June 13, 2016

Malassezia’s in horses’ ears, microbes in carnivorous plant pitchers, meta-analysis of arbuscular mycorrhizal fungi , and the metatranscriptome of an alkaline hot sulfur spring.

Pregnancy and birth

Early settlers – which E. coli strains do you not want at birth? – Thomas Secher – Am J Physiol Gastrointest Liver Physiol

Human gut microbiome

Intestinal Microbiota‐Generated Metabolite Trimethylamine‐N‐Oxide and 5‐Year Mortality Risk in Stable Coronary Artery Disease: The Contributory Role of Intestinal Microbiota in a COURAGE‐Like Patient Cohort – Vichai Senthong – Journal of the American Heart Association

ReviewGut microbiota, diet and obesity-related disorders – the good, the bad and the future challenges – Kevin J. Portune – Molecular Nutrition & Food Research

Animal experiments

Gut Microbiota are Linked to Increased Susceptibility to Hepatic Steatosis in Low Aerobic Capacity Rats Fed an Acute High Fat Diet – Matthew R Panasevich – Am J Physiol Gastrointest Liver Physiol

Animal microbiome

Don’t look a gift horse in the ear: Is Malassezia nana the main species in horses’ ear canal microbiome? – Ana Lúcia Aldrovandi – Brazilian Journal of Microbiology

Plant, root, and soil microbiome

Comparative Study of Bacterial Communities in Nepenthes Pitchers and Their Correlation to Species and Fluid Acidity – Pattanop Kanokratana – Microbial Ecology

Riparian reforestation: are there changes in soil carbon and soil microbial communities? – J.E. Mackay – Science of The Total Environment

Home-field advantage? evidence of local adaptation among plants, soil, and arbuscular mycorrhizal fungi through meta-analysis – Megan A. Rúa – BMC Evolutionary Biology

Associations between soil bacterial community structure and nutrient cycling functions in long-term organic farm soils following cover crop and organic fertilizer amendment – Adria L. Fernandez – Science of The Total Environment

Water and extremophile microbiome

Relationship of bacterial richness to organic degradation rate and sediment age in subseafloor sediment – Emily A. Walsh – Applied and Environmental Microbiology

Analysis of the metatranscriptome of microbial communities of an alkaline hot sulfur spring revealed different gene encoding pathway enzymes associated with energy metabolism – Swetaleena Tripathy – Extremophiles

Temperature effects on net greenhouse gas production and bacterial communities in arctic thaw ponds – Karita Negandhi – FEMS Microbiology Ecology

Differences in the sensitivity of fungi and bacteria to season and invertebrates affect leaf litter decomposition in a Mediterranean stream – Juanita Mora-Gómez – FEMS Microbiology Ecology

Microbes in the news

Living Bacteria Can Now Store Data – George Dvorsky – Gizmodo

Note that the images in this article have no sources, and that the second image is showing mice data instead of human: The Bacteria In Your Gut And Cancer – Jack Hidary – Huffington Post

The pioneering dental laser that blasts away bacteria – and could help millions of Brits eradicate chronic gum disease without the need for antibiotics – Hilary Freeman – Daily Mail

Science, publishing, and career

The Mistrust of Science – Commenceent Address at CalTech – Atul Gawande

June 11, 2016

Microbiome and virome of FMT patient over time, how well do animal models predict natural microbial activities, goats!, Neolithic vs. modern soil, truffles, and a medieval church.

Human gut microbiome

Long-term microbiota and virome in a Zürich patient after fecal transplantation against Clostridium difficile infection – Felix Broecker – Annals of the New York Academy of Sciences

Perspective: Nutrition and the microbiome – Karin Moelling – Annals of the New York Academy of Sciences

Entitled denigrating view of African research, unclear background or IRB approval of volunteers from Africa: Significant pharmacokinetic differences of berberine are attributable to variations in gut microbiota between Africans and Chinese – Raphael N. Alolga – Scientific Reports

Conference report: A Summary of The First HIV Microbiome Workshop 2015 – Brett Williams – AIDS Research and Human Retroviruses

Infection and microbes

No mention of extraction or PCR controls, and most OTUs are shared between samples, so suspicious for contamination. Proceed with caution: High-throughput sequencing of microbial diversity in implant-associated infection – Xin Wang – Infection, Genetics and Evolution

Animal experiments

Metabolomics insights into the modulatory effects of long term low calorie intake in mice – Junfang Wu – Journal of Proteome Research

Perspective: A synthetic ecology perspective: how well does behavior of model organisms in the laboratory predict microbial activities in natural habitats? – Zheng Yu – Frontiers in Microbiology

Animal microbiome

Age and feeding system (supplemental feeding versus grazing) modulates colonic bacterial succession and host mucosal immune maturation in goats – J. Jiao – Journal of Animal Science

Evaluation of 16S rRNA amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers – Phillip R. Myer – Journal of Microbiological Methods

Plant, root, and soil microbiome

A buried Neolithic paddy soil reveals loss of microbial functional diversity after modern rice cultivation – Yong-Guan Zhu – Science Bulletin

Mycorrhizal detection of native and non-native truffles in a historic arboretum and the discovery of a new North American species, Tuber arnoldianum sp. nov. – Rosanne A. Healy – Mycorrhiza

Beneficial native bacteria improve survival and mycorrhization of desert truffle mycorrhizal plants in nursery conditions – Alfonso Navarro-Ródenas – Mycorrhiza

Nutrient limitation drives response of Calamagrostis epigejos to arbuscular mycorrhiza in primary succession – Jana Rydlová – Mycorrhiza
http://link.springer.com/article/10.1007/s00572-016-0712-5

Ectomycorrhizal and saprotrophic fungal diversity are linked to different tree community attributes in a field-based tree experiment – Nhu H. Nguyen – Molecular Ecology

Long-term effect of plastic film mulching and fertilization on bacterial communities in a brown soil revealed by high through-put sequencing – John Farmer – Archives of Agronomy and Soil Science

Resilience of Fungal Communities to Elevated CO2 – Stavros D. Veresoglou – Microbial Ecology

Review: Life in heaps: A review of microbial responses to variable acidity in sulfide mineral bioleaching heaps for metal extraction – D.W. Shiers – Research in Microbiology

Review: Giving back to the community: Microbial mechanisms of plant-soil interactions – Sur Herrera Paredes – Functional Ecology

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

Water and extremophile microbiome

Characterizing and predicting cyanobacterial blooms in an 8-year amplicon sequencing time-course – Nicolas Tromas – bioRxiv

Response of a coastal tropical pelagic microbial community to changing salinity and temperature – Gurpreet Kaur-Kahlon – Inter-Research in Aquatic Microbial Ecology

Bacterial communities in Arctic first-year drift ice during the winter/spring transition – E. Eronen-Rasimus – Environmental Microbiology Reports

Diversity and distribution of prokaryotes within a shallow-water pockmark field – Donato Giovannelli – Frontiers in Microbiology

Mainly about animals: Life in a dark biosphere: a review of circadian physiology in “arrhythmic” environments – Andrew David Beale – Journal of Comparative Physiology B

Site-specific environmental factors control bacterial and viral diversity in stormwater retention ponds – Matthew A. Saxton – Inter-Research in Aquatic Microbial Ecology

Built environment microbiome

Profile of microbial communities on carbonate stones of the medieval church of San Leonardo di Siponto (Italy) by Illumina-based deep sequencing – Guglielmina Chimienti – Applied Microbiology and Biotechnology

Food microbiology

Cascade degradation of organic matters in brewery wastewater using a continuous stirred microbial electrochemical reactor and analysis of microbial communities – Haiman Wang – Scientific Reports

Bioinformatics and computational biology

Advancing microbial sciences by individual-based modelling – Ferdi L. Hellweger – Nature Reviews Microbiology

Microbes in the news

A Portrait of a Building and its External Inhabitants – Makayla Betts – MicroBEnet

Woman meets Winnipeg researchers whose Ebola treatment saved her life – Bill Redekop – Winnipeg Free Press

Tackling healthcare challenges in a changing world: an interview with Professor Jeremy Nicholson – News Medical

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:

Screen Shot 2016-06-10 at 9.31.50 PM.png

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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Screen Shot 2016-06-10 at 9.04.25 PM

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.

Screen Shot 2016-06-10 at 7.52.49 PM.png

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

Screen Shot 2016-06-10 at 7.59.02 PM.png

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

Screen Shot 2016-06-10 at 8.00.08 PM.png

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

Screen Shot 2016-06-10 at 8.03.28 PM

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

Screen Shot 2016-06-10 at 8.01.13 PM.png

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

Screen Shot 2016-06-10 at 8.02.20 PM

 

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

Techniques

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 9, 2016

Salivary microbiome in Behcet’s disease, microbial RNA in human blood, acetate implied in metabolic syndrome, effects of fire retardant on plant–microbe interactions, and a book about the marine microbiome.

Events

ASM Microbe TweetUp: Friday June 17, 11.45-12:30, in the Peer-to-Peer Exchange Zone (in the Exhibition Hall)

Focused meeting: Molecular Biology of Archaea 5, London, UK, 1-3 August 2016

Pregnancy and birth

Infant Early Gut Colonization by Lachnospiraceae: High Frequency of Ruminococcus gnavus – Valeria Sagheddu – Frontiers in Pediatrics

Review: The microbiome during pregnancy and early postnatal life – Josef Neu – Seminars in Fetal and Neonatal Medicine

Review: The human milk microbiome and factors influencing its composition and activity – Carlos Gomez-Gallego – Seminars in Fetal and Neonatal Medicine

Human blood microbiome

Total RNA Sequencing reveals microbial communities in human blood and disease specific effects – Serghei Mangul – bioRxiv

Human mouth microbiome

A Study of the Variation in the Salivary Peptide Profiles of Young Healthy Adults Acquired Using MALDI-TOF MS – Andrei Prodan – PLOS ONE

Sequencing of 16S rRNA reveals a distinct salivary microbiome signature in Behçet’s disease – Patrick Coit – Clinical Immunology

Human gut microbiome

Review: What’s bugging your teen? —The microbiota and adolescent mental health – Karen-Anne McVey Neufeld – Neuroscience & Biobehavioral Reviews

Bio-banking gut microbiome samples – Shankar Bolan – EMBO Reports

Animal experiments

Acetate mediates a microbiome–brain–β-cell axis to promote metabolic syndrome – Rachel J. Perry – Nature

Press: How altered gut microbes cause obesity – Science Daily
Fecal Transplant Shows Gut Microbes Cause Obesity – In Rats, Anyway – Science 2.0

Sex-specific Effects of Arsenic Exposure on the Trajectory and Function of the Gut Microbiome – Liang Chi – Chemical Research in Toxicology

Taxonomic assessment of rumen microbiota using total RNA and targeted amplicon sequencing approaches – Fuyong Li – Frontiers in Microbiology

Environmental filtering decreases with fish development for the assembly of gut microbiota – Qingyun Yan – Environmental Microbiology

Animal microbiome

Bacterial Community Diversity Harboured by Interacting Species – Mikaël Bili – PLOS ONE

Plant, root, and soil microbiome

Cascading effects of fire retardant on plant–microbe interactions, community composition, and invasion – Abigail Marshall – Ecological Applications

Temperature sensitivity of soil microbial communities: An application of macromolecular rate theory to microbial respiration – Charlotte J. Alster – Journal of Geophysical Research

Selection and evaluation of microorganisms for biocontrol of Verticillium dahliae in olive – A Varo – Journal of Applied Microbiology

Influence of plant genotype on the cultivable fungi associated to tomato rhizosphere and roots in different soils – Anna Poli – Fungal Biology

Arbuscular mycorrhizal fungal communities in buffelgrass pasture under intercropping and shading systems in Brazilian semiarid conditions – Karen M.S. Menezes – Agriculture, Ecosystems & Environment

Evolution of High Cellulolytic Activity in Symbiotic Streptomyces through Selection of Expanded Gene Content and Coordinated Gene Expression – Adam J. Book – PLOS Biology

Press: Chemistry lessons from bacteria may improve biofuel production – Science Daily

Review: Streptomyces as a plant’s best friend? – Tom Viaene – FEMS Microbiology Ecology

Water and extremophile microbiome

Light availability regulates the response of algae and heterotrophic bacteria to elevated nutrient levels and warming in a northern boreal peatland – Lily Y. Gu – Freshwater Biology

Metagenomic covariation along densely sampled environmental gradients in the Red Sea – Luke R Thompson – bioRxiv

Microbial community structure of Arctic seawater as revealed by pyrosequencing – Yang Li – Acta Oceanologica Sinica

A snapshot on spatial and vertical distribution of bacterial communities in the eastern Indian Ocean – Jing Wang – Acta Oceanologica Sinica

Pond Crash Forensics: Presumptive identification of pond crash agents by next generation sequencing in replicate raceway mass cultures of Nannochloropsis salina – Laura T. Carney – Algal Research

Detection of antibiotic-resistant bacteria endowed with antimicrobial activity from a freshwater lake and their phylogenetic affiliation – Zothanpuia – PeerJ

Microbial diversity in lake–river ecotone of Poyang Lake, China – Xiaolan Huang – Environmental Earth Sciences

Book: The Marine Microbiome. An Untapped Source of Biodiversity and Biotechnological Potential – Lucal J. Stal, Mariana Silvia Cretoiu – Springer

Food microbiology

Bacterial dynamics and functional analysis of microbial metagenomes during ripening of Dutch-type cheese – Davide Porcellato – International Dairy Journal

Pollution and waste microbiology

Chronic exposure to triclosan sustains microbial community shifts and alters antibiotic resistance gene levels in anaerobic digesters – Daniel Carey – Environ Sci Processes Impacts

Computational models of microbiome research, bioinformatics

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

A new way to publish metagenomics studies – Folker Meyer – BioMed Central

Techniques

RNA-stable isotope probing: from carbon flow within key microbiota to targeted transcriptomes – Tillmann Lueders – Current Opinion in Biotechnology

More microbiology

Centenary of the death of Elie Metchnikoff: A visionary and an outstanding team leader
Jean-Marc Cavaillon – Microbes and Infection

Microbes in the news

Worcester Polytechnic Institute Students Isolate Potentially Novel Soil-Dwelling Viruses – PR Web

Yuck factor may boost hand hygiene compliance: Interview with Ashley Gregory – EurekAlert

Europe orders Italians to cut down olive trees infected with bacteria – Nick Squires – The Telegraph

It’s Not Just Restaurants—Scientists Are Fascinated With Fermented Foods Too – Jane Lear – Take Part

Science, publishing, and career

Differences in incomes of physicians in the United States by race and sex: observational study – Dan P. Ly – British Medical Journal

Press: White male doctors earn 35 percent more than black male doctors – Jennifer Adaeze Okwerekwu – STAT News

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

Bioinformatics

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

Techniques

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

June 6, 2016

Human oral microbiome

Identification of oral bacteria on titanium implant surfaces by 16S rDNA sequencing – Fabiana de Melo – Clinical Oral Implants Research

Subgingival microbiota in individuals with severe chronic periodontitis – Chi-Ying Tsai – Journal of Microbiology, Immunology and Infection

Human gut microbiome

Gut to brain interaction in Autism Spectrum Disorders: a randomized controlled trial on the role of probiotics on clinical, biochemical and neurophysiological parameters – Elisa Santocchi – BMC Psychiatry

Review: Resource conflict and cooperation between human host and gut microbiota: implications for nutrition and health – Helen Wasielewski – Annals of the New York Academy of Sciences

Press: War and peace in the human gut: probing the microbiome -Biodesign

Animal and tissue culture experiments

Adult microbiota-deficient mice have distinct dendritic morphological changes: differential effects in the amygdala and hippocampus – Pauline Luczynski – European Journal of Neuroscience

Exposure to common respiratory bacteria alters the airway epithelial response to subsequent viral infection – Carla Bellinghausen – Respiratory Research

Animal microbiome

Gut microbiota of Busseola fusca (Lepidoptera: Noctuidae) – Maxi Snyman – World Journal of Microbiology and Biotechnology

Plant, root, and soil microbiome

The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages – Shengjing Shi – Ecology Letters

Functional Role of Bacteria from Invasive Phragmites australis in Promotion of Host Growth – M. A. Soares – Microbial Ecology

Design defines the effects of nanoceria at a low dose on soil microbiota and the potentiation of impacts by canola plant – Mohamed Hamidat – Environmental Science & Technology

Water and extremophile microbiome

Taxon interactions control the distributions of cryoconite bacteria colonizing a High Arctic ice cap – Jarishma K. Gokul – Molecular Ecology

Ectomycorrhizal and saprotrophic fungi respond differently to long-term experimentally increased snow depth in the High Arctic – Sunil Mundra – MicrobiologyOpen

Microbial sedimentary imprint on the deep Dead Sea sediment – Camille Thomas – The Depositional Record

Characterization of the cyanobacteria and associated bacterial community from an ephemeral wetland in New Zealand – Nick H. Secker – Journal of Phycology

Abundance of sulfur-degrading bacteria in a benthic bacterial community of shallow sea sediment in the off-Terengganu coast of the South China Sea – Zahar Marziah – MicrobiologyOpen

Pollution and waste microbiology

Responses of bacterial and archaeal communities to nitrate stimulation after oil pollution in mangrove sediment revealed by Illumina sequencing – Lei Wang – Marine Pollution Bulletin

Effects of erythromycin, trimethoprim and clindamycin on attached microbial communities from an effluent dominated prairie stream – M.J. Waiser – Ecotoxicology and Environmental Safety

Metagenomics and bioinformatics

MetaFast: fast reference-free graph-based comparison of shotgun metagenomic data – Vladimir I. Ulyantsev – Bioinformatics

MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses – Vanni Bucci – Genome Biology

Microbes in the news

New Bacterial Research May Help Reduce Excessive Amounts Of Phosphorus In Lakes
Catherine Cabral-Isabedra – Tech Times

About Nicholas Muzyczka, microbiology professor at the University of Florida: Inventor says fame is fine, but best reward is helping others – Anthony Clark – Gainesville.com

Bacteria has potential to clean up oil spills – Zia Lyle – Daily Texan Online

Clif Bars join list of products recalled over listeria concern – Debra Goldschmidt – CNN

Microbes in Space: JPL Researcher Explores Tiny Life – NASA

Jason Tetro aims to rehabilitate microbes’ bad reputation with The Germ Files – Rebecca Tucker – National Post

Science, publishing, and career

Publishing for academic refugeesPaul Ostwald: The Journal of Interrupted Studies – Emma Christie – Oxford Student

Postdoc mysteries: three recent developments raise puzzling uncertainties about postdocs’ present and future lives – Beryl Lieff Benderly – Science