September 22, 2017

Human Microbiome

Microbiome profile of the amniotic fluid as a predictive biomarker of perinatal outcome – Daichi Urushiyama – Scientific Reports

Role of gut microbiota on cardio-metabolic parameters and immunity in coronary artery disease patients with and without type-2 diabetes mellitus – Lidia Sanchez-Alcoholado – Frontiers in Microbiology

Perspective: Linking the gut microbial ecosystem with the environment: does gut health depend on where we live? – Nishat Tasnim – Frontiers in Microbiology

Effect of caloric restriction on gut permeability, inflammation markers, and fecal microbiota in obese women – Beate Ott – Scientific Reports

Perspective: The immunology of the allergy epidemic and the hygiene hypothesis – Bart N Lambrecht – Nature Immunology

Pearls: The microbiome and the hallmarks of cancer – Laura E. Fulbright – PLoS Pathogens

Exploring the salivary microbiome of children stratified by the oral hygiene index – Izumi Mashima – PLoS ONE

 

Built Site Microbiome

Metagenomic characterization of ambulances across the USA – Niamh B. O’Hara – Microbiome (BMC)

 

Food Microbiome

Review: A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies – Yu Cao – Frontiers in Microbiology

Bottled aqua incognita: microbiota assembly and dissolved organic matter diversity in natural mineral waters – Celine C. Lesaulnier – Microbiome (BMC)

 

Pathogen Research

An engineered bispecific DNA-encoded IgG antibody protects against Pseudomonas aeruginosa in a pneumonia challenge model – Ami Patel – Nature Communications

Illusions regarding Helicobacter pylori clinical trials and treatment guidelines – David Y Graham – Gut (BMJ)

 

Beneficial Microbes

Akkermansia muciniphila May Determine the Ameliorating or Aggravating Effects of Chondroitin Sulfate on Osteoarthritis – Qing-Ping Zeng – Frontiers in Microbiology

Minireview: Next-Generation Beneficial Microbes: The Case of Akkermansia muciniphila – Patrice D. Cani – Frontiers in Microbiology

The PGPR Stenotrophomonas maltophilia SBP-9 augments resistance against biotic and abiotic stress in wheat plants – Prabhat N. Jha – Frontiers in Microbiology

 

Beneficial Molecules

pH-dependant antifungal activity of valproic acid against the human fungal pathogen Candida albicans – Julien Chaillot – Frontiers in Microbiology

Dietary teasaponin ameliorates alteration of gut microbiota and cognitive decline in diet-induced obese mice – Sen Wang – Scientific Reports

Mulberry leaf alleviates streptozotocin-induced diabetic rats by attenuating NEFA signaling and modulating intestinal microflora – Yao Sheng – Scientific Reports

 

Microbial Evolution

New Insights into the Diversity of the Genus Faecalibacterium – Leandro Benevides – Frontiers in Microbiology

 

Environmental Microbiology

Insights into microalga and bacteria interactions of selected phycosphere biofilms using metagenomic, transcriptomic and proteomic approaches – Ines Krohn-Molt – Frontiers in Microbiology

 

Bioinformatics, Genomics and Methodologies

Genomic GC-content affects the accuracy of 16S rRNA gene sequencing based microbial profiling due to PCR bias – Martin I. Bahl – Frontiers in Microbiology

Preprint: Optimizing scoring function of dynamic programming of pairwise profile alignment using derivative free neural network – Kazunori D. Yamada – BioRxiv

Improving contig binning of metagenomic data using dS2 oligonucleotide frequency dissimilarity – Ying Wang – BMC Bioinformatics

A Laboratory Methodology for Dual RNA-Sequencing of Bacteria and their Host Cells In Vitro – James W. Marsh – Frontiers in Microbiology

 

Other

Review: A review of the relationship between the gut microbiota and amino acid metabolism – Rui Lin – Amino Acids (Springer)

 

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September 13,2017

Our midweek digest is a treat for wine drinkers- two studies looking at vineyard microbiomes and news of how Nestlé is moving into microbiome research. Lastly, read about an exciting workflow that makes it easier to map the resistome.

General Microbiome

Microbial communities in placentas from term normal pregnancy exhibit spatially variable profiles.

Parnell LA .Scientific Reports

Human gut microbiome

Host-microbe interaction in the gastrointestinal tract.

Parker A.Environmental Microbiology Report

Gut microbiota composition is associated with polypharmacy in elderly hospitalized patients.

Ticinesi A.Scientific Reports

Microbes in Infant Gut Development: Placing Abundance Within Environmental, Clinical and Growth Parameters.

Obermajer T.Scientific Reports

Animal experiments and microbiome

Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models.

Cekanaviciute E, PNAS

The microbiota influences cell death and microglial colonization in the perinatal mouse brain.

Castillo-Ruiz A. Brain, Behaviour, and Immunity

Microbial colonization is required for normal neurobehavioral development in zebrafish.

Phelps D,.Scientific Reports

Biotechnology 

Ozone-cathode microbial desalination cell; An innovative option to bioelectricity generation and water desalination.

Gholizadeh A. Chemosphere.

Plant and soil microbiome

Grape microbiome as a reliable and persistent signature of field origin and environmental conditions in Cannonau wine production.

Mezzasalma V. PLoS One.

Is microbial terroir related to geographic distance between vineyards?

Miura T. Environmental Microbiology Reports

Bacteria utilising plant-derived carbon in the rhizosphere of Triticum aestivum change in different depths of an arable soil.

Uksa M. Environmental Microbiology Reports

Mining the Volatilomes of Plant-Associated Microbiota for New Biocontrol Solutions.

Bailly A. Frontiers in Microbiology

More than 2500 years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis.

Michas A. Microbiome

Lung Microbiome

Functional characterization of the Mycobacterium abscessus genome coupled with condition specific transcriptomics reveals conserved molecular strategies for host adaptation and persistence.

Miranda-CasoLuengo AA.BMC Genomics

Mechanistic insight into the function of the microbiome in lung diseases.

Ubags NDJ. European Respiratory Journal

Antibiotics

A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity.

Ruiz VE.Nature Communications

Resistome

The recent emergence in hospitals of multidrug-resistant community-associated sequence type 1 and spa type t127 methicillin-resistant Staphylococcus aureus investigated by whole-genome sequencing: Implications for screening.

Earls MR. PLoS One

Rapid resistome mapping using nanopore sequencing.

van der Helm E.Nucleic Acids Research  

Network of microbial and antibiotic interactions drive colonization and infection with multidrug-resistant organisms

Wang J. PNAS

News

Nestlé moves into gut microbiome tests.

News- Nature Biotechnology

Protocol

Shotgun metagenomics, from sampling to analysis.

Quince C,Nature Biotechnology

Erratum 

Erratum to: Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey Species.

Hale VL. Microbial Ecology

September 5, 2017

Jobs

Postdoctoral fellow in genomics of uncultured microbial parasites (SciLifeLab, Sweden) via Science Careers

Call for Assistant Professors and Professors (IST Austria, including for Life Sciences) via Science Careers

 

Human Microbiome

Characterization of cervico-vaginal microbiota in women developing persistent high-risk Human Papillomavirus infection – Monica Di Paola – Scientific Reports

Collection of non-meconium stool on fecal occult blood cards is an effective method for fecal microbiota studies in infants – Wendy S.W. Wong – Microbiome (BMC)

Influence of Pregnancy History on the Vaginal Microbiome of Pregnant Women in their First Trimester – Dimitrios Nasioudis – Scientific Reports

Gut microbiome in ADHD and its relation to neural reward anticipation – Esther Aarts – PLoS ONE

A cross-sectional comparative study of gut bacterial community of Indian and Finnish children – Shreyas V. Kumbhare – Scientific Reports

Dysbiosis contributes to chronic constipation development via regulation of serotonin transporter in the intestine – Hailong Cao – Scientific Reports

Review article: the human intestinal virome in health and disease – S. R. Carding – Alimentary Pharmacology and Therapeutics

Review: Organ-specific protection mediated by cooperation between vascular and epithelial barriers – Ilaria Spadoni – Nature Reviews Immunology

Review: Microbiota of chronic diabetic wounds: ecology, impact and potential for innovative healing strategies – Sonia Gonçalves Pereira – Frontiers in Microbiology

Animal Microbiome

Comparative Analysis of the Gut Microbiota Composition between Captive and Wild Forest Musk Deer – Yimeng Li – Frontiers in Microbiology

High-fat diet increases pain behaviors in rats with or without obesity – Zongbin Song – Scientific Reports

Research Highlights: The microbiota maintains oxygen balance in the gut – Irene Vacca – Nature Reviews Microbiology

Studying the Differences of Bacterial Metabolome and Microbiome in the Colon between Landrace and Meihua Piglets – Zhuang Chen – Frontiers in Microbiology

Dietary heme induces gut dysbiosis, worsens colitis and potentiates the development of adenomas in mice – Marco Constante – Frontiers in Microbiology

Antibiotic-induced perturbations in microbial diversity during post-natal development alters amyloid pathology in an aged APPSWE/PS1ΔE9 murine model of Alzheimer’s disease – Myles R. Minter – Scientific Reports

Enrichment of beneficial bacteria in the skin microbiota of bats persisting with white-nose syndrome – Virginie Lemieux-Labonté – Microbiome (BMC)

 

Environmental and Soil Microbiome

Composted Cattle Manure Increases Microbial Activity and Soil Fertility More Than Composted Swine Manure in a Submerged Rice Paddy – Suvendu Das – Frontiers in Microbiology

Fermentative Bacteria Influence the Competition between Denitrifiers and DNRA Bacteria – Eveline M. van den Berg – Frontiers in Microbiology

Beneficial microbes

Lactobacillus casei BL23 produces microvesicles carrying proteins associated with its probiotic effect – Ana P. Domínguez Rubio – Frontiers in Microbiology

Probiotic mixture Golden Bifido prevents neonatal Escherichia coli K1 translocation via enhancing intestinal defense – Qing Zeng – Frontiers in Microbiology

Protective Effect of Akkermansia muciniphila against Immune-mediated Liver Injury in a Mouse Model – Wenrui Wu – Frontiers in Microbiology

 

Methods

Review: Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing – Luisa W. Hugerth – Frontiers in Microbiology

Total rRNA-Seq analysis gives insight into bacterial, fungal, protozoal and archaeal communities in the rumen using an optimized RNA isolation method – Chijioke O. Elekwachi – Frontiers in Microbiology

Non-Microbiology picks

The contribution of Nintendo Wii Fit series in the field of health: a systematic review and meta-analysis – Julien Tripette – PeerJ

August 28, 2017

Events and jobs
Research Specialist – Department of Microbiology – University of Illinois at Urbana-Champaign

Multi-site human microbiome
The nasal and gut microbiome in Parkinson’s disease and idiopathic rapid eye movement sleep behavior disorder – Anna Heintz-Buschart – Movement Disorders

Human gut microbiome
Cross sectional evaluation of the gut-microbiome metabolome axis in an Italian cohort of IBD patients – Maria Laura Santoru – Scientific Reports

Oxalobacter formigenes-associated host features and microbial community structures examined using the American Gut Project – Menghan Liu – Microbiome

Review: Gut Microbiota and Atherosclerosis – Daniel Y. Li – Current Atherosclerosis Reports

Animal experiments
Initial gut microbiota structure affects sensitivity to DSS-induced colitis in a mouse model – Min Li – Science China Life Sciences

Blood as a route of transmission of uterine pathogens from the gut to the uterus in cows – Soo Jin Jeon – Microbiome

Animal microbiome
Review: Health effects of feeding genetically modified (GM) crops to livestock animals: A review – CJ DeVos – Food and Chemical Toxicology
# The DOI does not seem to work yet, so included the Pubmed link

Plant, root, and soil microbiome
Bacterial Community Structure in the Asian Rice Gall Midge Reveals a Varied Microbiome Rich in Proteobacteria – Abhishek Ojha – Scientific Reports

Biodiversity of soil bacteria exposed to sub-lethal concentrations of phosphonium-based ionic liquids: Effects of toxicity and biodegradation – M Sydow – Ecotoxicology and Environmental Safety

Root-induced changes of Zn and Pb dynamics in the rhizosphere of sunflower with different plant growth promoting treatments in a heavily contaminated soil – SM Mousavi – Ecotoxicology and Environmental Safety
# The DOI does not seem to work yet, so included the Pubmed link

Food microbiology
Dietary fibers and protective lactobacilli drive burrata cheese microbiome – Fabio Minervina – Applied Environmental Microbiology

Exploring the microbial origins of p-cresol and its co-occurrence pattern in the Chinese liquor-making process – Hai Du – International Journal of Food Microbiology

Microbial ecology
Molecular determinants of the matrix thickening of a dual-species Pseudomonas aeruginosa and Enterococcus faecalis biofilm – Keehoon Lee – Applied Environmental Microbiology

Probiotics / prebiotics/ antibiotics
Lactolisterin BU, a novel Class II broad spectrum bacteriocin from Lactococcus lactis subsp. lactis bv. diacetylactis BGBU1-4 – Jelena Lozo – Applied Environmental Microbiology

Phages and viruses
Genomic and proteomic analysis of Human herpesvirus 6 reveals distinct clustering of acute versus inherited forms and reannotation of reference strain – Alexander Greninger – bioRxiv

Bioinformatics
EnSVMB: Metagenomics Fragments Classification using Ensemble SVM and BLAST – Yuan Jiang – Scientific Reports

GSimp: A Gibbs sampler based left-censored missing value imputation approach for metabolomics studies – Rumin Wei – bioRxiv

Techniques
A cytometric approach to follow variation and dynamics of the salivary microbiota – Susanna van Gelder – Methods

Microbes in the news
Gut bacteria may play role in fighting MS, Mayo researcher says – Jeremy Olson –
Star Tribune

Trillions of Bacteria in Your Body are Alien to Science, Study Finds – Wall Street Pit

Feeling anxious? Your gut bacteria might be to blame – Partha Nandi – WXYZ Detroit

August 25, 2017

Highlight of the day goes to Anna Karenina principle on microbiomes by J.R. Zaneveld as a Perspective in Nature Microbiology: “When healthy our microbiomes look alike, but when stressed each one of us has our own microbial snowflake”.

Events and jobs

Food Microbiology Microscopist II, EMSL Analytical, Inc. ,Cinnaminson, NJ 

Research Associate, University of Bristol – School of Biochemistry

General microbiome

Perspectives: Stress and stability: applying the Anna Karenina principle to animal microbiomes – Jesse R. Zaneveld – Nature Microbiology

Sugar metabolism of the first thermophilic Planctomycetes Thermogutta terrifontis: comparative genomic and transcriptomic approache – Alexander Elcheninov – bioRxiv

Horizontally Acquired Genes Are Often Shared between Closely Related Bacterial Species – Evgeni Bolotin –  Frontiers in Microbiology

Pregnancy and early life

Early gut mycobiota and mother-offspring transfer – Kasper Schei -Microbiome

Oral Microbiology

Genetic influences on the human oral microbiome – Brittany A. Demmitt – BMC Genomics

 

Human gut microbiome

Beyond gut feelings: how the gut microbiota regulates blood pressure – Francine Z. Marques – Nature Reviews Cardiology

Animal microbiome 

Upper and lower respiratory tract microbiota in horses: bacterial communities associated with health and mild asthma (inflammatory airway disease) and effects of dexamethasone – Stephanie L. Bond – BMC Microbiology

Plant, root, and soil microbiome

Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate-reducing benthic microbial populations – Zainab Abdulrahman Beiruti – Environmental Microbiology

Water and extremophile microbiome

Prey range and genome evolution of Halobacteriovorax marinus predatory bacteria from an estuary – Brett G. Enos – bioRxiv

Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments – Nina Dombrowski –  Microbiome

Prey range and genome evolution of Halobacteriovorax marinus predatory bacteria from an estuary – Brett G. Enos – bioRxiv

Bacteria-induced mixing in natural waters – T. Sommer – Geophysical Research Letters

Food microbiology

Unraveling the correlation between microbiota succession and metabolite changes in traditional Shanxi aged vinegar – Zhiqiang Nie – Scientific Reports

Microbes in the news

Space travel microbes turn urine into polymers

Is The Secret To A Healthier Microbiome Hidden In The Hadza Diet?

IBM: Your Computer Can Help Scientists Study Connection Between Body Bacteria and Autoimmune Diseases

 

August 23, 2017

Human Microbiome

The vaginal microbiome of pregnant women is less rich and diverse, with lower prevalence of Mollicutes, compared to non-pregnant women – Aline C. Freitas – Scientific Reports

The IBD interactome: an integrated view of aetiology, pathogenesis and therapy – Heitor S. P. de Souza – Nature Reviews Gastroenterology & Hepatology

Changes in the intestinal microbiota following the administration of azithromycin in a randomised placebo-controlled trial among infants in south India – Edward P. K. Parker – Scientific Reports

High intake of dairy during energy restriction does not affect energy balance or the intestinal microflora compared to low dairy intake in overweight individuals in a Randomized Controlled Trial – Line Quist Bendtsen – Applied Physiology, Nutrition, and Metabolism

Metabolic and functional paths of lactic acid bacteria in plant foods: get out of the labyrinth – Pasquale Filannino –  Current Opinion in Biotechnology

Differences of lung microbiome in patients with clinically stable and exacerbated bronchiectasis – Min Kwang Byun – PLoS ONE

Precision Nutrition: A Review of Personalized Nutritional Approaches for the Prevention and Management of Metabolic Syndrome – Juan de Toro-Martín – Nutrients

 

Animal Microbiome

Soy Improves Cardiometabolic Health and Cecal Microbiota in Female Low-Fit Rats – Tzu-Wen L. Cross – Scientific Reports

Modulatory influence of segmented filamentous bacteria on transcriptomic response of gnotobiotic mice exposed to TCDD – Robert Stedtfeld – Frontiers in Microbiology

Comparative analysis of the gut microbiota composition between captive and wild forest musk deer – Yimeng Li – Frontiers in Microbiology

Modulation of gut microbiome composition and function in experimental colitis treated with Sulphasalazine – Haihui Zheng – Frontiers in Microbiology

Respiratory Commensal Bacteria Corynebacterium pseudodiphtheriticum Improves Resistance of Infant Mice to Respiratory Syncytial Virus and Streptococcus pneumoniae Superinfection – Paulraj Kanmani – Frontiers in Microbiology

 

Pathogen research

Whole-genome sequencing for national surveillance of Shigella flexneri – Marie Anne Chattaway – Frontiers in Microbiology

SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data – Lennard Epping –  BioRxiv

In Vitro Antibacterial Activity of Unconjugated and Conjugated Bile Salts on Staphylococcus aureus – Thippeswamy H. Sannasiddappa –  Frontiers in Microbiology

Environmental Microbiology

Alleviation of heavy metal stress in plants and remediation of soil by rhizosphere microorganisms – Jitendra Mishra – Frontiers in Microbiology

From surface to deep-sea: Bacterial distribution to polymetallic nodule fields at 4000 m in the Clarion-Clipperton Zone of the Pacific Ocean – Markus V. Lindh – Frontiers in Microbiology

Analysis of Microbial Functions in the Rhizosphere Using a Metabolic-Network Based Framework for Metagenomics Interpretation – Shany Ofaim – Frontiers in Microbiology

 

Bioinformatics

Contradictory Results: Low rate of index hopping on the Illumina HiSeq X platform – Tom van der Valk – BioRxiv

Analyzing contentious relationships and outlier genes in phylogenomics – Joseph F. Walker – BioRxiv

Other

Metabolic Reconstruction and Modeling Microbial Electrosynthesis – Christopher W. Marshall – Scientific Reports

Receptor Uptake Arrays For Vitamin B12, Siderophores And Glycans Shape Bacterial Communities – Steven A. Frank – BioRxiv

Diversity of microbiota associated with symptomatic and non-symptomatic bacterial wilt-diseased banana plants determined using 16S rRNA metagenome sequencing – Nurul Shamsinah Mohd Suhaimi – World Journal of Microbiology and Biotechnology

News

Antarctic mystery microbe could tell us where viruses came from – Michael Marshall – New Scientist

Even the Eye Has a Microbiome – Jeff Lyon – JAMA

The Surprising Things Your Microbiome Reveals About You – Ashley Lewis – Readers Digest

Linking mental health and the gut microbiome – MedicalXpress

 

Non-microbiology picks

How to share data for collaboration – Shannon E Ellis – PeerJ preprints

 

August 22, 2017

Jobs

Postdoctoral Research Fellow in Microbiology/Molecular Ecology : Bremen, Germany (Soil microbial community interactions)

Postdoctoral Training Fellow : London, United Kingdom (M. tuberculosis and immunity)

 

Human Microbiome

Review: Human genetic variation and the gut microbiome in disease – Andrew Brantley Hall – Nature Reviews Genetics

Long-term taxonomic and functional divergence from donor bacterial strains following fecal microbiota transplantation in immunocompromised patients – Eli L. Moss – PLoS ONE

Intestinal colonisation patterns in breastfed and formula-fed infants during the first 12 weeks of life reveal sequential microbiota signatures – Harro M. Timmerman  – Scientific Reports

A prospective analysis of mucosal microbiome-metabonome interactions in colorectal cancer using a combined MAS 1HNMR and metataxonomic strategy – James Kinross – Scientific Reports

Inflammatory colonic innate lymphoid cells are increased during untreated hiv-1 infection and associated with markers of gut dysbiosis and mucosal immune activation – Stephanie Dilon- JAIDS Journal of Acquired Immune Deficiency Syndromes

The Maternal Infant Microbiome: Considerations for Labor and Birth – Alexis Dunn – MCN, American Journal of Maternal Child Nursing

Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome – Francesco Beghini – The ISME Journal

 

Animal Microbiome

The Maturing Development of Gut Microbiota in Commercial Piglets during the Weaning Transition – Limei Chen – Frontiers in Microbiology

Moderate-intensity exercise affects gut microbiome composition and influences cardiac function in myocardial infarction mice – Zuheng Liu – Frontiers in Microbiology  

Unveiling bifidobacterial biogeography across the mammalian branch of the tree of life – Christian Milani – The ISME Journal

 

Probiotics

In Vitro Evaluation of the Impact of the Probiotic E. coli Nissle 1917 on Campylobacter jejuni’s Invasion and Intracellular Survival in Human Colonic Cells – Yosra A. Helmy – Frontiers in Microbiology

 

Food Microbiology

Cell surface properties of Lactococcus lactis reveal milk protein binding specifically evolved in dairy isolates – Mariya Tarazanova – Frontiers in Microbiology

 

Pathogen Research

Metagenomic sequencing to replace semi-quantitative urine culture for detection of urinary tract infections: a proof of concept – Victoria A. Janes – BioRxiv

Burkholderia cenocepacia Infections in Cystic Fibrosis Patients: Drug Resistance and Therapeutic Approaches – Viola C. Scoffone –  Frontiers in Microbiology

 

Environmental Microbiome

Marine Microbial Gene Abundance and Community Composition in Response to Ocean Acidification and Elevated Temperature in Two Contrasting Coastal Marine Sediments – Ashleigh R. Currie – Frontiers in Microbiology

Heat Stress Dictates Microbial Lipid Composition along a Thermal Gradient in Marine Sediments – Miriam Sollich – Frontiers in Microbiology

Actinobacterial Rare Biospheres and Dark Matter Revealed in Habitats of the Chilean Atacama Desert – Hamidah Idris – Scientific Reports

A pivotal role for ocean eddies in the distribution of microbial communities across the Antarctic Circumpolar Current – – PLoS ONE

Microbial community analysis of apple rhizosphere around Bohai Gulf – Jihang Jiang – Scientific Reports

From virus isolation to metagenome generation for investigating viral diversity in deep-sea sediments – Cinzia Corinaldesi – Scientific Reports

 

Bioinformatics

PANINI: Pangenome Neighbor Identification for Bacterial PopulationsKhalil Abudahab  – BioRxiv

 

 

Non-Microbiology picks

The prehistory of biology preprints: a forgotten experiment from the 1960s – Matthew Cobb – PeerJ preprints