August 31, 2016

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ICU, Rudlavibizon, Flickr

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


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

Human gut microbiome

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

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

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

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

Animal and other model experiments

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

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

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

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

Animal microbiome

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

Plant, root, and soil microbiome

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

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

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

Water microbiome

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

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

Air microbiome

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

Bioinformatics and metagenomics

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

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

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

Microbial ecology

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

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

Microbes in the news

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

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

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

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

Peer review and science misconduct

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

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

Bik’s Non-Microbiology Picks

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

August 29, 2016

Breast milk protects against GBS colonization, niche segregation in the gut, drug detection and effects in streams, reconstruction of metabolic networks.

Pregnancy and birth

Role of human milk oligosaccharides in Group B Streptococcus colonisation – Nicholas J Andreas – Clinical & Translational Immunology

Press: Breast Milk Sugar May Protect Newborns Against Deadly Bacterial Infection – Dianne Depra – Tech Times

Human skin microbiome

News and Views: Microbiome: Ecology of eczema – Ian D. Odell – Nature Microbiology

Human respiratory microbiome

Changes in the prevalence and biofilm formation of Haemophilus influenzae and Haemophilus parainfluenzae from the respiratory microbiota of patients with sarcoidosis – Urszula Kosikowska – BMC Infectious Diseases

Human vaginal microbiome

The cervico-vaginal microbiota in women notified for Chlamydia trachomatis infection: A case-control study at the STI outpatient clinic in Amsterdam, the Netherlands – C van der Veer – Clinical Infectious Diseases

Human gut microbiome

Transcriptional interactions suggest niche segregation among microorganisms in the human gut – Damian Rafal Plichta – Nature Microbiology

Review: Alzheimer’s disease and gut microbiota – Xu Hu – Science China Life Sciences

Review: In Sickness and in Health: The Relationships Between Bacteria and Bile in the Human Gut – A.J. Hay – Advances in Applied Microbiology

Animal experiments

Enterococcus faecalis readily colonizes the entire gastrointestinal tract and forms biofilms in a germ-free mouse model – Aaron M.T. Barnes – Virulence

Animal microbiome

Distinct Bacterial Microbiomes in Sexual and Asexual Potamopyrgus antipodarum, a New Zealand Freshwater Snail – Cristina Takacs-Vesbach – PLOS ONE

Water and extremophile microbiome

Occurrence and Potential Biological Effects of Amphetamine on Stream Communities – Sylvia S. Lee – Environmental Science & Technology

Press: Ecological consequences of amphetamine pollution in urban streams – Cary Institute
Your drain on drugs: Amphetamines seep into Baltimore’s streams – Jen Christensen – CNN
Comment from PubMed Commons by Daniel Himmelstein 

Diversity of culturable bacteria recovered from Pico Bolívar’s glacial and subglacial environments, at 4950 m, in Venezuelan tropical Andes – Johnma Rondón – Canadian Journal of Microbiology


Efficient Reconstruction of Predictive Consensus Metabolic Network Models – Ruben G. A. van Heck – PLOS Computational Biology

Bioinformatics and Metagenomics

Review: Toward Accurate and Quantitative Comparative Metagenomics – Stephen Nayfach – Cell


Thousands of primer-free, high-quality, full-length SSU rRNA sequences from all domains of life – Soeren M Karst – bioRxiv

A method for assessing efficiency of bacterial cell disruption and DNA release – Olle M. de Bruin – BMC Microbiology

Microbes in the news

Findings from the American Physiological Society’s Inflammation, Immunity and Cardiovascular Disease conference: Targeting gut bacteria to reduce weight gain – Science Daily

Microbes at work in your Kimchi – Jennifer – The Microbial Menagerie

Artist’s 46-year-old loo paper to be studied: Billy Apple’s decades-old lavatory paper is now part of a scientific study at Auckland University – Jamie Morton – NZ Herald

BacteriaHysteriaThe ultimate embodiment of modern day germophobia: Squix – Jonathan Eisen – MicroBEnet

Science misconduct

Leading scientist suspended amid misconduct claims: Robert Ryan, award-winning Scottish microbiologist now under investigation – Victoria Weldon – Herald Scotland

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

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

Image duplication quartet

One of the topics discussed today on Twitter was a set of four very similar papers by the same group from Malaysia, all published around the same time, but with different titles and in different journals. The problems were first spotted by Dave Williamson on Twitter:

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Soon followed other tweets by Stuart Cantrill, Christophe Leterrier, Alexis Verger, and many others, who found more and more problems with papers by this group.

As already pointed out in posts in Retraction Watch, For Better Science by Leonid Schneider, and other blog posts, there are a lot of apparent problems with these studies. Not only do these papers contain a lot of very similar looking figures, most of the figures themselves appear to contain duplicated panels or parts of panels.

These 4 papers contain very similar examples of inappropriate image duplication as Arturo Casadevall, Ferric Fang and I wrote about in our paper that was published earlier this week in mBio:

The Prevalence of Inappropriate Image Duplication in Biomedical Research Publications – Elisabeth M. Bik, Arturo Casadevall, Ferric C. Fang – mBio

In our paper, we scanned over 20,000 published papers that contained the term “Western Blot” and screened all photographic images for duplicated panels, or lanes within panels. About 1:25 of the papers contained inappropriately duplicated images. That suggests that peer review and journal editors need to do a better job in catching these problems before publication.

The 4 papers that attracted attention today had very similar problems as the ones we encountered in our paper, but they also looked very similar to each other. The four-some were published respectively in Frontiers in Pharmacology, PeerJ, Scientific Reports, and Recent Patents on Anti-Cancer Drug Discovery. At the bottom of this post I will show the side-by-side screenshots of the 4 paper, showing how similar their figures are. But there are also a lot of potential problems with the figures, such as photos representing different cell lines that share similar features, or bands within the same Western Blot panel that look very similar to each other. What makes these papers unique is that they have so many apparent problems within one paper. Here are some examples (colored boxes are mine to point out similar looking features such as cells or bands):

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You can see more examples of what-seem-to-be inappropriate duplications on the PubPeer website, for the Frontiers in Pharmacology paper, and the Scientific Reports paper. Several people, including I, have left comments and concerns about the figures. I hope that by showing these examples, peer reviewers and editors will better recognize potential figure problems, and pay more attention in capturing these mistakes before they are published. I also hope that the authors will respond to our concerns.

To show how similar the papers are to each other, I have made screenshots of a side-by-side comparison of the 4 papers. In all screenshots below, you will see from left-t0-right: Frontiers in Pharmacology, PeerJ, Scientific Reports, and the Patents paper. Note that although the papers represent studies on different cell lines or chemicals, their figures look unexpectedly similar to each other.

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FPh Fig 2 – PeerJ Fig 2 – SciRep Fig 1 – Patent Fig 2

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FPh Fig 3 – PeerJ Fig 3 – SciRep Fig 2 – Patent Fig 3

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FPh, Fig 4 – PeerJ Fig 4 – SciRep Fig 3 – Patent Fig 4Screen Shot 2016-06-10 at 7.56.34 PM.png

NA -PeerJ Fig 5 – SciRep Fig 4 – Patent Fig 5

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NA -PeerJ Fig 6 – SciRep Fig 5 – Patent Fig 6

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NA – PeerJ Fig 7 – SciRep Fig 6 – Patent Fig 7

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NA – PeerJ Fig 8 – SciRep Fig 8 – Patent Fig 8

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FPh, Fig 5 – PeerJ Fig 10 – SciRep Fig 10 – Patent Fig 10

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FPh, Fig 6 – PeerJ Fig 11 – SciRep Fig 11 – Patent Fig 11

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FPh, Fig 7 – PeerJ Fig 12 – SciRep Fig 12  – Patent Fig 12

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FPh, Fig 8 – PeerJ Fig 13 – SciRep Fig 7  – Patent Fig 13

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June 10, 2016

Volunteers taking ETEC, 3 new E. coli phages, oral microbiomes of cats and dogs, skin microbes in Japanese amphibians, fungi and bacteria in floor dust.

Human oral microbiome

The oral microbiome of patients with axial spondyloarthritis compared to healthy individuals – Jordan E. Bisanz – PeerJ

Human vaginal microbiome

Association of Sexual Debut in Adolescents With Microbiota and Inflammatory Markers – Jespers, Vicky – Obstetrics & Gynecology

Human blood ‘microbiome’

Rapid identification of fungi in culture-negative clinical blood and respiratory samples by DNA sequence analyses – Farida Sidiq – BMC Research Notes

Human gut microbiome

Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment – Mihai Pop – BMC Genomics

Mucosa-Associated Ileal Microbiota in New-Onset Pediatric Crohn’s Disease – Assa, Amit – Inflammatory Bowel Diseases

Three New Escherichia coli Phages from the Human Gut Show Promising Potential for Phage Therapy – Marion Dalmasso – PLOS ONE

“Free living females” sounded… weird. Soluble Corn Fiber Increases Calcium Absorption Associated with Shifts in the Gut Microbiome: A Randomized Dose-Response Trial in Free-Living Pubertal Females – Corrie M Whisner – Journal of Nutrition

Similar Fecal Microbiota Signatures in Patients With Diarrhea-predominant Irritable Bowel Syndrome and Patients With Depression – Yixuan Liu – Clinical Gastroenterology and Hepatology

DGGE: Differences in the Biodiversity of the Fecal Microbiota of Infants With Rotaviral Diarrhea and Healthy Infants – Peng Fei – Jundishapur Journal of Microbiology

Opinion: How Our Other Genome Controls Our Epi-Genome – Antonella Celluzzi – Trends in Microbiology

Review: The role of the gut microbiota in NAFLD – Christopher Leung – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

Diet may influence the oral microbiome composition in cats – Christina J. Adler – Microbiome

Characterising the Canine Oral Microbiome by Direct Sequencing of Reverse-Transcribed rRNA Molecules – James E. McDonald – PLOS ONE

Bacterial microbiomes from vertically-transmitted fungal inocula of the leaf-cutting ant Atta texana – Lucas A. Meirelles – Environmental Microbiology Reports

Defensive insect symbiont leads to cascading extinctions and community collapse – Dirk Sanders – Ecology Letters

Plant, root, and soil microbiome

Subalpine conifers in two different geographic locations host highly similar foliar bacterial endophyte communities – Alyssa A. Carrell – FEMS Microbiology Ecology

Effect of plant growth-promoting bacteria on the growth and fructan production of Agave americana L. – Neyser De La Torre-Ruiz – Brazilian Journal of Microbiology

Composition of the Cutaneous Bacterial Community in Japanese Amphibians: Effects of Captivity, Host Species, and Body Region – Joana Sabino-Pinto – Microbial Ecology

Water and extremophile microbiome

Benthic protists: the under-charted majority – Dominik Forster – FEMS Microbiology Ecology

Methane release from sediment seeps to the atmosphere is counteracted by highly active Methylococcaceae in the water column of deep oligotrophic Lake Constance – Maren Bornemann – FEMS Microbiology Ecology

Review: How mutualisms arise in phytoplankton communities: building eco-evolutionary principles for aquatic microbes – Elena Kazamia – Ecology Letters

Review: All ecosystems potentially host electrogenic bacteria – Nicolas Chabert – Bioelectrochemistry

Pollution and waste and bioreactor microbiology

Arsenic metabolism and toxicity influenced by ferric iron in simulated gastrointestinal tract and the roles of gut microbiota – Haiyan Yu – Environmental Science & Technology

Pyrosequencing analysis of bacterial diversity in soils contaminated long-term with PAHs and heavy metals: Implications to bioremediation – Saranya Kuppusamy – Journal of Hazardous Materials

A strange combination of samples: Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies – Simon Güllert – Biotechnology for Biofuels

Monitoring the impact of bioaugmentation with a PAH-degrading strain on different soil microbiomes using pyrosequencing – S. Festa – FEMS Microbiology Ecology

Built environment microbiome

Fungal and bacterial growth in floor dust at elevated relative humidity levels – Karen C. Dannemiller – Indoor Air

Bioinformatics and statistics

An Introduction to Programming for Bioscientists: A Python-Based Primer – Berk Ekmekci – PLOS Computational Biology

Ten Simple Rules for Effective Statistical Practice – Robert E. Kass – PLOS Computational Biology

Bipartite Graphs for Visualization Analysis of Microbiome Data – Karel Sedlar – Evolutionary Bioinformatics


The source of SYBR green master mix determines outcome of nucleic acid amplification reactions – Jianxin Yang – BMC Research Notes

More microbiology

Ancestral Tryptophan Synthase Reveals Functional Sophistication of Primordial Enzyme Complexes – Florian Busch – Cell Chemical Biology

Press: Ancient enzyme resurrected from the ancestor of all bacteria – Conor Gearin – New Scientist
Bacteria perfected protein complexes more than 3.5 billion years ago – Science Daily

Microbes in the news

Tufts microbiologist Cecilia A. Silva-Valenzuela, Ph.D., named Pew Latin American Fellow
Silva-Valenzuela, in Andrew Camilli’s lab, will investigate novel approaches to prevent cholera outbreaks – EurekAlert

Bio-statistician Albert Parker with MSU’s Center for Biofilm Engineering earns top EPA award – Amanda Eggert – Montana State University

Video series with James Hamblin – The Atlantic
Should You Map Your Microbiome? A visit to uBiome
Your Probiotics Aren’t Doing Anything (Yet)
You Probably Don’t Need to Shower – James Hamblin – The Atlantic

Banking on stool despite an uncertain future – Tina Amirtha – Science

Science, publishing, and career

In effort to understand continuing racial disparities, NIH to test for bias in study sections – Jeffrey Mervis – Science

Triplicated paper with multiplicated cells and images – Leonid Schneider – For Better Science
Author denies accusations of blatant duplication – Shannon Palus – Retraction Watch

Bik’s Picks (it’s not microbiology, but pretty cool)

RhizoTubes as a new tool for high throughput imaging of plant root development and architecture: test, comparison with pot grown plants and validation – Christian Jeudy – Plant Methods

June 8, 2016

Obesity and microbiome patterns, universality of human microbial dynamics, intestinal fungal dysbiosis, pre-eclampsia, seaweed ice-ice disease.

Pregnancy and birth

Review: A dormant microbial component in the development of pre-eclampsia – Douglas B Kell – bioRxiv

General human microbiome

Universality of human microbial dynamics – Amir Bashan – Nature

News and Views: Host-microbe interaction: Rules of the game for microbiota – Karoline Faust – Nature

Perspectives: Accounting for reciprocal host–microbiome interactions in experimental science – Thaddeus S. Stappenbeck – Nature

Human gut microbiome

Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome – Marc Sze – bioRxiv

Animal and in vitro experiments

Immunological Consequences of Intestinal Fungal Dysbiosis – Matthew L. Wheeler – Cell Host & Microbe

Editorial: The Fungal Mycobiota: Small Numbers, Large Impacts – Carol A. Kumamoto – Cell Host & Microbe

Research Highlights: Love Thy Neighbor: Sharing and Cooperativity in the Gut Microbiota – Nathan T. Porter – Cell Host & Microbe

Animal microbiome

Overfishing and nutrient pollution interact with temperature to disrupt coral reefs down to microbial scales – Jesse R. Zaneveld – Nature Communications

Restructuring of the sponge microbiome favors tolerance to ocean acidification – M. Ribes – Environmental Microbiology Reports

Plant, root, and soil microbiome

Molecular identification of new bacterial causative agent of ice-ice disease on seaweed Kappaphycus alvarezii – Marlina Achmad – PeerJ Preprint

Effect of temperature (5 °C–25 °C) on epiphytic lactic acid bacteria populations and fermentation of whole-plant corn silage – Yiqin Zhou – Journal of Applied Microbiology

Conventional methanotrophs are responsible for atmospheric methane oxidation in paddy soils – Yuanfeng Cai – Nature Communications

More microbiology

Nondegenerative Evolution in Ancient Heritable Bacterial Endosymbionts of Fungi – Stephen J. Mondo – Molecular Biology and Evolution

Historical Y. pestis Genomes Reveal the European Black Death as the Source of Ancient and Modern Plague Pandemics – Maria A. Spyrou – Cell Host & Microbe

Microbes in the news

Arlington native Alexandra Worden named American Academy of Microbiology fellow – Arlington Wicked Local

Disease Researcher Finds New Home at Valencia — in the Classroom, with Dr. Hemangi Patil – Linda Shrieves Beaty – Valencia College

From the Congress of the European Academy of Neurology in Copenhagen, Denmark: Scientists Gather to Discuss Novel Connections Between Gut Microbiome and Brain Disorders – Patricia Inacio – Multiple Sclerosis News Today

Cooperative and Combative Behaviour in the Human Gut: Probing the Microbiome, with Athena Aktipis – SciCasts

Speeding Up Drug Discovery to Fight Tuberculosis – Seattle researchers created a genetic blueprint of the cunning tuberculosis bacteria, then used it to predict and rank potential drug targets – SystemsBiology

Science, publishing, and career

What does research reproducibility mean? – Steven N. Goodman – Science Translational Medicine

Editorial: Second chances – The line between compliance and misconduct is finer than you might think – Nature

Misconduct: Lessons from researcher rehab – James M. DuBois – Nature

June 7, 2016

Microbiomes of the lung, red coral, effect of invertebrates on water microbes, and bacteriophages are reservoirs of antibiotic resistance genes.

General microbiome

The vast unknown microbial biosphere – Carlos Pedrós-Alió – PNAS

Human respiratory microbiome

Review: The Lung Microbiome, Immunity, and the Pathogenesis of Chronic Lung Disease – David N. O’Dwyer – The Journal of Immunology

Review/Hypothesis: A Role for the Intestinal Microbiota and Virome in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)? – Navena Navaneetharaja – MDPI Journal of Clinical Medicine

Human gut microbiome

Review: The metabolic role of the gut microbiota in health and rheumatic disease: mechanisms and interventions – Shahla Abdollahi-Roodsaz – Nature Reviews Rheumatology

Animal experiments

Accelerated dysbiosis of gut microbiota during aggravation of DSS-induced colitis by a butyrate-producing bacterium – Qianpeng Zhang – Scientific Reports

Bacterial Adrenergic Sensors Regulate Virulence of Enteric Pathogens in the Gut – Cristiano G. Moreira – mBio

Animal microbiome

Spirochaetes dominate the microbial community associated with the red coral Corallium rubrum on a broad geographic scale – Jeroen A. J. M. van de Water – Scientific Reports

Plant, root, and soil microbiome

Mangrove succession enriches the sediment microbial community in South China – Quan Chen – Scientific Reports

Correlations between the composition of modular fungal communities and litter decomposition-associated ecosystem functions – Witoon Purahong – Fungal Ecology

History Leaves Its Mark on Soil Bacterial Diversity – Jennifer B. H. Martiny – mBio

Water and extremophile microbiome

Alteration of physico-chemical and microbial properties in freshwater substrates by burrowing invertebrates – Carolin Boeker – Limnologica – Ecology and Management of Inland Waters

Effects of the invasive clam Corbicula fluminea (Müller, 1774) on an estuarine microbial community – Adriana Novais – Science of The Total Environment

Delineating ecologically significant taxonomic units from global patterns of marine picocyanobacteria – Gregory K. Farrant – PNAS

Bacterial community composition and structure in an Urban River impacted by different pollutant sources – A. Mark Ibekwe – Science of The Total Environment

Population Dynamics and Community Composition of Ammonia Oxidizers in Salt Marshes after the Deepwater Horizon Oil Spill – Anne Bernhard – Frontiers in Microbiology

Review: Cannibalistic viruses in the aquatic environment: role of virophages in manipulating microbial communities – V. Marie – International Journal of Environmental Science and Technology

Built environment microbiome

Molecular investigation of bacterial communities: Data from two frequently used surfaces in the São Paulo Institute of Tropical Medicine – Tairacan Augusto Pereira da Fonseca – Data in Brief

The prevalence of foodborne pathogenic bacteria on cutting boards and their ecological correlation with background biota – Noor-Azira Abdul-Mutalib – AIMS Microbiology

Metagenomics and viruses

Metagenomic analysis reveals that bacteriophages are reservoirs of antibiotic resistance genes – Jéssica Subirats – International Journal of Antimicrobial Agents


SMART: Statistical Metabolomics Analysis—An R Tool – Yu-Jen Liang – Analytical Chemistry


Book: Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing – Editors: Ana M. Aransay, José Luis Lavín Trueba – Springer Books

More microbiology

Coupling spatiotemporal community assembly processes to ecosystem function – Emily Graham – PeerJ Preprint

Evolution of the archaeal and mammalian information processing systems: towards an archaeal model for human disease – Zhe Lyu – Cellular and Molecular Life Sciences

Species richness influences wine ecosystem function through a dominant species – Primrose J. Boynton – Fungal Ecology

Microbes in the news
New antimicrobial material joins fight against antibiotic-resistant bacteria – Michael Irving – GizMag

Note: PNAS paper not yet out: Distinguishing Deadly Staph Bacteria from Harmless Strains – Heather Buschman – UC San Diego

Scientists craft an artificial seawater concoction. New recipe facilitates marine microbe cultivation and characterization – EurekAlert

The man who can map the chemicals all over your body: Pieter Dorrestein uses mass spectrometry to eavesdrop on the molecular conversations between microbes and their world – Paul Tullis – Nature

Stockton Kimball Awardee is Noted Bacterial Pathogenesis Researcher – University of Buffalo

MSU doctoral student Jeffrey Simkins awarded National Science Foundation fellowship to research in Australia – Montana State University – KBZK

Vaccine watches bacteria, strikes only when trouble stirs – University of Buffalo

Bacteria hairs make excellent electrical wires – Science Daily

Science, publishing, and career

My paper got publishedThe Prevalence of Inappropriate Image Duplication in Biomedical Research Publications – Elisabeth M. Bik, Arturo Casadevall, Ferric C. Fang – mBio

May 4, 2016

Note: If you enjoy this blog, I would very much appreciate a comment here below. Without your support, I might not be able to continue MicrobiomeDigest in its current form and frequency. So please, show your love by leaving a sign of support at the end of this blog. Thank you from the bottom of my heart! – Elies

Culturing the unculturables, a review on social bee microbiotas, the needle mycobiome, and an improved phage search tool.

Jobs and events

Faculty Position – Phage Biology and Microbiome Research, McMaster University, Ontario – Science Careers

Postdoctoral Fellow in Mucosal Immunology and Host-Microbiome Interactions
Jill Roberts Institute for Research in Inflammatory Bowel Disease at Weill Cornell Medicine – New York City, United States of America

General microbiome

Review: Microbial contributions to chronic inflammation and metabolic disease – Shanahan, Fergus – Current Opinion in Clinical Nutrition and Metabolic Care

Review: The microbial-mammalian metabolic axis: a critical symbiotic relationship – Chilloux, Julien – Current Opinion in Clinical Nutrition and Metabolic Care

Human gut microbiome

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation – Hilary P. Browne – Nature

(Also oral samples) The role of the gastrointestinal microbiome in infectious complications during induction chemotherapy for acute myeloid leukemia – Jessica R. Galloway-Peña – Cancer

Ecological Effect of Solithromycin on the Normal Human Oropharyngeal and Intestinal Microbiota – Mamun-Ur Rashid – Antimicrobial Agents and Chemotherapy

Towards a functional hypothesis relating anti-islet cell autoimmunity to the dietary impact on microbial communities and butyrate production – David Endesfelder – Microbiome

Clostridium difficile Infection in Patients with Inflammatory Bowel Disease – Nancy Fu – Current Infectious Disease Reports

Review: Interplay between diet, gut microbiota, epigenetic events, and colorectal cancer – Scott J. Bultman – Molecular Nutrition & Food Research

Animal microbiome

Cecal microbiota of Tibetan Chickens from five geographic regions were determined by 16S rRNA sequencing – Xueyan Zhou – Microbiology Open

Variability of Bacterial Communities in the Moth Heliothis virescens Indicates Transient Association with the Host – Heike Staudacher – PLOS ONE

Review: Gut microbial communities of social bees – Waldan K. Kwong and Nancy A. Moran – Nature Reviews Microbiology

Plant, root, and soil microbiome

Mineral Type and Solution Chemistry Affect the Structure and Composition of Actively Growing Bacterial Communities as Revealed by Bromodeoxyuridine Immunocapture and 16S rRNA Pyrosequencing – L. C. Kelly – Microbial Ecology

Habitat conditions and phenological tree traits overrule the influence of tree genotype in the needle mycobiome–Picea glauca system at an arctic treeline ecotone – Pascal Eusemann – New Phytologist

Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes
Philip E. Long – Trends in Microbiology

Extremophile microbiome

Twenty-Three Species of Hypobarophilic Bacteria Recovered from Diverse Ecosystems Exhibit Growth under Simulated Martian Conditions at 0.7 kPa – Andrew C. Schuerger – Astrobiology


Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains – Yemin Lan – Microbiome

Phages and viruses

Inferring phage-bacteria infection networks from time series data – Luis Jover – bioRxiv preprint

PHASTER: a better, faster version of the PHAST phage search tool – David Arndt – Nucleic Acids Research


Digital Droplet Multiple Displacement Amplification (ddMDA) for Whole Genome Sequencing of Limited DNA Samples – Minsoung Rhee – PLOS ONE

Microbial Ecology

A conceptual framework for invasion in microbial communities – Marta Kinnunen – The ISME Journal

Microbes in the news

Most Gut Microbes Can Be Cultured. Contrary to the popular thought that many species are “unculturable,” the majority of bacteria known to populate the human gut can be grown in the lab, scientists show – Jyoti Madhusoodanan – The Scientist

Capturing the vast diversity of bacteria in our bodies – Megan Thielking – STAT News

A bitter pill. Josiah Zayner’s gut was making his life hell — so he embarked on an extreme DIY fecal transplant – Arielle Duhaime-Ross – The Verge

Article with video: Your mouth is full of bacteria blooming. And it’s beautiful – Hyacinth Empinado – STAT news

Explore this interactive map of the Gowanus Canal’s slightly scary microbiology – Jason Sayer – Architects Newspaper

The Friendly Viruses, and how they can help with the looming antimicrobial resistance crisis – Peter Speck and Anthony Smithyman – OUP blog

How the Gut Microbiome May be Key in Post-Surgery Organ Failure after Heart Surgery in Children – University of Arizona

Bugs as drugs: Harnessing novel gut bacteria for human health – Medical Xpress

Bacteria carrying bug threatens wine industry – John Bartell – ABC

Autonomous Super Mario-Themed Sewer Robots Live-Stream Neighborhood Microbiome Data – The answer to our health is in our excrement – Nickolaus Hines – Inverse

Bay Area Scientists Join Forces To Help Contain Zika Virus – CBS San Francisco

Breast milk hormones found to impact bacterial development in infants’ guts
Intestinal microbiome of children born to obese mothers significantly different from those born to mothers of healthy weight, CU Anschutz researchers find – EurekAlert

Science, publishing, and career

Dealing with retractions – Paul van der Vet – BioMed Central blog

Propagation of errors in citation networks: a study involving the entire citation network of a widely cited paper published in, and later retracted from, the journal Nature – Paul E. van der Vet and Harm Nijveen – Research Integrity and Peer Review

May 3, 2016

Counting the microbial species on Earth, goat rumen microbiome development, red kangaroos who died a tragic death, fungi in burgundy vineyards, Archaea in  Yellowstone, and image irregularities at a Pfizer lab in La Jolla.

Jobs and Events

Postdoctoral Fellowship Opportunity: Microbiology of the Built Environment – Sloan Foundation

Bioinformatics for the Microbiome, May 27 – Stanford Center for Genomics and Personalized Medicine, $49

General microbiology

Scaling laws predict global microbial diversity: Earth is home to as many as 1 trillion (10exp12) microbial species – Kenneth J. Locey – PNAS

Pregnancy and birth

Impact of Prematurity and Perinatal Antibiotics on the Developing Intestinal Microbiota: A Functional Inference Study – Silvia Arboleya – MDPI International Journal of Molecular Sciences

Review: Young microbes for adult obesity – M. Serino – Pediatric Obesity

Review: Microbial therapeutic interventions – Nicole G. Grady – Seminars in Fetal and Neonatal Medicine

Human oral microbiome

Microbiome of Deep Dentinal Caries Lesions in Teeth with Symptomatic Irreversible Pulpitis – Isabela N. Rôças – PLOS ONE

Human respiratory tract microbiome

Nasopharyngeal Microbiota, Host Transcriptome and Disease Severity in Children with Respiratory Syncytial Virus Infection – Wouter A.A. de Steenhuijsen Piters – Am J Respir Crit Care Med.

Human reproductive tract microbiome

Detection of DNA viruses in prostate cancer – Vitaly Smelov – Scientific Reports

Human gut microbiome

Effect of probiotic yoghurt on animal-based diet-induced change in gut microbiota: an open, randomised, parallel-group study – T. Odamaki – Beneficial Microbes

Fecal microbiota transplant for Clostridium difficile infection in older adults – William M. Tauxe – Therapeutic Advances in Gastroenterology

Review: Fine-tuning of the mucosal barrier and metabolic systems using the diet-microbial metabolite axis – Motoyoshi Nagai – International Immunopharmacology

Review: Gut Microbiome in CKD: challenges and opportunities – Anitha Nallu – Translational Research

Editorial: Transplanting a Microbial Organ: the Good, the Bad, and the Unknown – Dionysios A. Antonopoulos – mBio

Animal models
A polyphenol-rich fraction obtained from table grapes decreases adiposity, insulin resistance and markers of inflammation and impacts gut microbiota in high-fat-fed mice – Brian Collins – The Journal of Nutritional Biochemistry

Diet-induced obesity, energy metabolism and gut microbiota in C57BL/6J mice fed Western diets based on lean seafood or lean meat mixtures – Jacob Bak Holm – The Journal of Nutritional Biochemistry

Colonic Inflammation Accompanies An Increase of β-Catenin Signaling and Lachnospiraceae/Streptococcaceae in the Hind Gut of High-Fat Diet-Fed Mice – Huawei Zeng – The FASEB Journal

Gut commensal Bacteroides acidifaciens prevents obesity and improves insulin sensitivity in mice – J-Y Yang – Mucosal Immunology

Composition and Predicted Metabolic Capacity of Upper and Lower Airway Microbiota of Healthy Dogs in Relation to the Fecal Microbiota – Aaron C. Ericsson – PLOS ONE

Cultivation and qPCR Detection of Pathogenic and Antibiotic-Resistant Bacterial Establishment in Naive Broiler Houses – J. P. Brooks – Journal of Environmental Quality

Exploring the Goat Rumen Microbiome from Seven Days to Two Years – Lizhi Wang – PLOS ONE

Bacteriocin from epidemic Listeria strains alters the host intestinal microbiota to favor infection – Juan J. Quereda – PNAS

Animal microbiome

Spatial dynamics of the bacterial community structure in the gastrointestinal tract of red kangaroo (Macropus rufus) – Meirong Li – World Journal of Microbiology and Biotechnology

Assessment of Bacterial Communities in Thirteen Species of Laboratory-Cultured Domestic Mites (Acari: Acaridida) – Jan Hubert – Journal of Economic Entomology

Bacterial community in Haemaphysalis ticks of domesticated animals from the Orang Asli communities in Malaysia – Jing-Jing Khoo – Ticks and Tick-borne Diseases

Metabolomics of reef benthic interactions reveals a bioactive lipid involved in coral defence – Robert A. Quinn – Proceedings of the Royal Society B

Taxonomic and functional diversity of the culturable microbiomes of epigeic earthworms and their prospects in agriculture – Arjun Singh – Journal of Basic Microbiology

Methanogen Diversity in Indigenous and Introduced Ruminant Species on the Tibetan Plateau – Xiao Dan Huang – Archaea

Horse Species Symposium abstracts: Journal of Animal Science
Recent advances in the microbiome and physiology of the hindgut of the horse and dog – F. Camargo
Canine intestinal microbiology and metagenomics: From phylogeny to function – B. C. Guard – Journal of Animal Science
The microbiome of the horse hindgut: History and current knowledge – V. Julliand

Plant, root, and soil microbiome

Bacterial diversity and composition in major fresh produce growing soils affected by physiochemical properties and geographic locations – Jincai Ma – Science of the Total Environment

Microbial diversity limits soil heterotrophic respiration and mitigates the respiration response to moisture increase – Fen-Guo Zhang – Soil Biology and Biochemistry

Total and active microbial communities and phoD as affected by phosphate depletion and pH in soil – Sabine A. Ragot – Plant and Soil

Genetically modified WYMV-resistant wheat exerts little influence on rhizosphere microbial communities – Zhenhua Zhang – Applied Soil Ecology

Loss of testate amoeba functional diversity with increasing frost intensity across a continental gradient reduces microbial activity in peatlands – Vincent E.J. Jassey – European Journal of Protistology

Regional-scale analysis of arbuscular mycorrhizal fungi: the case of burgundy vineyards – Marie-Lara Bouffaud – Oeno One

Review: Role of Plant Growth Promoting Rhizobacteria in Agricultural Sustainability—A Review – Pravin Vejan – MDPI Molecules

Chapter: Mycorrhizas in Agroecosystems – Marcela C. Pagano – Recent Advances on Mycorrhizal Fungi

Water and extremophile microbiome

Next-Generation Sequencing Assessment of Eukaryotic Diversity in Oil Sands Tailings Ponds Sediments and Surface Water – Maria Aguilar – The Journal of Eukaryotic Microbiology

Drift in ocean currents impacts intergenerational microbial exposure to temperature – Martina A. Doblin – PNAS

Low Genome Content Diversity of Marine Planktonic Thaumarchaeota – Haiwei Luo – Environmental Microbiology Reports

The distribution, diversity and function of predominant Thermoproteales in high-temperature environments of Yellowstone National Park – Zackary J. Jay – Environmental Microbiology

Multidrug resistance phenotypes are widespread over different bacterial taxonomic groups thriving in surface water – Carlos Narciso-da-Rocha – Science of the Total Environment

A 150-year record of phytoplankton 1 community succession controlled by hydroclimatic variability in a tropical lake – Kweku Afrifa Yamoah – Biogeosciences

Review: Hydrothermal Vents and Methane Seeps: Rethinking the Sphere of Influence – Lisa A. Levin – Frontiers in Marine Science

ReviewMicrobial associations with macrobiota in coastal ecosystems: patterns and implications for nitrogen cycling – Orissa M Moulton – Frontiers in Ecology and the Environment

Book: Biotechnology of Extremophile – Springer

Waste and pollution microbiology

Revealing colonisation and biofilm formation of an adherent coal seam associated microbial community on a coal surface – Silas H.W. Vick – International Journal of Coal Geology

Enhanced Degradation of Diesel in the Rhizosphere of Lupinus luteus after Inoculation with Diesel-Degrading and Plant Growth-Promoting Bacterial Strains – María Balseiro-Romero – Journal of Environmental Quality

Built environment microbiology

Urban Microbiomes and Urban Agriculture: What Are the Connections and Why Should We Care? – Gary M. King – Sowing Seeds in the City

Bioinformatics, transcriptomics, metagenomics

rnaQUAST: a quality assessment tool for de novo transcriptome assemblies – Elena Bushmanova – Bioinformatics

Feature: Microbiology: the road to strain-level identification – Vivien Marx – Nature Methods

Protocol BookData Mining Techniques for the Life Sciences – Springer
Bacterial Genomic Data Analysis in the Next-Generation Sequencing Era – Massimiliano Orsini
Update on Genomic Databases and Resources at the National Center for Biotechnology Information – Tatiana Tatusova
Big Data, Evolution, and Metagenomes: Predicting Disease from Gut Microbiota Codon Usage Profiles – Maja Fabijanić

More microbiology

Riches of phenotype computationally extracted from microbial colonies – Tzu-Yu Liu – PNAS

Microbes in the news

UB’s microbiome hunters. These are exciting times at UB as its work on the human genome and microbiome matures. – Research Foundation for The State University of New York

Video: How Your City Has Its Own Unique Microbiome – Discovery News – YouTube

Wrapping up multiple sclerosis at UCSF – Claire Conway – UC San Francisco

Stalking Cave Bacteria to Make Secret Weapons Against Superbugs: Dr. Naowarat Cheeptham – Sam Grobart – Bloomberg

Seres Therapeutics Announces Achievement of Target Enrollment of SER-109 Phase 2 Study for the Prevention of Recurrent Clostridium difficile Infection – Business Wire

Bacteria use traffic-cop-like mechanism to infect gutWSU scientists discover mechanism critical to pathogens’ success – EurekAlert

Tesla’s Bioweapon Defense Mode can protect you from bacteria, and reduce pollution
Cars. Tesla’s AC unit is available on the Model X and the new Model S – Alphr

Bacteria Hysteria

This odor-fighting, bacteria-killing underwear is made with pure silver – Christian de Looper – Yahoo Digital Trends
Millions of people are drinking mold and bacteria with their coffee. This is how to avoid it! – David Wolfe

Science, publishing and career

Image integrity concerns in papers from a Pfizer lab – Leonid Schneider – For Better Science