yogurt on your face? The benefits of probiotics go beyond improved digestion – Victoria Dawson Hoff – Elle Beauty

My Archaea, My Brother – Genome Web

“This Idle No More movement is like bacteria, it has grown a life of its own all across this nation,” – RCMP apologizes for Idle No More ‘bacteria’ comparison – APTN

Calls for global database on bacteria contained in food – Channel News Asia

Antibiotic-Resistant Typhoid Spreading Abroad – Dennis Thompson – WebMD

“You may not want to eat lunch with Misty Bever”: Intestinal fortitude: There’s an illness lurking that causes chronic, debilitating pain. The cure, however, comes from deep within.– Dan England – The Tribune

Bik’s Picks

Mars sunsets are beautiful — and blue, NASA photo shows – Matthew T. Hall – UT San Diego

What do these new alien photos reveal about Roswell UFO crash – Sam Catherman – State Column

Google says its self-driving cars have had 11 crashes – Chris Woodyard – USA Today

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May 8, 2015

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Human oral microbiome

Published in Gut but also oral: Human buccal epithelium acquires microbial hyporesponsiveness at birth, a role for secretory leukocyte protease inhibitor – Celia L Menckeberg – Gut

 

Human gut microbiome

Cholesterol gallstones and bile host diverse bacterial communities with potential to promote the formation of gallstones – Yuhong Peng – Microbial Pathogenesis

Development of an enhanced human gastrointestinal epithelial culture system to facilitate patient-based assays – Kelli L VanDussen – Gut

Gut microbiome and innate immune response patterns in IgE-associated eczema – Christina E West – Clinical & Experimental Allergy

Review: The gut microbiome in autoimmunity: Sex matters – Andres Gomez – Clinical Immunology

Review: Chemical communication in the gut: Effects of microbiota-generated metabolites on gastrointestinal bacterial pathogens – Stefanie L. Vogt – Anaerobe

Special issue of Clinical Liver Disease about “Liver and the Microbiome”. Reviews include:

Human genital microbiome

The vaginal and gastrointestinal microbiomes in gynecologic cancers: A review of applications in etiology, symptoms and treatment – Dana Chase – Gynecologic Oncology

Animal models of microbiome

Effects of dietary inulin on bacterial growth, short-chain fatty acid production and hepatic lipid metabolism in gnotobiotic mice – Karolin Weitkunat – The Journal of Nutritional Biochemistry

Plant root and soil microbiome

Covariation of soil bacteria functional diversity and vegetation diversity along an altitudinal climatic gradient in the Western Carpathians – Beata Klimek – Pedobiologia

Changes in fungal communities along a boreal forest soil fertility gradient – Erica Sterkenburg – New Phytologist

Water microbiome

Editorial without citation to the original Nature paper: Deep-ocean microbe is closest living relative of complex cells – Mitch Leslie – Science

Parasites

Not all parasites are protective – Derek M. McKay – Parasite Immunology

Helminths and the microbiota: parts of the hygiene hypothesis – P. Loke – Parasite Immunology

Bioinformatics

Testing in Microbiome-Profiling Studies with MiRKAT, the Microbiome Regression-Based Kernel Association Test – Ni Zhao – AJHG

Sparse and Compositionally Robust Inference of Microbial Ecological Networks – Zachary D. Kurtz – PLOS Computational Biology

Demystifying computer science for molecular ecologists – Mahdi Belcaid and Robert J. Toonen

Techniques

TM7 detection in human microbiome: Are PCR primers and FISH probes specific enough? – Maria V. Sizova – Journal of Microbiological Methods

Microbes in the news

Man’s Best Germs: Does Your Dog Influence Your Health? – Heather Buschman – UC San Diego

Video: Can Poop Cure an Infection? – Anna Rothschild – Gross science

Science, publishing, and career

The Hitchhiker’s Guide to a Neuroscience Career – Marian Joels – Neuron

Recommendation letters: Give women an even chance – Marcia McNutt – Science

Bik’s Picks
Spiders Sprayed with Graphene Spin Super-Strong Silk – Renee Morad – Discovery

Mmm, I always have mixed feelings about papers using these types of animal models. “We made this mouse blind. And then we cured it!” Light in sight: A step towards a potential therapy for acquired blindness – Science Daily

Grocery lists may help shoppers stick to healthier diet, lower weight – Reuters

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May 7, 2015

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Events

Human Gut Microbiome and Diseases Congress – 25-26 June 2015, Milano, Italy

Pregnancy and birth microbiome

The Canadian Healthy Infant Longitudinal Development (CHILD) birth cohort study: assessment of environmental exposures – Tim K Takaro – Journal of Exposure Science and Environmental Epidemiology

The Impact of Infancy Antibiotic Intake on Childhood Obesity; Review of Studies – Mohammad Reza Vafa – Advances in Obesity, Weight Management & Control

Human respiratory microbiome

The Host Response to the Lung Microbiome in Chronic Obstructive Pulmonary Disease
Marc A Sze – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

Approaches to studying and manipulating the enteric microbiome to improve autism symptoms – Richard E. Frye – Microbial Ecology in Health and Disease

Plant root and soil microbiome

Heading to the Origins – Rice Microbiome as Functional Extension of the Host – Pablo R. Hardoim – Journal of Rice Research

Inoculation of Phaseolus vulgaris with the nodule-endophyte Agrobacterium sp. 10C2 affects richness and structure of rhizosphere bacterial communities and enhances nodulation and growth – Saif-Allah Chihaoui – submitted paper

Biochar in Co-Contaminated Soil Manipulates Arsenic Solubility and Microbiological Community Structure, and Promotes Organochlorine Degradation – Samuel J. Gregory – PLOS ONE

Microbial quality of soil from the Pampa biome in response to different grazing pressures – Rafael S. Vargas – Genetics and Molecular Biology

Built environment microbiome

Dysbiotic drift: mental health, environmental grey space, and microbiota – Alan C Logan – Journal of Physiological Anthropology

Extremophiles

Sub-Ice Microalgal and Bacterial Communities in Freshwater Lake Baikal, Russia – Maria V. Bashenkhaeva – Microbial Ecology

Phages and viruses

Protist predation can select for bacteria with lowered susceptibility to infection by lytic phages – Anni-Maria Örmälä-Odegrip – BMC Evolutionary Biology

Microbial Ecology

Evolutionary ecology of microorganisms: from the tamed to the wild – Jay T Lennon – PeerJ

Metagenomics and bioinformatics

MyPro: A seamless pipeline for automated prokaryotic genome assembly and annotation – Yu-Chieh Liao – Journal of Microbiological Methods

PrePrint: Infer Metagenomic Abundance and Reveal Homologous Genomes Based on the Structure of Taxonomy Tree – Yu-Qing Qiu – IEEE/ACM Transactions on Computational Biology and Bioinformatics

Metabolomics

Effects of Uremic Toxins from the Gut Microbiota on Bone: A Brief Look at Chronic Kidney Disease – Ana Paula Black – Therapeutic Apheresis and Dialysis

Microbes in the news

Ulcer-causing bacteria induces stomach stem cell growth in mice, researchers find – Stanford Medicine

Newly named bacteria help honey bee larvae thrive – Kim Kaplan – Phys.org

The smell of death: Scientist reveals how 400 compounds mix to create heady mixture of scents as bacteria rips apart rotting flesh – Moheb Costandi – Daily Mail

Eat your vegetables, feed your microbiome – David Charbonneau – EyeViewKamloops

Microbiome Portrait Experiment for High School Students – Tufts

Bacteria redefine reinforced concrete – RSC Advances Blog

Possible role of gut bacteria in autism – Science Daily

Environmental exposures study tracks more than 3,200 Canadian babies – Simon Fraser University

Final Report Summary – TORNADO (Molecular Targets Open for Regulation by the gut flora – New Avenues for improved Diet to Optimize European health) – CORDIS Europa

Measles Vaccination Saves You From More Than Measles – Maggie Fox – NBC News

Microbes and money

‘Gut microbiome’ startup moving to science accelerator, seeks study volunteers: Prince William Science Accelerator – ISOThrive – Inside Nova

UBiome Seeks Academic Partnerships with the Launch of the uBiome Academic Consortium – WDRB

Science, publishing, and career

Science forum: RIPOSTE: a framework for improving the design and analysis of laboratory-based research – Nicholas G D Masca – eLife

Bik’s Picks

Listen To These Eerie ‘X-Files’ Sounds Recorded At The Edge Of Space – Macrina Cooper-White – Huffington Post

Finding That Babies Born at 22 Weeks Can Survive Could Change Abortion Debate – Lucy Westcott – Newsweek

Samantha Cristoforetti: 5 Memorable Moments From the Italian Astronaut’s Time in Space – Alyssa Newcomb – ABC News
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May 6, 2015

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Human oral microbiome

The Impact of Various Time Intervals on the Supragingival Plaque Dynamic Core Microbiome – Wen-xin Jiang – PLOS ONE

Dental and Microbiological Risk Factors for Hospital-Acquired Pneumonia in Non-Ventilated Older Patients – Victoria C. Ewan – PLOS ONE

Human gut microbiome

Unraveling the Influence of Gut Microbes on the Mind – M.J. Friedrich – JAMA

Gut Microbiota and Colorectal Cancer – Yu Y.-N. – Gastrointestinal Tumors

Gut Microbiota and Hepatocellular Carcinoma – Tao X – Gastrointestinal Tumors

Editorial: Gut microbiota and inflammation in chronic kidney disease patients – Denise Mafra – Clinical Kidney Journal

Animal models

Chronic Trichuris muris Infection in C57BL/6 Mice Causes Significant Changes in Host Microbiota and Metabolome: Effects Reversed by Pathogen Clearance – Ashley Houlden – PLOS ONE

Animal microbiome

Bacterial Diversity Associated with Cinachyra cavernosa and Haliclona pigmentifera, Cohabiting Sponges in the Coral Reef Ecosystem of Gulf of Mannar, Southeast Coast of India – C. Jasmin – PLOS ONE

Plant microbiome

Shifts in Symbiotic Endophyte Communities of a Foundational Salt Marsh Grass following Oil Exposure from the Deepwater Horizon Oil Spill – Demetra Kandalepas – PLOS ONE

Endophytic and Epiphytic Microbes as “Sources” of Bioactive Agents – David J. Newman and Gordon M. Cragg – Frontiers in Chemistry

Review: Pivotal roles of phyllosphere microorganisms at the interface between plant functioning and atmospheric trace gas dynamics – Françoise Bringel – Frontiers in Microbiology

Soil and sediment microbiome

Metabolic Activity and Functional Diversity Changes in Sediment Prokaryotic Communities Organically Enriched with Mussel Biodeposits – Thomas Pollet – PLOS ONE

Impacts of dimethyl phthalate on the bacterial community and functions in black soils – Zhi-Gang Wang – Frontiers in Microbiology

Aquatic / Extremophile microbiome

Benthic microbial communities of coastal terrestrial and ice shelf Antarctic meltwater ponds – Stephen D. Archer – Frontiers in Microbiology

Microbial food web components, bulk metabolism, and single-cell physiology of piconeuston in surface microlayers of high-altitude lakes – Hugo Sarmento – Frontiers in Microbiology

Microbial communities of the Lemon Creek Glacier show subtle structural variation yet stable phylogenetic composition over space and time – Cody S. Sheik – Frontiers in Microbiology

Bioreactor microbiome

Bacterial Pathogens and Community Composition in Advanced Sewage Treatment Systems Revealed by Metagenomics Analysis Based on High-Throughput Sequencing – Xin Lu – PLOS ONE

Metagenomics, metabolomics, and bioinformatics

Expression of heterologous sigma factors enables functional screening of metagenomic and heterologous genomic libraries – Stefan M. Gaida – Nature Communications

TreeSeq, a Fast and Intuitive Tool for Analysis of Whole Genome and Metagenomic Sequence Data – Bastiaan Wintermans – PLOS ONE

Covariation is a poor measure of molecular coevolution – David Talavera – Molecular Biology and Evolution

Review: Data-driven integration of genome-scale regulatory and metabolic network models – Saheed Imam – Frontiers in Microbiology

Archaea

Complex archaea that bridge the gap between prokaryotes and eukaryotes – Anja Spang – Nature

More microbiology papers

The passenger-associated transport repeat promotes virulence factor secretion efficiency and delineates a distinct autotransporter subtype – Matthew Thomas Doyle – Molecular Microbiology

Microbes and art

Intestine-inspired 3D printed fashion will hold glowing bacteria – Chris Baraniuk – New Scientist

Microbes in the news

Who are the bioaerosols in your neighborhood? Find out by entering a chamber … – Jonathan Eisen – MicroBEnet

Exploring bacterial genes: New technique helps uncover useful functions in microbial genomes – University of Delaware

Newly discovered ‘missing link’ shows how humans could evolve from single-celled organisms: A new microbe found a mile and a half below the Atlantic Ocean  – Rachel Feltman – The Washington Post

Treating a bacterial infection with bacteria lowers chances of recurrence – Meryl Lin McKean – Fox4kc

Toxic Gut Bacteria: New Treatment Could Prevent Repeat Infections – Rachael Rettner – Live Science

Researchers produce jet fuel compounds from fungus – Science Daily

Molecular Homing Beacon Redirects Human Antibodies to Fight Pathogenic Bacteria – Heather Buschman – UC San Diego

Bacteria research opens way for new antibiotics: common building block, called the Passenger-associated Transport Repeat (PATR) present in many pathogens – University of Adelaide

Science, publishing, and career

‘Living figures’ make their debut: Published chart integrates data from outside scientists – Dalmeet Singh Chawla – Nature

The trouble with reference rot: Computer scientists are trying to shore up broken links in the scholarly literature – Jeffrey M. Perkel – Nature

The retirement debate: Stay at the bench, or make way for the next generation: When and how to exit research has become a charged issue in science – Megan Scudellari – Nature

Pint-sized DNA sequencer impresses first users: Portable device offers on-the-spot data to fight disease, catalogue species and more – Erika Check Hayden – Nature

Bik’s Picks

Recovering Sea Lions at Marine Center Deliberately Injured By Chlorine, Police Say – Avianne Tan – ABC News

People with Depression and Bipolar Disorder Feel Sadness Differently – Tanya Lewis – Live Science

Feasting on fruits may leave you craving for more – Silvia Fernandez – Pierce Pioneer News

Trouble Falling Asleep? Doctor Says This Trick Will Put You to Sleep in One Minute – Zachary Stieber – The Epoch Times
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May 5, 2015, part 2

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There was so much literature today (more than 600 papers!) that I am doing a second digest today.

Human reproductive tract microbiome

Investigation and Characterization of the Microbiome of the Upper Female Reproductive Tract [10] – Shana M. Miles – Obstetrics & Gynecology

Animal and other models

Akkermansia muciniphila Adheres to Enterocytes and Strengthens the Integrity of the Epithelial Cell Layer – Justus Reunanen – Applied and Environmental Microbiology

Animal microbiome

Effect of Diet on the Rumen Microbial Community Composition of Growing Cattle and the Role It Plays in Methane Emissions – Allison L. Knoell – Digital Commons University of Nebraska – Lincoln

Amphibian Symbiotic Bacteria Do Not Show a Universal Ability To Inhibit Growth of the Global Panzootic Lineage of Batrachochytrium dendrobatidis – Rachael E. Antwis – Applied and Environmental Microbiology

Reptiles as Reservoirs of Bacterial Infections: Real Threat or Methodological Bias? – Giulia Zancolli – Microbial Ecology

Plant root, soil and sediment microbiome

Effects of cultivation ages and modes on microbial diversity in the rhizosphere soil of Panax ginseng – Chunping Xiao – Journal of Ginseng Research

Soil-foraging animals alter the composition and co-occurrence of microbial communities in a desert shrubland – David J Eldridge – The ISME Journal

The bacterial community inhabiting temperate deciduous forests is vertically stratified and undergoes seasonal dynamics – Rubén López-Mondéjar – Soil Biology and Biochemistry

Diversity of active microbial communities subjected to long-term exposure to chemical contaminants along a 40-year-old sediment core – Assia Kaci – Environmental Science and Pollution Research

Soil moisture and land use are major determinants of soil microbial community composition and biomass at a regional scale in northeastern China – L. Ma – Biogeosciences

Bacterial Community Diversity in Soil Under two Tillage Practices as Determined by Pyrosequencing – Aditi Sengupta – Microbial Ecology

Soil Microorganisms Contribute to Plant Nutrition and Root Health – Mark S. Coyne and Robert Mikkelsen – Better Crops

Changes in northern Gulf of Mexico sediment bacterial and archaeal communities exposed to hypoxia – R. Devereux – Geobiology

Effect of Nitrogen Management on Soil Microbial Community and Enzymatic Activities in Jatropha curcas L. Plantation – Doongar Ram Chaudhary – CLEAN – Soil, Air, Water

Response of maize and soil microorganisms to decomposing poplar root residues after shallow or homogenous mixing into soil – Hikal Gad – Journal of Plant Nutrition and Soil Science

Water microbiome

Metagenome Sequencing of a Coastal Marine Microbial Community from Monterey Bay, California – Ryan S. Mueller – Genome Announcements

Enrichment experiment changes microbial interactions in an ultra-oligotrophic environment – Gabriel Y. Ponce-Soto – Frontiers in Microbiology

Review: Marine-derived fungi: diversity of enzymes and biotechnological applications
Rafaella C. Bonugli-Santos – Frontiers in Microbiology

Review, but contains mostly plagiarized text: The Importance of Marine Genomics to Life – Popoola Raimot Titilade – Journal of Ocean Research

Extremophiles

Spatial microbial community structure and biodiversity analysis in “extreme” hypersaline soils of a semiarid Mediterranean area – Loredana Canfora – Applied Soil Ecology

Ecoenzymatic stoichiometry at the extremes: How microbes cope in an ultra-oligotrophic desert soil – Yunuen Tapia-Torres – Soil Biology and Biochemistry

Microbial and Enzyme Activities of Saline and Sodic Soils – Kripal Singh – Land Degradation & Development

Identification of Anthraquinone-Degrading Bacteria in Soil Contaminated with Polycyclic Aromatic Hydrocarbons – Elyse A. Rodgers-Vieira – Applied and Environmental Microbiology

Carbon Source Preference in Chemosynthetic Hot Spring Communities – Matthew R. Urschel – Applied and Environmental Microbiology

Isolating the effects of storm events on arctic aquatic bacteria: temperature, nutrients, and community composition as controls on bacterial productivity – Heather E. Adams – Frontiers in Microbiology

Bioreactor microbiology

Analysis of microbial communities in the oil reservoir subjected to CO2-flooding by using functional genes as molecular biomarkers for microbial CO2 sequestration – Jin-Feng Liu – Frontiers in Microbiology

Viruses

Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions – Cheryl-Emiliane T. Chow – Frontiers in Microbiology

More microbiology

Global trends in antimicrobial use in food animals – Thomas P. Van Boeckel – PNAS USA

Review: Sugar coating: bacterial protein glycosylation and host–microbe interactions – Felicia Y.Y. Tan – Trends in Biochemical Sciences

Assay for estimating total bacterial load: relative qPCR normalization of bacterial load with associated clinical implications – Ivan Brukner – Diagnostic Microbiology and Infectious Disease

Review: A review on computational systems biology of pathogen–host interactions – Saliha Durmuş – Frontiers in Microbiology

Metagenomics and bioinformatics

Contact genomics: Scaffolding and phasing (meta)genomes using chromosome 3D physical signatures – Jean-Francois Flot – FEBS Letters

Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations – Hong Xue – mBio

Whole genome sequencing of extended-spectrum β-lactamase producing Klebsiella pneumoniae isolated from a patient in Lebanon – Sima Tokajian – Frontiers in Cellular and Infection Microbiology

A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data – Stefan Spring – Frontiers in Microbiology

Review: Strategies and approaches in plasmidome studies – uncovering plasmid diversity disregarding of linear elements? – Julian R. Dib – Frontiers in Microbiology

Microbes in the news

Your Beard Is Covered in Bacteria: So is everything else. Don’t fall for the latest viral freak-out – David Coil – Slate

Longread: Gut Feelings – The Mysteries of the Microbiome – Jo Chandler – The Monthly

Bik’s Picks

Dolphins Living in Closer Quarters Are Friendlier – Lori Cuthbert – Discovery

Space might make astronauts dumber, study shows – Craig Hlavaty – Chron.com

We could use some in California – pipeline, please! Where does all the water go? Watch Oregon’s mysterious Lost Lake disappear down a lava tube – Aileen Donnelly – National Post
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May 5, 2015

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General human microbiome

Review: The Human Microbiota: The Rise of an “Empire” – Gidon Berger – Rambam Maimonides Medical Journal

Human gut microbiome

Human colon-derived soluble factors modulate gut microbiota composition – Arancha Hevia – Frontiers in Oncology

Dysbiosis of Intestinal Microbiota Associated With Inflammation Involved in the Progression of Acute Pancreatitis – Tan, Chaochao – Pancreas

Review: Does the Gut Microbiota Contribute to Obesity? Going beyond the Gut Feeling – Marisol Aguirre and Koen Venema – Microorganisms

Review: Alcohol Effects on the Composition of Intestinal Microbiota – Phillip A. Engen – The Gastrointestinal Microbiome – NIH

Human respiratory microbiome

Prevalence of oropharyngeal antibiotic-resistant flora among residents of aged care facilities: a pilot study – Christopher D. Etherton-Beer – Respirology

Animal models of microbiomes

Modulatory effects of a cranberry extract co-supplementation with Bacillus subtilis CU1 probiotic on phenolic compounds bioavailability and gut microbiota composition in high-fat diet-fed mice – Stéphanie Dudonné – PharmaNutrition

Animal microbiome

Characterization of the cellulolytic bacteria communities along the gastrointestinal tract of Chinese Mongolian sheep by using PCR-DGGE and real-time PCR analysis – Yan Zeng – World Journal of Microbiology and Biotechnology

Soil microbiome

Soil microbial community structure is unaltered by plant invasion, vegetation clipping, and nitrogen fertilization in experimental semi-arid grasslands – Chelsea J. Carey – Frontiers in Microbiology

Water microbiome

A metagenome for lacustrine Cladophora (Cladophorales) reveals remarkable diversity of eukaryotic epibionts and genes relevant to materials cycling – Linda E. Graham – Journal of Phycology

Bacterial and archaeal biogeography of the deep chlorophyll maximum in the South Pacific Gyre – Emily A. Walsh – Aquatic Microbial Ecology

Extremophiles

The influence of surface soil physicochemistry on the edaphic bacterial communities in contrasting terrain types of the Central Namib Desert – S. Gombeer – Geobiology

Microbial diversity and metabolic networks in acid mine drainage habitats – Celia Mendez-Garcia – Frontiers in Microbiology

Metabolomics

Structuring Microbial Metabolic Responses to Multiplexed Stimuli via Self-Organizing Metabolomics Maps – Cody R. Goodwin – Chemistry & Biology

Techniques

Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data – Jake Jervis-Bardy – Microbiome

More microbes

Antibacterial activity of silver-killed bacteria: the “zombies” effect – Racheli Ben-Knaz Wakshlak

Review: The dormant blood microbiome in chronic, inflammatory diseases – Marnie Potgieter – FEMS Microbiology Reviews

Microbes and art

Faecal transplants and bio-art – Eden Project’s latest exhibition Invisible You explores the science of microbes – Nicola Davis – The Guardian

Microbiology printable labels or buffet cards blue and black – LoveBacteriaArt – Etsy

Microbes in the news

1h Video: Seth Bordenstein: The microbiome and Darwin’s Mystery of Mysteries – University of Michigan Early Career Scientists Symposium

Cervicovaginal microbiome holds promise in preventing preterm birth – interview with Dr. Michal Elovitz at the annual meeting of the American Congress of Obstetricians and Gynecologists – Mary Ellen Schneider #ACOG15

Episode 6 of The Microbiome Podcast: The microbiome, autism, and serotonin production with Dr. Elaine Hsiao – MicrobiomeInstitute

Some beards as dirty as toilets: Microbiologist tests beards for germs – Royale Da – KOAT

(See more beard microbiome articles from these past days in The Beard Microbiome)

“You’re covered in poo bacteria.” No, your beard isn’t full of poop (probably) – Rachel Feltman – The Washington Post

HuMiX – Emulating human microbiome on a chip – Bactavatchalou Sivakumar

Nanoparticles in consumer products can significantly alter normal gut microbiome – Phys.org

Never a dull day for microbiologist – Kathryn Bernard up for Women of Distinction prize – Winnipeg Free Press

Agricultural microbiology draws Chinese researchers to Argentina – Xinhua – Want China Times

Expert’s Corner: Physician-scientist on why he recommends probiotics – University of Massachusetts

Gut Wars: One Man’s Adventure With Antibiotics and Ulcerative Colitis – Alexandra Carmichael – uBiome blog

Show Me Your Moves: Updated classics and new techniques help microbiologists get up close and quantitative – Marissa Fessenden – The Scientist

‘Zombie’ Bacteria May Help Heal Wounds – Discovery

Ocean currents disturb methane-eating bacteria – Phys.org

Bacteria could prove key in the fight against cholesterol – Paul Healy – Independent

Free book (for a limited time): The Squid, the Vibrio & the Moon – Small Friends Books

Science, publishing, and career

DNA editing takes a serious step forward — for better or worse – Eryn Brown – LA Times

Bik’s Picks

Llamas as Lab Rats: From diagnostics to vaccines, llama antibodies point to new directions in HIV research – Jenny Rood – The Scientist

Big whales have stretchy nerves to help them gulp – Jonathan Webb – BBC

Is sleepwalking genetic? Study suggests it runs in the family – ZME Science

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May 4, 2015

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Grant opportunities

Newborn and Infant Gut Health – Application deadline : May 13, 2015 – Bill & Melinda Gates Foundation

Events

Free Webinar: The Human Microbiome: Beyond the Gut – May 5, 2:30 pm ET – The Scientist

General microbiome

Review: Sequencing and beyond: integrating molecular ‘omics’ for microbial community profiling – Eric A. Franzosa – Nature Reviews Microbiology

Reproductive Parasitism: Maternally Inherited Symbionts in a Biparental World
Gregory D.D. Hurst and Crystal L. Frost – Cold Spring Harbor Perspectives in Biology

Human oral microbiome

Editorial: Defining functional signatures of dysbiosis in periodontitis progression
Gary P Wang – Genome Medicine
belongs to:
Functional signatures of oral dysbiosis during periodontitis progression revealed by microbial metatranscriptome analysis – Susan Yost – Genome Medicine

Human gut microbiome

Intestinal dysbiosis in children with short bowel syndrome is associated with impaired outcome – Helene Engstrand Lilja – Microbiome

Intestinal Microbiota Signatures Associated With Histological Liver Steatosis in Pediatric-Onset Intestinal Failure – Katri Korpela – Journal of Parenteral & Enteral Nutrition

Differences of the Fecal Microflora With Clostridium difficile Therapies – Thomas J. Louie – Clinical Infectious Diseases

Review: The human gut resistome – Willem van Schaik – Philosophical Transactions B

Animal models

The intestinal microbiota influences Campylobacter jejuni colonization and extra-intestinal dissemination in mice – Jason L. O’Loughlin – Applied and Environmental Microbiology

Animal microbiome

Fish: Selection in the host structures the microbiota associated with developing cod larvae (Gadus morhua) – Ingrid Bakke – Environental Microbiology

Plant and soil microbiome

Crustose coralline algal species host distinct bacterial assemblages on their surfaces – Jennifer M Sneed – The ISME Journal

Influence of plant communities and soil properties during natural vegetation restoration on arbuscular mycorrhizal fungal communities in a karst region – Yueming Liang – Ecological Engineering

Contrasting spatial patterns and ecological attributes of soil bacterial and archaeal taxa across a landscape – Florentin Constancias – Microbiology Open

Predictable communities of soil bacteria in relation to nutrient concentration and successional stage, in a laboratory culture experiment – Woojin Song – Environmental Microbiology

Water microbiome

Accumulation of Clinically Relevant Antibiotic Resistant Genes, Bacterial load and Metals from a Freshwater Lake Sediments in Central Europe – Naresh Devarajan – Environmental Science & Technology

Effects of Heavy Metal and Nutrients on Benthic Microbial Communities in Freshwater Sediment of Poyang Lake (China) – Cho Yu – Journal of Residuals Science & Technology

Review: Stream microbial diversity responds to environmental changes: Review and synthesis of existing research – Lydia Zeglin – Frontiers in Microbiology

Built environment microbiome

Indoor air bacterial communities in Hong Kong households assemble independently of occupant skin microbiomes – David Wilkins – Environmental Microbiology

Bioreactor microbiology

Bacterial community structure in treated sewage sludge with mesophilic and thermophilic anaerobic digestion – Hana Stiborova – Folia Microbiologica

Performance and microbial community dynamics in bioaugmented aerated filter reactor treating with coking wastewater – Shengnan Shi – Bioresource Technology

Phages and viruses

My life with Mu – Ariane Toussaint – Bacteriophage

Fungi

Fungal artificial chromosomes for mining of the fungal secondary metabolome – Jin Woo Bok – BMC Genomics

Review: The Human Mycobiome – Patrick C. Seed – Cold Spring Harbor Perspectives in Medicine

Antibiotic resistance

Antibiotic resistance genes in the environment: prioritizing risks – Johan Bengtsson-Palme & D. G. Joakim Larsson – Nature Reviews Microbiology

Review: The human gut resistome – Willem van Schaik – Philosophical Transactions B

Metagenomics

Under-detection of endospore-forming Firmicutes in metagenomic data – Sevasti Filippidou – Computational and Structural Biotechnology Journal

Microbes in the news

Each Vineyard Has a Unique Microbiome – University of Chicago – The Epoch Times

Viruses: You’ve heard the bad; here’s the good – American Society for Microbiology – Science Daily

Silver turns bacteria into deadly zombies – Emily Conover – Science Magazine

Rare plague outbreak in Colorado linked to pit bull, CDC says – CNN Wire

Science, publishing, and career

A time limit on postdoctoral contracts: The French experience – Elisabeth Pain – Science Careers

Follow the Funding – Bob Grant – The Scientist

Women Scientists Share Their Awful Stories Of Sexism In Publishing – Cat Ferguson – BuzzFeed Science

Science and art

The Microbiome Votes: I mixed my microbiome with the candidates and asked them to vote – Exploring the Invisible

Bik’s Picks

Horribly bleak study sees ‘empty landscape’ as large herbivores vanish at startling rate – Fred Barbash and Justin Wm. Moyer – Washington Post

Here’s How Coffee Cups in Space Could Help Save Lives on Earth – Helen Regan – Time

Why Hawaiians are protesting construction of the world’s second-largest telescope – Joseph Stromberg – Vox.com

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May 1, 2015

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A late post today – I was in meetings all day, and had no time to look at the 474 papers in my inbox until late. But let’s catch up!

General microbiome

Editorial: Bacteria make us human – Mohsin Ali – The Lancet

Microbiome of pregnancy and birth

Spotlight: Gut bacteria and necrotizing enterocolitis: cause or effect? – Christopher James Stewart – Trends in Microbiology

Editorial Harnessing the Early-Life Microbiota to Protect Children with Cystic Fibrosis – Leopoldo N. Segal and Martin J. Blaser – The Journal of Pediatrics

Human oral microbiome

Review: Dental Chatter: Bacterial Cross-Talk in the Biofilm of the Oral Cavity – Doron Steinberg – Israel Journal of Chemistry

The interaction between Streptococcus spp. and Veillonella tobetsuensis in the early stages of oral biofilm formation – Izumi Mashima – Journal of Bacteriology

Human gut microbiome

Antibiotic treatment of diarrhoea is associated with decreased time to the next diarrhoea episode among young children in Vellore, India – Elizabeth T Rogawski – International Journal of Epidemiology

High throughput sequencing reveals distinct microbial populations within the mucosal and luminal niches in healthy individuals – Yehuda Ringel – Gut Microbes

Gut Microbiota-Mediated Drug-Antibiotic Interactions – Dong-Hyun Kim – Drug Metabolism & Disposition

Humoral Immunity in the Gut Selectively Targets Phenotypically Virulent Attaching-and-Effacing Bacteria for Intraluminal Elimination – Nobuhiko Kamada – Cell Host & Microbe

MicroRNA-193a-3p Reduces Intestinal Inflammation in Response to Microbiota via Down-regulation of Colonic PepT1 – Xin Dai – The Journal of Biological Chemistry

Editorial: Some Reflections on the Microbiome and Obesity – Richard I. Shader – Clinical Therapeutics

Review: Regulation of body fat mass by the gut microbiota: Possible mediation by the brain – Erik Schéle – Peptides

Review: Role of Intestinal Microbiome in Lipid and Glucose Metabolism in Diabetes Mellitus – Casper van Olden – Clinical Therapeutics

Review: Gut microbiome, gut function, and probiotics: Implications for health – Neerja Hajela – Indian Journal of Gastroenterology

Review: Gut microbiota and the development of pediatric diseases – Chun-Yi Lu – Journal of Gastroenterology

Review: Regulation of body fat mass by the gut microbiota: Possible mediation by the brain – Erik Schéle – Peptides

Animal models

Transcriptional Modulation of Intestinal Innate Defense/Inflammation Genes by Preterm Infant Microbiota in a Humanized Gnotobiotic Mouse Model – Lei Lu – PLOS ONE

Pharmaceuticals and personal care products alter the holobiome and development of a medically important mosquito – Marcus J. Pennington – Environmental Pollution

Differences in the faecal microbiome of non-diarrhoeic clinically healthy dogs and cats associated with Giardia duodenalis infection: impact of hookworms and coccidia – Jan Šlapeta – International Journal for Parasitology

Ezetimibe and simvastatin modulate gut microbiota and expression of genes related to cholesterol metabolism – Emilie Catry – Life Sciences

Animal microbiome

Review: Tick microbiome: the force within – Sukanya Narasimhan – Trends in Parasitology

16S rRNA Amplicon Sequencing Demonstrates that Indoor-Reared Bumblebees (Bombus terrestris) Harbor a Core Subset of Bacteria Normally Associated with the Wild Host – Ivan Meeus – PLOS ONE

Plant microbiome

Plant and soil effects on bacterial communities associated with Miscanthus × giganteus rhizosphere and rhizomes – Dongfang Li – GCB Bioenergy

Soil microbiome

Distinct microbial populations are tightly linked to the profile of dissolved iron in the methanic sediments of the Helgoland mud area, North Sea – Oluwatobi Oni – Frontiers in Microbiology

Ecological effects of combined pollution associated with e-waste recycling on the composition and diversity of soil microbial communities – Jun Liu – Environmental Science & Technology

Water microbiome

Differences in organic matter and bacterioplankton between sections of the largest Arctic river: Mosaic or continuum? – Michail I. Gladyshev – Limnology and Oceanography

Extremophile microbiome

Insights from the Metagenome of an Acid Salt Lake: The Role of Biology in an Extreme Depositional Environment – Sarah Stewart Johnson – PLOS ONE

The microbial diversity, distribution, and ecology of permafrost in China: a review – Weigang Hu – Extremophiles

Bioreactor microbiology

Illumina MiSeq Sequencing Reveals Diverse Microbial Communities of Activated Sludge Systems Stimulated by Different Aromatics for Indigo Biosynthesis from Indole – Xuwang Zhang – PLOS ONE

Effects of garlic oil, nitrate, saponin and their combinations supplemented to different substrates on in vitro fermentation, ruminal methanogenesis, and abundance and diversity of microbial populations – A.K. Patra – Journal of Applied Microbiology

Food microbiology

Technological implications of reducing nitrate and nitrite levels in dry-fermented sausages: typical microbiota, residual nitrate and nitrite and volatile profile – Xavier F. Hospital – Food Control

Review: New Approaches for Bacteriotherapy: Prebiotics, New-Generation Probiotics, and Synbiotics – Rachna Patel – Clinical Infectious Diseases

Metagenomics and bioinformatics

DIDA: Distributed Indexing Dispatched Alignment – Hamid Mohamadi – PLOS ONE

Hybrid De Novo Genome Assembly Using MiSeq and SOLiD Short Read Data – Tsutomu Ikegami – PLOS ONE

Using populations of human and microbial genomes for organism detection in metagenomes – Sasha K Ames – Genome Research

Metabolomics

Systems biology of host–microbe metabolomics – Almut Heinken and Ines Thiele – Wiley Interdisciplinary Reviews: Systems Biology and Medicine

Microbes in the news

Don’t douche, and other lessons about the vaginal microbiome: Exploring the microscopic world between our legs – Susan Keown – Fred Hutch

Gut bacteria easy scapegoat to explain diseases, but connections hard to prove – Meredith Knight – Genetic Literacy Project

Find Out Just How Bacteria-Infested Houston Street Is During This Weekend of Walking Tours – Jaime Cone – Bedford and Bowery
and
The Artist & The Scientist: Microbial Maps – Festival Walk in New York City with Chris Mason – Jane’s Walk

Video: The Microbiome Project: Hospitals – Bacteria may actually be beneficial to hospitals – Argonne National Laboratory

Freshmen participate in huge research study on tiny viruses – University of Colorado Boulder

uBiome is launching an academic consortium to bring together researchers and industry teams with the hope of accelerating scientific understanding of the microbiome – uBiome

Each vineyard has a unique microbiome – Louise Lerner – Futurity

Science, publishing, and career

Ten Simple (Empirical) Rules for Writing Science – Cody J. Weinberger – PLOS Computational Biology

Honors Thesis: Students’ Knowledge and Opinions Concerning Genetically Modified Organisms: A Survey at University of Colorado Boulder – Connor Folkerth – University of Colorado at Boulder

Sexism in science: Peer editor tells female researchers their study needs a male author – Rachel Feltman – Washington Post

Bik’s Picks

How This Beetle Creates 500 Explosions Per Second In Its Bum – Ed Yong – National Geographic

Evidence that premature girls thrive more than premature boys – Science Daily

House GOP Wants to Eviscerate NASA Earth Sciences in New Budget – Phil Plait – Bad Astronomy – Slate
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April 30, 2015

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General human microbiome

Microbiome Analysis: Trends in Cancer Epidemiology, Challenges and Opportunities – Elizabeth F. Hebert – International Journal of Cancer Research and Molecular Mechanisms

Human respiratory microbiome

Still under embargo/technical difficulties: Swine Farming Is a Risk Factor for Infection With and High Prevalence of Carriage of Multidrug-Resistant Staphylococcus aureus – Shylo E. Wardyn – Clinical Infectious Diseases

The Culturome of the Human Nose Habitats Reveals Individual Bacterial Fingerprint Patterns – Ursula Kaspar – Environmental Microbiome

Human gut microbiome

Determining the Long-term Effect of Antibiotic Administration on the Human Normal Intestinal Microbiota Using Culture and Pyrosequencing Methods – Mamun-Ur Rashid – Clinical Infectious Diseases

Animal models of microbiome research

Modulation of growth performances, survival, digestive enzyme activities and intestinal microbiota in common carp (Cyprinus carpio) larvae using short chain fructooligosaccharide – Seyed Hossein Hoseinifar – Aquaculture Research

Plant microbiome

Simulation of the evolution of the legume-rhizobia symbiosis under the conditions of ecological instability – N. I. Vorobyov – Russian Journal of Genetics: Applied Research

Review: Plant-associated fungal communities in the light of meta’omics – Derek Peršoh – Fungal Diversity

Water microbiome

Editorial : Roles and mechanisms of parasitism in aquatic microbial communities – Télesphore Sime-Ngando – Frontiers in Microbiology

Picoplankton and nanoplankton variability in an Antarctic shallow coastal zone (Admiralty Bay) during the austral summer of 2010/2011 – Mariana Vanzan – Polar Biology

Relationships between Microbial Compositions and Hydrochemical Factors in Nitrate Contaminated Groundwater of Hun River Alluvial Proluvial Fan, China – A.X. Zhou – Journal of Agricultural Science and Technology

Extremophile microbiome

Picoplankton and nanoplankton variability in an Antarctic shallow coastal zone (Admiralty Bay) during the austral summer of 2010/2011 – Mariana Vanzan – Polar Biology

Microbiome of the built environment

Screening of bacteria and concrete compatible protection materials – Yusuf Çağatay Erşan – Construction and Building Materials

Bioreactor microbiology

Metal Oxide Nanoparticles Induce Minimal Phenotypic Changes in a Model Colon Gut Microbiota – Alicia A Taylor – Environmental Engineering Science

Metagenomics

Genome mining: Prediction of lipopeptides and polyketides from Bacillus and related Firmicutes – Gajender Aleti – Computational and Structural Biotechnology Journal

Book: VIRONOMICS: The Study of Viral Genomics in Human Cancer and Disease – Dirk P. Dittmer – Next Generation Sequencing in Cancer Research, Volume 2

Microbes in the news

An Atlas of the Bacteria and Fungi We Breathe Every Day – Neel V. Patel – Wired

Deadly Gut Bacteria Infections Peak in Spring – Rachael Rettner – Live Science

Study finds swine farming is a risk factor for drug-resistant staph infections – University of Iowa

Turning to Bacteria to Fight the Effects of Climate Change – Esther Ngumbi – Scientific American

Are We Less “Gutsy” Than we Used to Be? New Clues about the Evolution of the Human Microbiome from Research in Apes – Sharon Greenblum – Food Insight

How Fluid Flow Affects Bacteria – Science 2.0

Four Exceptional Contributions to the Advancement of Clinical Microbiology and Infectious Diseases Recognised at ECCMID – Select Science

Microbiome Hypome (articles that overstate microbiome importance)

The Cure for Brain Diseases Is in Your Gut – David Perlmutter – The Daily Beast

Microbes and money

Irish Microbiome Research Institute Partners With San-Francisco Based Second Genome On Bowel Disease Research – IBD News Today

Bik’s Picks

Low Sunlight Increases Pancreatic Cancer Risk; Why It’s Important To Get Enough Vitamin D – Justin Caba – Medical Daily

Bat Wings Harbor Special Sensory Cells – Stephanie Pappas – Live Science

Sea Lion Pup Waddling Around San Francisco’s Marina District Safely Captured – KPIX / KCBS

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April 29, 2015

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Events

Friday May 1: Del Mar College, Corpus Christi, TX Hosts a Day of Science with “How to Train Your Superorganism: Via the Microbiome” – Record Star

Pregnancy and birth microbiome

Colostrum of Healthy Slovenian Mothers: Microbiota Composition and Bacteriocin Gene Prevalence – Tanja Obermajer – PLOS ONE

Human respiratory microbiome

The Importance of Bacterial and Viral Infections Associated with Adult Asthma Exacerbations in Clinical Practice – Motoyasu Iikura – PLOS ONE

Human gut microbiome

Fat, fibre and cancer risk in African Americans and rural Africans – Stephen J. D. O’Keefe – Nature Communications

Characterization of Bacterial and Fungal Microbiome in Children with Hirschsprung Disease with and without a History of Enterocolitis: A Multicenter Study – Philip K. Frykman – PLOS ONE

Animal models of microbiome research

Editorial: Host–microbe interactions and the enteric nervous system: a new connection? – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Animal gut microbiome

Integrated Community Profiling Indicates Long-Term Temporal Stability of the Predominant Faecal Microbiota in Captive Cheetahs – Anne A. M. J. Becker – PLOS ONE

Plant microbiome

The Intracellular Scots Pine Shoot Symbiont Methylobacterium extorquens DSM13060 Aggregates around the Host Nucleus and Encodes Eukaryote-Like Proteins – Janne J. Koskimäki – mBio

Extremophile microbiome

Deep groundwater and potential subsurface habitats beneath an Antarctic dry valley –
J. A. Mikucki – Nature Communications

Microbial Diversity in a Permanently Cold and Alkaline Environment in Greenland – Mikkel A. Glaring – PLOS ONE

Bioinformatics

A Robust ANOVA Approach to Estimating a Phylogeny from Multiple Genes – Ximing Xu – Molecular Biology and Evolution

Maximum likelihood tree estimation using codon substitution models with multiple partitions – Stefan Zoller – Molecular Biology and Evolution

Techniques

Estimating Bacterial Diversity for Ecological Studies: Methods, Metrics, and Assumptions – Julia Birtel – PLOS ONE

From Benchtop to Desktop: Important Considerations when Designing Amplicon Sequencing Workflows – Dáithí C. Murray – PLOS ONE

Microbes in the news

Diet swap has dramatic effects on colon cancer risk for Americans and Africans – Science Daily

Mapping Genomes of Pine Bacteria Yields Unexpected Results – UC Merced

Salty aquifer, previously unknown microbial habitat discovered under Antarctica – Science Daily

Chemistry of seabed’s hot vents could explain emergence of life – Eureka Alert
and
Hydrothermal Vents Able to Create Simple Organic Molecules, Study Says – Sci-News

Understanding genetic diversity of bacteriophages – Phys.org

Deadly Gut Bacteria Peak in Spring (about C. difficile) – Rachael Rettner – LiveScience

30 min podcast about Antonie van Leeuwenhoek: The ‘first’ microbiologist and climate modelling – SocGenMicro – SoundCloud

Drug resistant bacteria common for nursing home residents with dementia – Science Daily

Rubella Has Been Eliminated From the Americas, Health Officials Say – Donald G. McNeil Jr. – New York Times

Science, publishing, and career

Symposium overview: Raising standards – International Symposium on Research Assessment and Evaluation in Shanghai, China – Michelle Grayson – Nature

Collateral damage: How one misconduct case brought a biology institute to its knees – The fall out from the STAP case is still being felt across Japan – David Cyranoski – Nature

Bik’s Picks

‘Obesity Signature’ Written in Pee – Rachael Rettner – LiveScience

Childhood bullying: Worse long-term mental health than maltreatment by adult – Science Daily

FDA Approves Double-Chin Eliminator Injection, Kybella – Sydney Lupkin – ABC News

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