August 27, 2016

Gut microbiome in pre-Columbian mummies, spacecraft assembly cleanrooms, smokeless tobacco products, time series data, and a return of the Musical Microbes.

Human skin microbiome

Skin fungal community and its correlation with bacterial community of urban Chinese individuals – Marcus H. Y. Leung – Microbiome

Human oral microbiome

High-throughput quantitative method for assessing coaggregation among oral bacterial species – E. Levin-Sparenberg – Letters in Applied Microbiology

Human gut microbiome

Taxonomic and predicted metabolic profiles of the human gut microbiome in pre-Columbian mummies – Tasha M. Santiago-Rodriguez – FEMS Microbiology Ecology

Note: unclear definition of “redemption”; means that a medication prescription was filled. Broad-Spectrum Antibiotic Treatment and Subsequent Childhood Type 1 Diabetes: A Nationwide Danish Cohort Study – Tine D. Clausen – PLOS ONE

Animal experiments

Impact of dietary fibre:starch ratio in shaping caecal archaea revealed in rabbits – Y. Zhu – Journal of Animal Physiology and Animal Nutrition

Plant, root, and soil microbiome

Endolithic microbial diversity in sandstone and granite from the McMurdo Dry Valleys, Antarctica – Stephen D. J. Archer – Polar Biology

Dry Season Constrains Bacterial Phylogenetic Diversity in a Semi-Arid Rhizosphere System – Rodrigo Gouvêa Taketani – Microbial Ecology

Review: Bacteria in decomposing wood and their interactions with wood-decay fungi – Sarah R. Johnston – FEMS Microbiology Ecology

Water microbiome

Multitaxon activity profiling reveals differential microbial response to reduced seawater pH and oil pollution – Francisco J. R. C. Coelho – Molecular Ecology

High-throughput metabarcoding of eukaryotic diversity for environmental monitoring of offshore oil-drilling activities – Anders Lanzén – Molecular Ecology

Microbial source tracking in impaired watersheds using PhyloChip and machine-learning classification – Eric A. Dubinsky – Water Research

Spacecraft microbiome

Functional metagenomics of spacecraft assembly cleanrooms: Presence of virulence factors associated with human pathogens – Mina Bashir – Frontiers in Microbiology

Tobacco microbiome

Bacterial Populations Associated with Smokeless Tobacco Products – Jing Han – Applied and Environmental Microbiology

Bacteria in smokeless tobacco products may be a health concern – American Society for Microbiology

Development of an Integrated Pipeline for Profiling Microbial Proteins from Mouse Fecal Samples by LC-MS/MS – Jing Wu – Journal of Proteome Research

Bioinformatics, metagenomics, and statistics

Modeling time-series data from microbial communities – Benjamin J Ridenhour – bioRxiv

Improving ancient DNA genome assembly – Alexander Seitz – PeerJ Preprint

More microbiology

The Musical Microbes are back! Influence of a mono-frequency sound on bacteria can be a function of the sound-level – Vijay Kothari – bioRxiv

Microbes in the news

Focus: California drought reducing beach bacteria: Reduced runoff has meant fewer health advisories, data show – Daniel Wheaton – San Diego Union Tribune
Mystery Solved: How Lyme Disease Bacteria Spread Around the Body – Rachael Rettner – LiveScience

In sub-Saharan Africa, cancer can be an infectious disease – ScienceDaily

#BacteriaHysteria: You Should Never Ask For a Slice Of Lemon In Your Drink – Alice Sholl – Yahoo

Science, publishing, and career

There Was A Huge Outpouring Of Support For This Little Girl Who Got Bullied For Loving Bugs. Let Sophia play with her bugs! – Ishmael N. Daro – BuzzFeed

August 26, 2016

MRI scans of colonic contents in setting of diet or defaecation, fecal transplants, the microbiome of ambulances, and a core taxa tool.

Pregnancy and birth

Longitudinal study on clinical and microbial analysis of periodontal status in pregnancy – Fernanda Campos Machado – Brazilian Oral Research

Review: Role of microbiota function during early life and children neurodevelopment – Tomás Cerdó – Trends in Food Science & Technology

Human oral microbiome (also see above)

Evaluation of oral microbiota in undernourished and eutrophic children using checkerboard DNA-DNA hybridization – M. Testa – Anaerobe

Review: Human neutrophils and oral microbiota: a constant tug-of-war between a harmonious and a discordant coexistence – Silvia M. Uriarte – Immunological Reviews

Human skin microbiome

Temporal stability in chronic wound microbiota is associated with poor healing – Michael Loesche – Journal of Investigative Dermatology

Human gut microbiome

Colonic content: effect of diet, meals, and defecation – R. A. Bendezú – Neurogastroenterology & Motility

Gut microbiota associated with HIV infection is significantly enriched in bacteria tolerant to oxygen – Grégory Dubourg – BMJ Open Gastroenterology

Prevalence and genetic diversity of Blastocystis in family units living in the United States – Pauline D. Scanlan – Infection, Genetics and Evolution

Nitrogen fixation and nifH diversity in human gut microbiota – Katsura Igai – Scientific Reports

Letter: Intestinal Microbiota and Health of Adults Who Were Born by Cesarean Delivery – James J. Goedert – JAMA Pediatrics

Opinion: The microbiome, microbial generated pro-inflammatory neurotoxins, and Alzheimer’s disease – Walter J. Lukiw – Journal of Sport and Health Science

Review: Estrogen and Microbiota Crosstalk: Should We Pay Attention? – Karen L. Chen – Trends in Endocrinology & Metabolism

Review: Gender, aging and longevity in humans: an update of an intriguing/neglected scenario paving the way to a gender-specific medicine – Rita Ostan – Clinical Science

Fecal transplants

Estimating the risks of faecal transplants – K. Patel – The Journal of Hospital Infection

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

Plant, root, and soil microbiome

Arbuscular mycorrhizal fungi communities from tropical Africa reveal strong ecological structure – Susana Rodríguez-Echeverría – New Phytologist

Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria – Edward W. Davis II – PeerJ

Water microbiome

Structure and function of methanogenic microbial communities in sediments of Amazonian lakes with different water types – Yang Ji – Environmental Microbiology

Built environment microbiome

Detection and characterization of surface microbial contamination in emergency ambulances – Aketza Varona-Barquin – American Journal of Infection Control

Fitness and recovery of bacterial communities and antibiotic resistance genes in urban wastewaters exposed to classical disinfection treatments – Andrea Di Cesare – Environmental Science & Technology

Bioinformatics and metagenomics

PhyloCore: A phylogenetic approach to identifying core taxa in microbial communities – Tiantian Ren – Gene

Microbes in the news

Gut reaction: the surprising power of microbes – Ed Yong – The Guardian

Want to feel better? Be kind to your bugs. Ed Yong’s new book will give you a positive outlook on your body’s trillions of bacteria – Kate Womersley – The Spectator

The world’s largest bacterial study of baby poo – MedicalXpress

What’s in Your Poo? The nonmicrobial components of feces may have important consequences as we try to grapple with microbiome research – Kevin Bonham – Scientific American

Solving a 48-year-old mystery: scientists succeed at growing noroviruses in human intestinal cell cultures in the lab – Graciela Gutierrez – Baylor College of Medicine

MSU researchers spread the buzz about bee viruses – Marshall Swearingen – Montana State University

Science, publishing, and career

Family ties ‘help scientists to get ahead’ in some countries. Levels of nepotism in scientific publishing have been revealed by report – Jack Grove  – Times Higher Education

Supervisors can do a lot more to support PhD students. Many doctoral candidates feel poorly looked after. More awareness and empathy from academics can help fight that – Geoffrey Cantor – Times Higher Education

New leader of NIH’s research watchdog faces staff revolt – Jocelyn Kaiser – Science

Microbiome Blogs, Tweeps, and Books

I just wrote a new page called “Microbiome Blogs, Tweeps, and BooksMicrobiome Blogs, Tweeps, and Books“. You can find it at the grey bar under the picture at the top of this page, by clicking on Microbiome Collection. Or just by clicking here. The page features microbiome books I like (either by having read them or by reading the abstract), people who like to tweet about microbial communities (both scientists as well as science writers), and blogs that focus on, or regularly feature microbiomes.


August 25, 2016

Microbiome of the Graduate Student Gut, allergic cats, tree phyllosphere, milk tanker trucks, and microbes of soda lakes.

Pregnancy and birth

Review: Role of microbiota function during early life and children neurodevelopment – Tomás Cerdó – Trends in Food Science & Technology

General microbiome

Now published after preprint earlier this year and article in Cell: Revised Estimates for the Number of Human and Bacteria Cells in the Body – Ron Sender – PLOS Biology

Enemies and brothers in arms: Candida albicans and gram-positive bacteria – Toni M. Förster – Cellular Microbiology

Human respiratory microbiome

General antibiotic exposure is associated with increased risk of developing chronic rhinosinusitis – Alice Z. Maxfield – The Laryngoscope

Evidence and Role for Bacterial Mucin Degradation in Cystic Fibrosis Airway Disease – Jeffrey M. Flynn – PLOS Pathogens

Human gut microbiome

Master Thesis: Characterizing Microbiome Changes in the Graduate Student Gut – Justin Roy Lund – University of Oklahoma

Altered Fecal Microbiota Correlates with Liver Biochemistry in Nonobese Patients with Non-alcoholic Fatty Liver Disease – Baohong Wang – Scientific Reports

Prosteatotic and Protective Components in a Unique Model of Fatty Liver: Gut Microbiota and Suppressed Complement System – Long Liu – Scientific Reports

Is there a role for stool metabolomics in cystic fibrosis? – Nadeem O Kaakoush – Pediatrics International

Animal microbiome

Allergic to humans? Characterization of the cutaneous mycobiota in healthy and allergic cats using next generation sequencing – Courtney Meason-Smith – Veterinary Dermatology

Fish: The influence of weight and gender on intestinal bacterial community of wild largemouth bronze gudgeon (Coreius guichenoti, 1874) – Xuemei Li – BMC Microbiology

Plant, root, and soil microbiome

Tree phyllosphere bacterial communities: exploring the magnitude of intra- and inter-individual variation among host species – Isabelle Laforest-Lapointe – PeerJ

Long-Term Recovery of Microbial Communities in the Boreal Bryosphere Following Fire Disturbance – Nick A. Cutler – Microbial Ecology

Autochthonous Microbiota in Arsenic-Bearing Technosols from Zemianske Kostoľany (Slovakia) and Its Potential for Bioleaching and Biovolatilization of Arsenic – Alexandra Šimonovičová – Water, Air, & Soil Pollution

Built environment microbiology

Fungi and Bacteria in Indoor Cultural Heritage Environments: Microbial-related Risks for Artworks and Human Health – Enza Di Carlo – Environment and Ecology Research

Fitness and recovery of bacterial communities and antibiotic resistance genes in urban wastewaters exposed to classical disinfection treatments – Andrea Di Cesare – Environmental Science & Technology

Bacterial diversity and antibiotic resistances of abundant aerobic culturable bacteria in input and output samples of fifteen German biogas plants – Thorsten Schauss – Journal of Applied Microbiology

Food microbiology

The Core and Seasonal Microbiota of Raw Bovine Milk in Tanker Trucks and the Impact of Transfer to a Milk Processing Facility – Mary E. Kable – mBio

Water and extremophile microbiome

Microbial community diversity and composition varies with habitat characteristics and biofilm function in macrophyte-rich streams – Peter S. Levi – Oikos

Evaluation of Alternative High-Throughput Sequencing Methodologies for the Monitoring of Marine Picoplanktonic Biodiversity Based on rRNA Gene Amplicons – Isabel Ferrera- Frontiers in Marine Science

Book Chapter: Bacteria, Archaea and Viruses of Soda Lakes – William D. Grant – Soda Lakes of East Africa

Bioinformatics and metagenomics

ResistoMap – online visualization of human gut microbiota antibiotic resistome – Konstantin Yarygin – bioRxiv

Techniques Virtual Communities for Protocol Development and Discussion – Leonid Teytelman – PLOS Biology

More microbiology

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

Microbes in the news

How Designers and Scientists Are Using Bees to Map NYC’s Microbes – Liz Stinson – Wired

Graphic novel about World War I depicts gross realities of dysentery – Carolyn Webb – The Age Victoria

The newest food trend: fermentation – Ted Weesner – Boston Globe



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