Welcome to my weird brain. Here is another visual association I had yesterday, as I was going through a bunch of bioinformatics papers.
To the left: A figure from Bipartite Graphs for Visualization Analysis of Microbiome Data – Karel Sedlar – Evolutionary Bioinformatics
On the right: the wing of a macaw (large, colorful parrot) as found on Birds of a feather – Dan4Kent.
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:
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):
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.
FPh Fig 2 – PeerJ Fig 2 – SciRep Fig 1 – Patent Fig 2
FPh Fig 3 – PeerJ Fig 3 – SciRep Fig 2 – Patent Fig 3
FPh, Fig 4 – PeerJ Fig 4 – SciRep Fig 3 – Patent Fig 4
NA -PeerJ Fig 5 – SciRep Fig 4 – Patent Fig 5
NA -PeerJ Fig 6 – SciRep Fig 5 – Patent Fig 6
NA – PeerJ Fig 7 – SciRep Fig 6 – Patent Fig 7
NA – PeerJ Fig 8 – SciRep Fig 8 – Patent Fig 8
FPh, Fig 5 – PeerJ Fig 10 – SciRep Fig 10 – Patent Fig 10
FPh, Fig 6 – PeerJ Fig 11 – SciRep Fig 11 – Patent Fig 11
FPh, Fig 7 – PeerJ Fig 12 – SciRep Fig 12 – Patent Fig 12
FPh, Fig 8 – PeerJ Fig 13 – SciRep Fig 7 – Patent Fig 13
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
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
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
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
Welcome to my brain. Another weird association I had this morning.
On the left: 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 (Figure 2).
On the right: Bayside21 – 8′ Rainbow Tilt Beach Marked Umbrella – ShadeUSA – Amazon
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
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 published: The Prevalence of Inappropriate Image Duplication in Biomedical Research Publications – Elisabeth M. Bik, Arturo Casadevall, Ferric C. Fang – mBio
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 refugees: Paul 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
A very late Saturday digest, after a fun day at the pool and dinner with family. Germ-free jewel wasps, tooth extraction in horses, dormancy in lakes, subways and urban biomes.
Pregnancy and birth
Review: Fetal, neonatal, and infant microbiome: Perturbations and subsequent effects on brain development and behavior – Rochellys Diaz Heijtz – Seminars in Fetal and Neonatal Medicine
Determination of Bifidobacterium and Lactobacillus in breast milk of healthy women by digital PCR – L. Qian – Beneficial Microbes
Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants – Tali Raveh-Sadka – The ISME Journal
Human gut microbiome
Capturing One of the Human Gut Microbiome’s Most Wanted: Reconstructing the Genome of a Novel Butyrate-Producing, Clostridial Scavenger from Metagenomic Sequence Data – Patricio Jeraldo – Frontiers in Microbiology
Identification, recovery, and refinement of hitherto undescribed population-level genomes from the human gastrointestinal tract – Cedric C. Laczny – Frontiers in Microbiology
Cryptic functional variation in the human gut microbiome – Patrick H Bradley – bioRxiv Preprint
Review: The gut microbiome in human immunodeficiency virus infection – Gili Zilberman-Schapira – BMC Medicine
Review: The Gut Microbiome and Obesity – George Kunnackal John – Current Oncology Reports
Animal experiments
An optimized approach to germ-free rearing in the jewel wasp Nasonia – J. Dylan Shropshire – PeerJ Preprints
Bacteraemia before, during and after tooth extraction in horses in the absence of antimicrobial administration – I. Kern – Equine Veterinary Journal
Effects of Diets Supplemented with Ensiled Mulberry Leaves and Sun-Dried Mulberry Fruit Pomace on the Ruminal Bacterial and Archaeal Community Composition of Finishing Steers – Yuhong Niu – PLOS ONE
Uncovering the composition of microbial community structure and metagenomics among three gut locations in pigs with distinct fatness – Hui Yang – Scientific Reports
Animal microbiome
Gut microbial communities associated with the molting stages of the giant freshwater prawn Macrobrachium rosenbergii – Eleni Mente
DGGE: A comparison of microbial profiles of different regions of the equine hindgut –
K. Fliegerova – Livestock Science
Diversity and composition of cultivable gut bacteria in an endemic island bird and its mainland sister species – Elisa Lobato – Symbiosis
Bacterial Community Diversity Harboured by Interacting Species – Mikaël Bili – PLOS ONE
Plant, root, and soil microbiome
Structure of Fungal Communities in Sub-Irrigated Agricultural Soil from Cerrado Floodplains – Elainy Cristina A. M. Oliveira – Diversity
Phylogenetic and multivariate analyses to determine the effect of agricultural land-use intensification and soil physico-chemical properties on N-cycling microbial communities in drained Mediterranean peaty soils – Valentina Ciccolini – Biology and Fertility of Soils
The impact of pasture systems on soil microbial biomass and community-level physiological profiles – Francisco Marques Cardozo Junior – Land Degradation & Development
Effect of Heavy Metals Pollution on Soil Microbial Diversity and Bermudagrass Genetic Variation – Yan Xie – Frontiers in Plant Science
Isolation, identification and oenological characterization of non-Saccharomyces yeasts in a Mediterranean island – G. Polizzotto – Letters in Applied Microbiology
Water and extremophile microbiome
Diversity and distribution of cultured endolichenic fungi in the Ny-Ålesund Region, Svalbard (High Arctic) – Tao Zhang – Extremophiles
Bacterial dormancy is more prevalent in freshwater than hypersaline lakes – Zachary T. Aanderud – Frontiers in Microbiology
Changes in the water quality and bacterial community composition of an alkaline and saline oxbow lake used for temporary reservoir of geothermal waters – Andrea K. Borsodi – Environmental Science and Pollution Research
Responses of aquatic bacteria to terrestrial runoff: effects on community structure and key taxonomic groups – Huong T. Le – Frontiers in Microbiology
Metagenomics accelerates species discovery and unravel great biodiversity of benthic invertebrates in marine sediments in Campos basin, Brazil – Milena Marcela D P Schettini – PeerJ Preprint
Built environment microbiome
Microbial communities in dairy processing environment floor-drains are dominated by product-associated bacteria and yeasts – Kerstin Schön – Food Control
The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report – The MetaSUB International Consortium – Microbiome
Bioinformatics and metagenomics
The Pepsi Challenge, Metagenomics style? COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment, and paired-end read LinkAge – Yang Young Lu – Bioinformatics
Microbial Ecology
A stable genetic polymorphism underpinning microbial syntrophy – Tobias Großkopf – The ISME Journal
Microbes in the news
Two Stanford microbiology and immunology professors elected to National Academy of Sciences – Stanford Medicine
Crowds of crows spread C. jejuni: Are humans vulnerable? – EurekAlert
Antimicrobial Kills E. Coli Within 30 Seconds – Greg Watry – RD Magazine
Detlef Weigel (@PlantEvolution) attended me on Twitter to a nice #LabStockPhotoFail in the New York Times – who should know better than to blindly use stock photos with incorrect labels. His tweet included a screenshot of the New York Times article, in which an image of a protein gel is used to portray a DNA sequence.
The source of the stock photo was listed as Science Source, which describes themselves as “The best in stock photography, specializing in Science, Medical and Nature images and video”. Not a site where you would expect to see this:
Note: the “DNA gel” photo has been quickly replaced as of today in both the New York Times article as well as on the Science Source website.
Here is a link to the New York Times article as it appeared yesterday, as archived by the WayBack Machine on Archive.org.
Microbiome Digest - Bik's Picks 