August 24, 2016

Revisiting obesity and microbiome links, movies of Vibrio growing in biofilms, and decomposing chickens (yum)!

My apologies for not having had a lot of time to keep up with the literature. I’m now running all searches after work hours. This week we have friends over from Europe, and after 7 pm, my friends go before work ! Here is what I have so far, but it’s not as recent as I would like it to be. Hopefully I will have some time in the weekend to catch up.

Jobs and events

Postdoc Position in Bioinformatics, Metagenomics and the Human Microbiome – Jeroen Raes group, Leuven, Belgium

Human Microbiome Journal Club, Friday August 26: What is the most appropriate method for associating microbiome data with health and disease?

Human gut microbiome

Previously on bioRxiv, now publishedLooking for a Signal in the Noise: Revisiting Obesity and the Microbiome – Marc A. Sze, Patrick D. Schloss – mBio

No, your gut bacteria ISN’T making you fat: Scientists find ‘no difference’ between the microbes in obese and thin people’s stomachs – Daily Mail

Effect of Fecal Microbiota Transplantation on Recurrence in Multiply Recurrent Clostridium difficile Infection: A Randomized Trial – Colleen R. Kelly – Annals of Internal Medicine

Systematic Review: Adverse Events of Fecal Microbiota Transplantation – Sinan Wang – PLOS ONE

Animal microbiome

Nutrition mediates the expression of cultivar–farmer conflict in a fungus-growing ant – Jonathan Z. Shik – PNAS

Water microbiome

Distinct bacterial communities in surficial seafloor sediments following the 2010 Deepwater Horizon blowout – Tingting Yang – Frontiers in Microbiology

Microbiome of death

Effect of Substrate on Identification of Microbial Communities in Poultry Carcass Composting and Microorganisms Associated with Poultry Carcass Decomposition – Jie Wang – Journal of Agricultural and Food Chemistry

Bioinformatics and metagenomics

Using Dendritic Heat Maps to Simultaneously Display Genotype Divergence with Phenotype Divergence – Matthew Kellom – PLOS ONE

Microbial Ecology

Review: Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System – Adrian Ho – Frontiers in Microbiology

More microbiology

Vibrio cholerae biofilm growth program and architecture revealed by single-cell live imaging – Jing Yan – PNAS

Comparative genomics of biotechnologically important yeasts – Robert Riley – PNAS

Microbes in the news

Great Moments in Science: The microscopic high-tech wizardry of bacteria – Karl Kruszelnicki – ABC Australia

Bacteria are the probably cause of barnacles sticking to boats – battling biofouling with biology – Mary Beth Griggs – PopSci

Bacteria Hysteria

Your Bed Is A Hotbed Of Bacteria – Joy D’Souza – Huffington Post Canada
Bacteria in your Bed – “study” sponsored by AmeriSleep (huge CoI)

Science, publishing, and career

Including Diverse Voices in Science Stories –  Christina Selby – The Open Notebook


August 23, 2016

The bagpipe microbiome, antibiotic disturbance and diabetes risk, tubeworm metamorphosis, and immune tolerance to intestinal bacteria.


Assistant or Associate Professor in Immunology (Tenure Track), Division of Immunology of the Department of Microbiology & Immunobiology at Harvard Medical School, Boston, MA

Assistant/Associate/Professor of Microbiology and Infectious Disease, Lincoln Memorial University, Harrogate, TN

Respiratory microbiome

Bagpipe lung; a new type of interstitial lung disease? – Jenny King – Thorax

Human gut microbiome / bioinformatics

Bioinformatics support for the Tübiom community gut microbiome project – Sina Beier- PeerJ Preprint

Review: Eosinophils, probiotics, and the microbiome – Helene F. Rosenberg – Journal of Leukocyte Biology

Animal experiments

Antibiotic-mediated gut microbiome perturbation accelerates development of type 1 diabetes in mice – Alexandra E. Livanos – Nature Microbiology

Antibiotic Therapy During Infancy Increases Type 1 Diabetes Risk in Mice – Alison F. Takemura – The Scientist

Life Inside an Acorn: How Microclimate and Microbes Influence Nest Organization in Temnothorax Ants – Joseph Karlik – Ethology

Stepwise metamorphosis of the tubeworm Hydroides elegans is mediated by a bacterial inducer and MAPK signaling – Nicholas J. Shikuma – PNAS

Strange experimentGut microbiota can transfer fiber characteristics and lipid metabolic profiles of skeletal muscle from pigs to germ-free mice – Honglin Yan – Scientific Reports

pH drop impacts differentially skin and gut microbiota of the Amazonian fish tambaqui (Colossoma macropomum) – François-Étienne Sylvain – Scientific Reports

Immune tolerance to an intestine-adapted bacteria, Chryseobacterium sp., injected into the hemocoel of Protaetia brevitarsis seulensis – Jiae Lee – Scientific Reports

Alternative for antibiotics: Predatory bacteria are nontoxic to the rabbit ocular surface – Eric G. Romanowski – Scientific Reports

Animal microbiome

Multi-marker metabarcoding of coral skeletons reveals a rich microbiome and diverse evolutionary origins of endolithic algae – Vanessa Rossetto Marcelino – Scientific Reports

Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data – Ran Blekhman – Scientific Reports

Microbes in the news

Why We Sit on One Type of Stool but, Ideally, Not on Another – Julie Taylor – uBiome Blog
Gene-modified soil bacteria promise eco-friendly computing. The US Navy is creating nanowires from one of the most renewable resources on the planet – Jon Fingas – EnGadget

Inaugural ACS Infectious Diseases Young Investigator Awards Winners Announced: Audrey Odom, Timothy Wencewicz, Marcos Pires – ACS Axial

Ghent scientist uses bacteria to remove methane from air – Andy Furniere – Flanders Today

Microbes are More Social Than You Think, But Not Always in a Good Way – Jeffrey Marlow – Discover

Science, publishing, and career

More Faculty Diversity, Not on Tenure Track – Colleen Flaherty – InsideHigherEd


the Macroscope – a Big Picture view of Planet Earth… articles, essays, and photographs by Jonathan Foley

August 22, 2016

Human skin microbiome

Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis – Mercedes E. Gonzalez – Journal of the American Academy of Dermatology

Animal microbiome

Yeasts from the microbiota of bats: a focus on the identification and antimicrobial susceptibility of cryptic species of Candida – Raimunda S. N. Brilhante – Journal of Medical Microbiology

Plant, root, and soil microbiome

Intrinsic factors of Peltigera lichens influence the structure of the associated soil bacterial microbiota – Diego Leiva – FEMS Microbiology Ecology

Bacterial succession on decomposing leaf litter exhibits a specific occurrence pattern of cellulolytic taxa and potential decomposers of fungal mycelia – Vojtěch Tláskal – FEMS Microbiology Ecology

Local Environmental Factors Drive Divergent Grassland Soil Bacterial Communities in the Western Swiss Alps – Erika Yashiro – Applied and Environmental Microbiology

Watershed Assessment with Beach Microbial Source Tracking (MST) and Outcomes of Resulting Gull Management – Kelly D. Goodwin – Environmental Science & Technology

Microbial ecology

The importance of neutral and niche processes for bacterial community assembly differs between habitat generalists and specialists – Jingqiu Liao – FEMS Microbiology Ecology

Bioinformatics and metagenomics

A scalable assembly-free variable selection algorithm for biomarker discovery from metagenomes – Anestis Gkanogiannis – BMC Bioinformatics

Microbes in the news

The Strange Case of the Butterfly and the Male-Murdering Microbe – Ed Yong – The Atlantic

Bigelow Lab’s role in algae industry is growing – Kevin Miller – Press Herald

Science, publishing, and career

Why academics should make time for social media – Andy Miah – Times Higher Education

Introducing our special section on “The Integrity of Science” – The New Atlantis

August 20, 2016

Microbial eukaryotes along a pollution gradient, bacteria binding to ice, and testing the neutral theory.

Jobs and events

Assistant Professor in Genomics and Ecology of Microbial Pathogens in Food Systems Department of Food Science & Technology, University of California, Davis (via Jonathan Eisen –

Human gut microbiome

Gastrointestinal microbial populations can distinguish pediatric and adolescent Acute Lymphoblastic Leukemia (ALL) at the time of disease diagnosis – Seesandra V. Rajagopala – BMC Genomics

Review: Diet and Gut Microbial Function in Metabolic and Cardiovascular Disease Risk – Katie A. Meyer – Current Diabetes Reports

Review: Other Helicobacters and gastric microbiota – Chloë De Witte – Helicobacter

Plant, root, and soil microbiome

Spatial Distribution of Eukaryotic Communities Using High-Throughput Sequencing Along a Pollution Gradient in the Arsenic-Rich Creek Sediments of Carnoulès Mine, France – A. Volant – Microbial Ecology

Water and extremophile microbiome

Putting life on ice: bacteria that bind to frozen water – Maya Bar Dolev – Journal of the Royal Society Interface

Genetic signatures of ecological diversity along an urbanization gradient – Ryan P. Kelly – PeerJ Preprint

Surveys, simulation and single-cell assays relate function and phylogeny in a lake ecosystem – Sarah P. Preheim – Nature Microbiology

Book: Microbes from Hell: archaea and hyperthermophiles – Patrick Forterre

Drinking water and water treatment microbiology

Elucidation of Taste- and Odor-Producing Bacteria and Toxigenic Cyanobacteria in a Midwestern Drinking Water Supply Reservoir by Shotgun Metagenomic Analysis – Timothy G. Otten – Applied and Environmental Microbiology

Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics – Johan Bengtsson-Palme – Science of the Total Environment

Microbial Ecology

Testing the Neutral Theory of Biodiversity with Human Microbiome Datasets – Lianwei Li – Scientific Reports

Review: The Ecology and Evolution of Microbial Competition – Melanie Ghoul – Trends in Microbiology

Microbes in the news

We need to stop sanitizing everything and let bacteria back in our lives – Joselin Linder – New York Post

Bacteria may be key to environmentally friendly extraction of minerals – Angela Kean – S&P Capital IQ

Science, publishing, and career

What lurks in ageing academics’ unvisited personal archives? – Ron Iphofen – Times Higher Education
Army report says science director creating ‘environment of fear’ at USAMRIID – Sylvia Carignan – Frederick News Post

August 19, 2016

Gingivitis and periodontitis in Malawian cohort, gut Bifidobacteria during aging, picornaviruses in rats from 2 locations.

Jobs and events

QIIME 2 workshop Nov 4-5 (just prior to SSSA meeting) in Phoenix, AZ – Greg Caporaso –

Three postdoctoral researchers and one Ph.D. student: role of microbes in post-fire soil organic matter dynamics – University of Wisconsin-Madison

Human oral microbiome

Distinguishing the Signals of Gingivitis and Periodontitis in Supragingival Plaque: A Cross-Sectional Cohort Study in Malawi – Liam Shaw – Applied and Environmental Microbiology

Press: Investigators chart microbial ecology of gingivitis, periodontitis – EurekAlert

Association of metabolic syndrome and chronic periodontitis in Colombians – Adriana Jaramillo – Clinical Oral Investigations

Microbial Signatures of Oral Dysbiosis, Periodontitis and Edentulism Revealed by Gene Meter Methodology – M Colby Hunter – bioRxiv

Human gut microbiome

Review: Gut Bifidobacteria Populations in Human Health and Aging – Silvia Arboleya – Frontiers in Microbiology

Review: Correlations of host genetic and gut microbiome composition – Krystyna Dabrowska – Frontiers in Microbiology

Review: Gut Microbiota: a contributing factor to obesity – Steve M. Harakeh – Frontiers in Cellular and Infection Microbiology

Animal microbiome

High diversity of picornaviruses in rats from different continents revealed by deep sequencing – Thomas Arn Hansen – Emerging Microbes & Infections

Composition of Ileal Bacterial Community in Grazing Goats Varies across Non-rumination, Transition and Rumination Stages of Life – Jinzhen Jiao – Frontiers in Microbiology

Spatial and temporal dynamics of Pacific oyster hemolymph microbiota across multiple scales – Ana Lokmer – Frontiers in Microbiology

Plant, root, and soil microbiome

Unexpectedly high beta-diversity of root-associated fungal communities in the Bolivian Andes – Christopher J. Barnes – Frontiers in Microbiology

Fungal Assemblages in Different Habitats in an Erman’s Birch Forest – Teng Yang – Frontiers in Microbiology

Water microbiome

Chronic Polyaromatic Hydrocarbon (PAH) Contamination Is a Marginal Driver for Community Diversity and Prokaryotic Predicted Functioning in Coastal Sediments – Mathilde Jeanbille – Frontiers in Microbiology

Microbes in space

The theory and application of space microbiology: China’s experiences in space experiments and beyond – Changting Liu – Environmental Microbiology

Bioreactor microbiology

Colonic Transit Time Is a Driven Force of the Gut Microbiota Composition and Metabolism: In Vitro Evidence – William Tottey – Journal of Neurogastroenterology and Motility


Resolving microbial membership using Abundance and Variability In Taxonomy (‘AVIT ) – Anirikh Chakrabarti – Scientific Reports

Microbes in the news

Trillions of Tiny Dictators. Microbes have taken over our bodies and maybe even our minds. What, exactly, are they? – Emily Willingham – The Wall Street Journal
With a little help from my friends. The microbiome gets a worthy biography – The Economist
Eating Yogurt Is Not Enough: Rebalancing The Ecosystem Of ‘The Microbes Within Us’ – Terry Gross – NPR Fresh Air (Transcript of interview with Ed Yong)

Prebiotics Take Front and Center Stage on the 700 Club – PR NewsWire

Uncovering the female body’s secret protection against HIV – Heather Boerner – PBS Newshour

Scientific Studies Using Mice May Be Hard to Replicate Due to Gut Microbes – Paul Ratner – BigThink

Scientists Investigate How Multidrug-Resistant Pathogens are Brought into Hospitals – SciCasts

MSU team shows biofilm and mineral-producing bacteria have potential for plugging oil and gas leaks – Marshall Swearingen – Montana State University

Montana Officials Close Yellowstone River To Fight Fish-Killing ParasiteMontana Officials Close Yellowstone River To Fight Fish-Killing Parasite – Richard Gonzales – NPR

Science, publishing, and career

Peer Review Week September 2016 #RecognizeReview – Alice Meadows – The Scholarly Kitchen

With Kate Rubins, a former PhD student in our lab: NASA Astronauts Successfully Install New Space Station Docking Port – Samantha Mathewson –

August 18, 2016

Human gut microbiome

Aberrant IgA responses to the gut microbiota during infancy precedes asthma and allergy development – Majda Dzidic – The Journal of Allergy and Clinical Immunology

Plasmid metagenomics reveals multiple antibiotic resistance gene classes among the gut microbiomes of hospitalised patients – Tossawan Jitwasinkul – Journal of Global Antimicrobial Resistance

Review: The Role of the Microbiome in Gastrointestinal Cancer – Lydia E. Wroblewski – Gastroenterology Clinics of North America

Animal experiments

The Spectrum and Regulatory Landscape of Intestinal Innate Lymphoid Cells Are Shaped by the Microbiome – Meital Gury-BenAri – Cell

Animal microbiome

The Gut Microbiomes of Two Pachysoma MacLeay Desert Dung Beetle Species (Coleoptera: Scarabaeidae: Scarabaeinae) Feeding on Different Diets – Philippa Z. N. Franzini – PLOS ONE

A different gut microbial community between larvae and adults of a wild bumblebee nest (Bombus pascuorum) – Anneleen Parmentier – Insect Science

Plant, root, and soil microbiome

Plant Growth Promotion and Suppression of Bacterial Leaf Blight in Rice by Inoculated Bacteria – Sumera Yasmin – PLOS One


NCBI prokaryotic genome annotation pipeline – Tatiana Tatusova – Nucleic Acids Research

More microbiology

Design, synthesis, and testing toward a 57-codon genome – Nili Ostrov – Science

Microbes in the news

New polio cases in Nigeria spur massive response – Leslie Roberts – Science

Science, publishing, and career

This woman may know a secret to saving the brain’s synapses – Emily Underwood – Science


August 17, 2016

Beneficial bacteria in the nose suppress pathogenic bacteria,  gut microbiome and Entamoeba histolytica infection, viromes of the Earth.


Assistant/Associate Professor in Microbiology & Immunology, University of Illinois at Chicago – Science Careers

Internship: Coral microbiome under ocean acidification – King Abdullah University of Science and Technology – Saudi Arabia

Pregnancy and birth

Microbiota in Breast Milk of Chinese Lactating Mothers – Olga Sakwinska – PLOS ONE

Human skin microbiome

ReviewFactors shaping the composition of the cutaneous microbiota – K. Szabó – British Journal of Dermatology

Human respiratory microbiome

Staphylococcus aureus Shifts toward Commensalism in Response to Corynebacterium Species – Matthew M. Ramsey – Frontiers in Microbiology

Press: New findings detail how beneficial bacteria in the nose suppress pathogenic bacteria– Science Daily

Human gut microbiome

Disease Severity and Immune Activity Relate to Distinct Interkingdom Gut Microbiome States in Ethnically Distinct Ulcerative Colitis Patients – Jordan S. Mar – mBio

Stool microbiome reveals diverse bacterial ureases as confounders of oral urea breath testing for Helicobacter pylori and Mycobacterium tuberculosis in Bamako, Mali – Mamoudou Maiga – Journal of Breath Research

Review: Antibiotics as deep modulators of gut microbiota: between good and evil – Gianluca Ianiro – Gut

Review: The Intestinal Bacterial Microbiome and E. histolytica Infection – Stacey L. Burgess – Curr Trop Med Reports

Review: The microbiome and immune regulation after transplantation – Tabibian, James H. – Transplantation

Review: Experimental design considerations in microbiota/inflammation studies – Robert J Moore – Clin Transl Immunology

Animal experiments

Wolbachia Endosymbionts Modify Drosophila Ovary Protein Levels in a Context-Dependent Manner – Steen Christensen – Applied and Environmental Microbiology

Composition of the Cockroach Gut Microbiome in the Presence of Parasitic Nematodes – Cláudia S. L. Vicente – Microbes and Environments

Animal microbiome

Link of a ubiquitous human coronavirus to dromedary camels – Victor M. Corman – PNAS

Plant, root, and soil microbiome

Changes in the composition of the RNA virome mark evolutionary transitions in green plants – Arcady Mushegian – BMC Biology

ReviewIdentifying the role of soil microbes in plant invasions – Wayne Dawson – Journal of Ecology

Water microbiome

Uncovering Earth’s virome – David Paez-Espino – Nature

Press: Unveiled: Earth’s Viral Diversity. Environmental datasets help researchers double the number of microbial phyla known to be infected by viruses.- Joint Genome Institute
Researchers complete unprecedented study of the global virome – Katherine Lindemann – Research Gate Blog

290 Metagenome-assembled Genomes from the Mediterranean Sea: Ongoing Effort to Generate Genomes from the Tara Oceans Dataset – Benjamin J Tully – bioRxiv

The Microbiome and Mental Health: Looking Back, Moving Forward with Lessons from Allergic Diseases – Alan C. Logan

Extremophile microbiome

Yeasts from macroalgae and lichens that inhabit the South Shetland Islands, Antarctica
Alysson Wagner Fernandes Duarte – Environmental Microbiology Reports

Bioinformatics and metagenomics

Comparison of bacterial genome assembly software for MinION data and their applicability to medical microbiology – Kim Judge – Microbial Genomics

Fast comparison of genomic and meta-genomic reads with alignment-free measures based on quality values – Matteo Comin – BMC Medical Genomics

Gifted microbes for genome mining and natural product discovery – Richard H. Baltz – Journal of Industrial Microbiology & Biotechnology

Microbial Ecology

Biodiversity at multiple trophic levels is needed for ecosystem multifunctionality – Santiago Soliveres – Nature

Extrapolating abundance curves has no predictive power for estimating microbial biodiversity – Amy Willis – PNAS

Synergistic elimination of bacteria by phage and the immune system – Chung Yin (Joey) Leung – bioRxiv

Microbes in the news

The Counterintuitive Way That Microbes Survive in Antarctica – And what it could mean for the search for life on other worlds – Ed Yong – The Atlantic

Human Cells Make Up Only Half Our Bodies. A New Book Explains Why – Jonathan Weiner – New York Times

Journalist Edmund Soon-Weng Yong awarded 2016 Byron H. Waksman Award for excellence in the public communication of Life Sciences – NewsWise

Mouse microbes may make scientific studies harder to replicate – Kelly Servick – Science Mag

Biome, Genome, Microbiome…Houdinisome? – Jason Tetro – Germ Guy

Tiny Stanford invention purifies water in minutes using the sun – CNET

The importance of quality pre-analytical factors and their impact on microbiome analysis – Lisa Gamwell – DNA Genotek’s Microbiome Collection and Stabilization Blog

Behind paywall: Brazilian Researchers Profile Microbiome of Rio Before, During, After Olympic Games – Genome Web
Rio 2016 organizers are confident everything is fine. I’m not reassured – Sally Jenkins – Washington Post

Science, publishing, and career

Stanford programs prepare underrepresented high schoolers for careers in science, engineering and medicine – Victoria Chesley – Stanford News