Category Archives: Fungi

December 7, 2016

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Microbiota of migratory birds, blue fungus living in snow, migrating from SSU rRNAs to metagenomics.

Jobs

Awesome job at awesome institute: Postdoctoral Research Fellow, Microbiology – California Academy of Sciences

Human gut microbiome

Special issue of Trends in Food Science & Technology; several papers have appeared here before but worth checking out: Unravelling the role of the gut microbiome in energy balance and brain development and function: the European project MyNewGut

Review: Homeostasis of the Gut Barrier and Potential Biomarkers – Jerry M Wells – American Journal of Physiology, Gastrointestinal and Liver Physiology

Review: Challenges in simulating the human gut for understanding the role of the microbiota in obesity – M. Aguirre – Beneficial Microbes

Animal models

Integrated Role of Bifidobacterium animalis subsp. lactis Supplementation in Gut Microbiota, Immunity, and Metabolism of Infant Rhesus Monkeys – Xuan He – mSystems

Review: Dissecting the interplay between intestinal microbiota and host immunity in health and disease: Lessons learned from germfree and gnotobiotic animal models – Ulrike Fiebiger – European Journal of Microbiology and Immunology

Animal microbiome

* Changes in gut microbiota of migratory passerines during stopover after crossing an ecological barrier – William B. Lewis – The Auk

Plant, root, and soil microbiome

* Microbial Community Structure and Function of Soil following Ecosystem Conversion from Native Forests to Teak Plantation Forests – Vidya De Gannes – Frontiers in Microbiology

Drought tolerance of bioenergy grass Saccharum spontaneum L. enhanced by arbuscular mycorrhizae – P.P. Mirshad – Rhizosphere

Perspective: Microbiome selection could spur next-generation plant breeding strategies – Murali Gopal – Frontiers in Microbiology

Water and extremophile microbiome

Siderophore-based microbial adaptations to iron scarcity across the eastern Pacific Ocean – Rene M. Boiteau – PNAS

Phylogenetic diversity of microbial communities of the Posolsk Bank bottom sediments, Lake Baikal – S. M. Chernitsyna – Microbiology

Dampened copepod-mediated trophic cascades in a microzooplankton-dominated microbial food web: A mesocosm study – Bernadette Pree – Limnology and Oceanography

* Antarctomyces pellizariae sp. nov., a new, endemic, blue, snow resident psychrophilic ascomycete fungus from Antarctica – Graciéle C. A. de Menezes – Extremophiles

Temporal variability of bacterial communities in cryoconite on an Alpine glacier – Andrea Franzetti – Environmental Microbiology Reports

Intraclade Heterogeneity in Nitrogen Utilization by Marine Prokaryotes Revealed Using Stable Isotope Probing Coupled with Tag Sequencing (Tag-SIP) – Michael Morando – Frontiers in Microbiology

Pollution microbiology

Effect of metal concentration on the microbial community in acid mine drainage of a polysulfide ore deposit – V. V. Kadnikov – Microbiology

Metagenomics and bioinformatics (viruses too)

MEGARes: an antimicrobial resistance database for high throughput sequencing – Steven M. Lakin – Nucleic Acids Research

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center – Alice R. Wattam – Nucleic Acids Research

Alignment-free d2* oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences – Nathan A. Ahlgren – Nucleic Acids Research

*  Crystal Ball: Migrating SSU rRNA gene surveys to the metagenomics era – Josh D. Neufeld – Environmental Microbiology Reports

Techniques

DNA extraction from benthic Cyanobacteria: comparative assessment and optimization – V. Gaget – Journal of Applied Microbiology

Microbial ecology

Microbial Community Coalescence for Microbiome Engineering – Matthias C. Rillig – Frontiers in Microbiology

More microbiology

How to Define Pathogenicity, Health, and Disease? – Mauno Vihinen – Human Mutation-Variation, Informatics, and Disease

Crystal Ball: Accessories make the microbe – Lisa Y. Stein – Environmental Microbiology Reports

Validating Regulatory Predictions from Diverse Bacteria with Mutant Fitness Data – Shiori Sagawa – bioRxiv

Microbes in the news

With my former Stanford co-worker Fiona Strouts: New farmers’ market baker knows art, science of bread-making. Stanford fellow brings baking know-how to Portola Valley farmers’ market – Dave Boyce – Mountain View Voice

New Mechanism to Control Human Viral Infections Discovered – Sean Nealon – University of California Riverside

Uterine microbiota play a key role in implantation and pregnancy success in in vitro fertilization – EurekAlert (see digest October 12)

Understanding microbiome impact on pig health – National Hog Farmer

Syphilis is coming back – Juha Wahlstedt – Clinical Laboratory Blogspot

November 25, 2016

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Human multisite microbiome (of dead bodies)

Thesis: Understanding the relationship between the human microbiome and urban decay/recovery among autopsied adults in Detroit, Michigan – Amanda T. Rzotkiewicz – Michigan State University

Human oral microbiome

The autoimmunity–oral microbiome connection – NG Nikitakis – Oral Diseases

Human reproductive and urinary tract microbiome

Potential contribution of the uterine microbiome in the development of endometrial cancer – Marina R. S. Walther-António – Genome Medicine

Proinflammatory Cytokines as Regulators of Vaginal Microbiota – E. A. Kremleva – Bulletin of Experimental Biology and Medicine

Seven Bacteriophages Isolated from the Female Urinary Microbiota – Kema Malkia – Genome Announcements

Human gut microbiome

Altered intestinal microbiota–host mitochondria crosstalk in new onset Crohn’s disease – Walid Mottawea – Scientific Reports

Metagenomics of two severe foodborne outbreaks provides diagnostic signatures and signs of co-infection not attainable by traditional methods – Andrew D. Huang – Applied and Environmental Microbiology

Review: Gut Microbiota and Autism: Key Concepts and Findings – Helen T. Din – Journal of Autism and Developmental Disorders

Review: Intestinal Microbiota as an Alternative Therapeutic Target for Epilepsy – Jiaying Wu – Canadian Journal of Infectious Diseases and Medical Microbiology

Review: Irritable Bowel Syndrome: A gut microbiota-related disorder? – Yogesh Bhattarai – American Journal of Physiology – Gastrointestinal and Liver Physiology

Review: Gut Microbiota, Bacterial Translocation, and Interactions with Diet: Pathophysiological Links between Major Depressive Disorder and Non-Communicable Medical Comorbidities – Slyepchenko A. – Psychotherapy and Psychosomatics

Review: Microbiome, metabolites and host immunity – Maayan Levy – Current Opinion in Microbiology

Animal and in vitro models

* Persistent microbiome alterations modulate the rate of post-dieting weight regain – Christoph A. Thaiss – Nature

Press: Yo-yo weight gain driven by gut bacteria’s ‘memory’ of obesity, says study – Hannah Devlin – The Guardian
Breakthrough in Dieting Science: Gut Bacteria Are Behind Relapsing Obesity – Ido Efrati and Ruth Schuster – Haaretz

Effects of a gut pathobiont in a gnotobiotic mouse model of childhood undernutrition – Vitas E. Wagner – Science Translational Medicine

Antibiotics impair murine hematopoiesis by depleting intestinal microbiota – Kamilla S. Josefsdottir – Blood

Pre- and post-weaning diet alters the faecal metagenome in the cat with differences vitamin and carbohydrate metabolism gene abundances – Wayne Young – Scientific Reports

Mucosa-associated biohydrogenating microbes protect the simulated colon microbiome from stress associated with high concentrations of poly-unsaturated fat – Rosemarie De Weirdt – Environmental Microbiology

Differential fecal microbiota are retained in broiler chicken lines divergently selected for fatness traits – Qiangchuan Hou – Scientific Reports

Evolutionary biologic changes of gut microbiota in an ‘adenoma-carcinoma sequence’ mouse colorectal cancer model induced by 1, 2-Dimethylhydrazine – Teng Sun – Oncotarget

Mini review: All Together Now: Experimental Multispecies Biofilm Model Systems – Chuan Hao Tan – Environmental Microbiology

Animal microbiome

The stable microbiome of inter and sub-tidal anemone species under increasing pCO2 – Erinn M. Muller – Scientific Reports

An Enrichment of CRISPR and Other Defense-Related Features in Marine Sponge-Associated Microbial Metagenomes – Hannes Horn – Frontiers in Microbiology

Plant, root, and soil microbiome

Soil Bacterial Community Response to Short-Term Manipulation of the Nitrogen Deposition Form and Dose in a Chinese Fir Plantation in Southern China – Caixia Liu – Water, Air, & Soil Pollution

Microbial community composition but not diversity changes along succession in arctic sand dunes – Anbu Poosakkannu – Environmental Microbiology

Soil-covered strategy for ecological restoration alters the bacterial community structure and predictive energy metabolic functions in mine tailings profiles – Yang Li – Applied Microbiology and Biotechnology

Contrasting effects of two mammalian soil engineers on microbial communities – David J. Eldridge – Austral Ecology

* Habitat-driven variation in mycorrhizal communities in the terrestrial orchid genus Dactylorhiza – Hans Jacquemyn – Scientific Reports

 * Are there keystone mycorrhizal fungi associated to tropical epiphytic orchids? – Stefania Cevallos – Mycorrhiza

Water and extremophile microbiome

Stromatolites from the Aptian Crato Formation, a hypersaline lake system in the Araripe Basin, northeastern Brazil – Lucas Veríssimo Warren – Facies

Diversity, abundance, and possible sources of fecal bacteria in the Yangtze River – Haohao Sun – Applied Microbiology and Biotechnology

Climate-related changes of soil characteristics affect bacterial community composition and function of high altitude and latitude lakes – Carina Rofner – Global Change Biology

Viruses and phages

Ultrastructure and Viral Metagenome of Bacteriophages from an Anaerobic Methane Oxidizing Methylomirabilis Bioreactor Enrichment Culture – Lavinia Gambelli – Frontiers in Microbiology

Seven Bacteriophages Isolated from the Female Urinary Microbiota – Kema Malkia – Genome Announcements

Metabolomics

The role of metabolism (and the microbiome) in defining the clinical efficacy of dietary flavonoids – Aedín Cassidy – The American Journal of Clinical Nutrition

Metagenomics and bioinformatics

Alignment-free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains – Weinan Liao – Scientific Reports

Techniques

ITS all right mama: investigating the formation of chimeric sequences in the ITS2 region by DNA metabarcoding analyses of fungal mock communities of different complexities –
Anders Bjørnsgaard Aas – Molecular Ecology Resources

Microbes in the news

Stockholmers’ poop wanted in fight against drug-resistant bacteria – RT

The modern microbiome: Are we undoing evolution? – Maria Gloria Dominguez-Bello – ASM Cultures

PhD student finds surprising secret to detecting staph infections earlier – Breanne Grady – USC News

November 22, 2016

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Vaginal Mirobiome in PPROM, Prevotella copri and rheumatoid arthritis, mice transplanted with stool from lean or obese humans, archaea in a pond.

Pregnancy and early life

High Diversity and Variability in the Vaginal Microbiome in Women following Preterm Premature Rupture of Membranes (PPROM): A Prospective Cohort Study – Teenus Paramel Jayaprakash – PLOS ONE

Human oral microbiome

Review: The oral microbiome – an update for oral healthcare professionals – M. Kilian – British Dental Journal

Human gut microbiome

Chronic opioid use is associated with altered gut microbiota and predicts readmissions in patients with cirrhosis – C. Acharya – Alimentary Pharmacology and Therapeutics

In vitro fermentation of B-GOS: Impact on faecal bacterial populations and metabolic activity in autistic and non-autistic children – Roberta Grimaldi – FEMS Microbial Ecology

Evidence for Immune Relevance of Prevotella copri, a Gut Microbe, in Patients with Rheumatoid Arthritis – Annalisa Pianta – Arthitis & Rheumatology

Review: Human gut microbiota: the links with dementia development – Rashad Alkasir – Protein & Cell

Review: Gut hormones and gut microbiota: implications for kidney function and hypertensionGut hormones and gut microbiota: implications for kidney function and hypertension – Baris Afsar – Journal of the American Society of Hypertension

Review: Dysbiosis in the intensive care unit: Microbiome science coming to the bedside – Georgios D Kitsios – Journal of Critical Care

Review: Interactions between gut microbes and host cells control gut barrier and metabolism – P D Cani – International Journal of Obesity Supplements

Review: Life history and eco-evolutionary dynamics in light of the gut microbiota – Emilie Macke – Oikos

Animal experiments

Environmental spread of microbes impacts the development of metabolic phenotypes in mice transplanted with microbial communities from humans – Li Zhang – ISME Journal

Gut bacteria affect our metabolism – Science Daily

Animal microbiome

Gut microbiota of dung beetles correspond to dietary specializations of adults and larvae
– Shantanu P. Shukla – Molecular Ecology

Thesis: Characterization of the juvenile green turtle (Chelonia mydas) microbiome associated with the ontogenic shift from pelagic habitats to inshore resident areas – James T. Price – Purdue University

Tick microbiome and pathogen acquisition altered by host blood meal – Andrea Swei – The ISME Journal

Plant, root, and soil microbiome

Investigation of Endophytic Bacterial Community in Supposedly Axenic Cultures of Pineapple and Orchids with Evidence on Abundant Intracellular Bacteria – Natalia Pimentel Esposito-Polesi – Current Microbiology

Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest – Witoon Purahong – Scientific Reports

High-methionine soybean has no adverse effect on functional diversity of rhizosphere microorganisms -J.G. Liang – Plant Soil Environment

Illumina sequencing-based community analysis of bacteria associated with different bryophytes collected from Tibet, China – Jing Yan Tang – BMC Microbiology
https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-016-0892-3
Networks Depicting the Fine-Scale Co-Occurrences of Fungi in Soil Horizons – Hirokazu Toju – PLOS ONE

Isolation and Identification of Keratinolytic Bacteria that Exhibit Feather-degrading Potentials – F. O. Iruolaje – Journal of Advances in Biology & Biotechnology

Water and extremophile microbiome

Cryo-protective effect of an ice-binding protein derived from Antarctic bacteria – Marco Mangiagalli – The FEBS Journal

Unusually High Archaeal Diversity in a Crystallizer Pond, Pomorie Salterns, Bulgaria, Revealed by Phylogenetic Analysis – Margarita Kambourova – Archaea

Polymetallic nodules, sediments, and deep waters in the equatorial North Pacific exhibit highly diverse and distinct bacterial, archaeal, and microeukaryotic communities – Christine N. Shulse – Microbiology Open

Conference abstract: Defining the boarders of extreme life: The study of microbial communities and their settings gives insights into Mars analogue life within the MASE project – A Perras – 16th International Symposium on Microbial Ecology

Pollution microbiology

Influence of plantation on microbial community in porous concrete treating polluted surface water – Yan Long – International Biodeterioration & Biodegradation

Food microbiology

Study of the bacterial diversity of foods: PCR-DGGE versus LH-PCR – Cristiana Garofalo – International Journal of Food Microbiology

Viruses and phages

Viral coinfection is shaped by host ecology and virus-virus interactions across diverse microbial taxa and environments – Samuel L Diaz-Munoz – bioRxiv

More microbiology

Uncovering new drugs and targets – Andrea Du Toit – Nature Reviews Microbiology

Microbiota under pressure – Andrea Aguilar – Nature Reviews Nephrology

Microbes in the news

‘Bacteria beaters’ win Longitude Prize Discovery Award – Shan Ross – The Scotsman

Bacteria for bio-toilets by February 15 – The Times of India

Your Office Has a Microbiome, and It Might Make You Sick – Zoe Schlanger – Wired

Tomato plants are more resistant against nematodes when colonized by a fungus – Farming Futures

Scientists use bacteria to map out NZ. A team of scientists growing bacteria in the shape of New Zealand have caught the attention of their colleagues across the globe – News Australia

The cover image is a map of New Zealand drawn with pyoverdine-producing P. aeruginosa cells in an ocean of indigoidine-synthesizing E. coli. – Cell Chemical Biology

Science, publishing, and career

Citizen science: The people behind the data – Mary Goodchild – NERC Planet Earth

November 21, 2016

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Why is the human vaginal microbiome unique, multiple sclerosis, fiber-deprived gut microbes eating mucus, vertical structure of the phyllospere, cave microbiome, resistome.

Pregnancy and early life

Associations between changes in the maternal gut microbiome and differentially methylated regions of diabetes-associated genes in fetuses: A pilot study from a birth cohort study – Kaori Tachibana – Journal of Diabetes Investigation

Human vaginal microbiome

Lactobacilli Dominance and Vaginal pH: Why is the Human Vaginal Microbiome Unique? – Elizabeth A. Miller – Frontiers in Microbiology

Human gut microbiome

Prevalence of Small Intestinal Bacterial Overgrowth in Multiple Sclerosis: a Case-Control Study from China – Yongbo Zhang – Journal of Neuroimmunology

MyNewGut: Insulin resistance as key factor for linking modulation of gut microbiome to health claims and dietary recommendations to tackle obesity – Stoffer Loman -Trends in Food Science & Technology

Review: The Multibiome: The Intestinal Ecosystem’s Influence on Immune Homeostasis, Health, and Disease – Heather A Filyk – EBioMedicine

Review: Microbiome and nutrition in autism spectrum disorder: current knowledge and research needs – Kirsten Berding – Nutrition Reviews

Review: Th Role of Short-Chain Fatty Acids in Kidney Injury Induced by Gut-derived Inflammatory Response – Wei Huang – Metabolism

Review: Role of Gastrointestinal Microbiota on Kidney Injury and the Obese Condition – Keerati Wanchai – The American Journal of the Medical Sciences

Animal and in vitro experiments

A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility – Mahesh S. Desai – Cell
Editorial: Veggies and Intact Grains a Day Keep the Pathogens Away – Francesca S. Gazzaniga – Cell
Press: High-fiber diet keeps gut microbes from eating the colon’s lining, protects against infection, animal study shows – Science Daily

Coevolutionary dynamics between a defensive microbe and a pathogen driven by fluctuating selection – Suzanne A. Ford – Molecular Ecology

Gut microbiota in Drosophila melanogaster interacts with Wolbachia but does not contribute to Wolbachia-mediated antiviral protection – Yixin H. Ye – Journal of Invertebrate Pathology

Modulation of the cytokine profile in Caco-2 cells by faecal lactobacilli and bifidobacteria from individuals with distinct dietary habits – Diomira Luongo – Cytokine

An Alteration in the Cecal Microbiota Composition by Feeding of 1-Kestose Results in a Marked Increase in the Cecal Butyrate Content in Rats – Takumi Tochio – PLOS ONE

Animal microbiome

Proteome data on the microbial microbiome of grasshopper feces – Nico Jehmlich – Data in Brief

Plant, root, and soil microbiome

Vertical Structure of Phyllosphere Fungal Communities in a Tropical Forest in Thailand Uncovered by High-Throughput Sequencing – Ayako Izuno – PLOS ONE

Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities – Rafal Zgadzaj – PNAS

Press: Nitrogen-fixing symbiosis is crucial for legume plant microbiome assembly – EurekAlert

Influence of salt tolerant Trichoderma spp. on growth of maize (Zea mays) under different salinity conditions – Krishna Kumar – Journal of Basic Microbiology

Review: Recent changes to the classification of symbiotic, nitrogen-fixing, legume-associating bacteria: a review – Abdelaal Shamseldin – Symbiosis

Review: Forest microbiome: diversity, complexity and dynamics – Petr Baldrian – FEMS Microbiology Reviews

Review: The cave microbiome as a source for drug discovery: reality or pipe dream? – Soumya Ghosh – Biochemical Pharmacology

Extremophile microbiome

Opinion: Colonization of Black Smokers by Hyperthermophilic Microorganisms – Reinhard Wirth – Trends in Microbiology

Food microbiology

Biofilms formed by microbiota recovered from fresh produce: Bacterial biodiversity, and inactivation by benzalkonium chloride and enterocin AS-48 – Mª José Grande Burgos – LWT – Food Science and Technology

Metabolomics

Comparative in silico analysis of butyrate production pathways in gut commensals and pathogens – Swadha Anand – Frontiers in Microbiology

Resistome

Prevalence of antibiotic resistance genes among human gut-derived bifidobacteria – Sabrina Duranti – Applied and Environmental Microbiology

Review: Genomic and metagenomic technologies to explore the antibiotic resistance mobilome
– José L. Martínez – Annals of the New York Academy of Sciences

Microbes in the news

I got my gut sequenced – and found out I need to go to the dentist – Liam Mannix – Sydney Morning Herald

Bighorn sheep transfer OK’d despite concerns about disease – Brett French – Missoulian
http://missoulian.com/news/state-and-regional/bighorn-sheep-transfer-ok-d-despite-

High-Fat Diets Alter Gut Microbiota, Leading to Increased Choroidal Neovascularization – Dava Stewart – HCP Live

Student scientists engineer bacteria to break down plastic, hope to help clean Baltimore harbor – Scott Dance – The Baltimore Sun

Soil bacteria helps protect rice plants from arsenic and fungus. ‘Cocktail’ of soil bacteria can protect rice plants from deadly forces – Science Daily
Bacteria Might Be Able To Help Rice Affected By Fungus – Rodney Rafols – iTechPost

November 7, 2015

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Colon cancer tumor location and Fusobacterium nucleatum abundance, eczema in infants, fungi in Crohn’s disease, pH 4 in Yellowstone.

Pregnancy and early life

Altered Gut Microbiota Composition Associated with Eczema in Infants – Huajun Zheng – PLOS ONE

Predominant Lactobacillus species types of vaginal microbiota in pregnant Korean women: quantification of the five Lactobacillus species and two anaerobes – Jeong Hyun Kim – The Journal of Maternal-Fetal & Neonatal Medicine

Human respiratory microbiome

The endotracheal tube microbiome associated with Pseudomonas aeruginosa or Staphylococcus epidermidis – An Hotterbeekx – Scientific Reports

Human gut microbiome

Fungal Microbiota Profile in Newly-diagnosed Treatment-naïve Children with Crohn disease – Mohammad El Mouzan – Journal of Crohn’s and Colitis

Analysis of the Duodenal Microbiome in Autistic Individuals: Association with Carbohydrate Digestion – Kushak, Rafail I. – Journal of Pediatric Gastroenterology and Nutrition

Fusobacterium nucleatum in Colorectal Carcinoma Tissue According to Tumor Location – Kosuke Mima – Clinical and Translational Gastroenterology

Short chain fatty acids and gut microbiota differ between patients with Parkinson’s disease and age-matched controls – Marcus M. Unger – Parkinsonism & Related Disorders

Impact of Cystic Fibrosis Disease on Archaea and Bacteria Composition of Gut Microbiota  – Francesco Miragoli – FEMS Microbiology Ecology

Title is confusing; “No change in mucosal gut Mycobiome” would have been more clear. No Change in the Mucosal Gut Microbiome is Associated With Celiac Disease-Specific Microbiome Alteration in Adult Patients – Valeria D’Argenio – American Journal of Gastroenterology

Assessing the Airway Microbiota in Cystic Fibrosis – Jordana E. Hoppe – Clinical Microbiology Newsletter

Review: Role of vitamin D on gut microbiota in cystic fibrosis – Mansi Kanhere – The Journal of Steroid Biochemistry and Molecular Biology

Review: Nutrition and the Gut Microbiome in the Elderly – Nuria Salazar – Gut Microbes

Addendum: Support for the Microgenderome Invites Enquiry into Sex Differences – Amy Wallis – Gut Microbes

Animal models

Genomic Variants Associated with Resistance to High Fat Diet Induced Obesity in a Primate Model – R. Alan Harris – Scientific Reports

Mice Fed a High-Fat Diet Supplemented with Resistant Starch Display Marked Shifts in the Liver Metabolome Concurrent with Altered Gut Bacteria – Dorothy A Kieffer – Journal of Nutrition

Animal microbiome

Identifying bacterial predictors of honey bee health – Giles E. Budge – Journal of Invertebrate Pathology

Plant, root, and soil microbiome

Over-winter dynamics of soil bacterial denitrifiers and nitrite ammonifiers influenced by crop residues with different carbon to nitrogen ratios – Enrico Tatti – Applied Soil Ecology

Bacterial and fungal community structure and diversity in a mining region under long-term metal exposure revealed by metagenomics sequencing – Ramya Narendrula-Kotha – Ecological Genetics and Genomics

Conversion of grassland to arable decreases microbial diversity and alters community composition – Katherine E. French – Applied Soil Ecology

Water and extremophile microbiome

Differences in Bacterial Diversity and Communities Between Glacial Snow and Glacial Soil on the Chongce Ice Cap, West Kunlun Mountains – Guang Li Yan – Scientific Reports

Microbial community analysis of pH 4 thermal springs in Yellowstone National Park – Xiaoben Jiang – Extremophiles

Food microbiology

Microbiota of high-pressure-processed Serrano ham investigated by culture-dependent and culture-independent methods – N. Martínez-Onandia – International Journal of Food Microbiology

Applicability of commercial phage-based products against Listeria monocytogenes for improvement of food safety in Spanish dry-cured ham and food contact surfaces – Diana Gutiérrez – Food Control

Pollution and waste microbiology

Limited Bacterial Diversity within a Treatment Plant Receiving Antibiotic-Containing Waste from Bulk Drug Production – Nachiket P. Marathe – PLOS ONE

Microbes in the news

Costa Rican ants might have the secret to better antibiotics – L. Arias – TicoTimes

Waterfowl Worry: Recurring disease kills loons, other birds – Washington Times

STEM Gets Marvelous for a Local Student – how the microbes on the scalp could impact the hair growth – NCTV17.com

Best-selling cleanser recalled over dangerous levels of bacteria. Liz Earle’s ‘Cleanse & Polish Hot Cloth Cleanser’ found to contain potentially dangerous bacteria – Ben Kentish – Interdependent

Microbes and the market

APC Microbiome Institute: Alimentary discoveries produce a gut reaction among investors – Companies aim to exploit one of the 21st century’s big advances – Financial Times

October 24, 2016

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Strain-level associations of gut microbes, symbiosis in a coral reef sponge, halophilic microbiota of table salt, and microbiota of the red snapper.

Pregnancy and early life

Studying vertical microbiome transmission from mothers to infants by strain-level metagenomic profiling – Francesco Asnicar – bioRxiv Preprint

Human oral microbiome

Salivary microbiota and caries occurrence in Mutans Streptococci-positive school children – M. ElSalhy – European Journal of Paediatric Dentistry

Microbiological and bioinformatics analysis of primary Sjögren’s syndrome patients with normal salivation – Huma Siddiqui – Journal of Oral Microbiology

Evaluation of buccal cell samples for studies of oral microbiota – Guoqin Yu – Cancer Epidemiology, Biomarkers & Prevention

Human gut microbiome

Unusual sub-genus associations of faecal Prevotella and Bacteroides with specific dietary patterns – Francesca De Filippis – Microbiome

Review: The role of the commensal microbiota in adaptive and maladaptive stressor-induced immunomodulation – Amy R. Mackos – Hormones and Behavior

Review: Health Disparities and the Microbiome – Keisha Findley – Trends in Microbiology

Review: Emerging Technologies for Gut Microbiome Research – Jason W. Arnold – Trends in Microbiology

Review: Tiny microbes, enormous impacts: what matters in gut microbiome studies? – Justine Debelius – Genome Biology

Animal models

Illumina Miseq platform analysis caecum bacterial communities of rex rabbits fed with different antibiotics – Fuqin Zou – AMB Express

Animal microbiome

Draft Genomes Shed Light on the Dual Bacterial Symbiosis that Dominates the Microbiome of the Coral Reef Sponge Amphimedon queenslandica – Marie-Emilie A. Gauthier – Frontiers in Marine Science

Plant, root, and soil microbiome

Assessing the role of endophytic bacteria in the halophyte Arthrocnemum macrostachyum salt tolerance – S. Navarro-Torre – Plant Biology

Control of Cortaderia selloana with a glyphosate-based herbicide led to a short-term stimulation of soil fungal communities – M. Anza – Environmental Monitoring and Assessment

Water and extremophile microbiome

Trade-off between taxon diversity and functional diversity in European lake ecosystems
– Lars Grossmann – Molecular Ecology

Diversity of retrievable heterotrophic bacteria in Kongsfjorden, an Arctic fjord –
Rupesh Kumar Sinha – Brazilian Journal of Microbiology

Atmospheric aerosol deposition influences marine microbial communities in oligotrophic surface waters of the western Pacific Ocean – Teruya Maki – Deep Sea Research Part I: Oceanographic Research Papers

Long-term dynamics in microbial eukaryotes communities: a paleolimnological view based on sedimentary DNA – Eric Capo – Molecular Ecology

Shifts in bacterial community structure during succession in a glacier foreland of the High Arctic – Mincheol Kim – FEMS Microbiology Ecology

Food microbiology

Microbial culturomics unravels the halophilic microbiota repertoire of table salt: Description of Gracilibacillus massiliensis sp. nov. – Awa Diop – Microbial Ecology in Health and Disease

Microbiota of wild-caught Red Snapper Lutjanus campechanus – Andrea M. Tarnecki – BMC Microbiology

Archaea

Archaea in Natural and Impacted Brazilian Environments – Thiago Rodrigues – Archaea

Fungi

Sequence-based classification and identification of Fungi – David Hibbett – Mycologia

Metagenomics and bioinformatics

Filtration and Normalization of Sequencing Read Data in Whole-Metagenome Shotgun Samples – Philippe Chouvarine – PLOS ONE

Review: Genomic and functional techniques to mine the microbiome for novel antimicrobials and antimicrobial resistance genes – Boahemaa Adu-Oppong – Annals of the New York Academy of Sciences

Review: Translational metagenomics and the human resistome: confronting the menace of the new millennium – Matthias Willmann – Journal of Molecular Medicine

Metabolomics

Review: The Human Microbiome and Metabolomics: Current Concepts and Applications – Eric Banan-Mwine Daliri – Critical Reviews in Food Science and Nutrition

Microbes in the news

Post publication peer review of mSystems migraine paper – Jonathan Eisen – Storify

Woods Hole Oceanographic Institution Teams Up on Coral Study – Cape Cod

Costly detox programmes slammed by nutrition experts – Susan Strongman – NZ Herald

The Nose Knows Beneficial Bacteria – Lindsey Bomar – ASM blog

Ph.D. student creates new way to treat antibiotic resistance – CCTV America

‘My father’s poo saved my life’: Woman who could not leave her bed due to her agonising chronic constipation reveals how a VERY personal transplant saved her life – Sophie Haslett – Daily Mail

 

October 20, 2016

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Events

2016-2017 Dannon Gut Microbiome, Yogurt and Probiotics Fellowship Grant Application Form
Also see: Leading Yogurt Company Challenges Students to Unearth New Data on the Gut Microbiome, Yogurt and Probiotics with $50K Grant Program. Dannon® will award two $25K grants to further scientific research – PR Newswire

Third Annual Microbiome Symposium – Penn Vet – October 26 and 27, 2016
Penn’s microbiome conference turns eye toward antibiotic use in livestock
Text by Katherine Unger Baillie – Penn Current

Q4 microbiome conferences roundup: Are you looking for a good scientific microbiome research symposium? Over the next three months, you have six exciting microbiome conferences from which to choose. – Megan M. MacBride – Taconic

Disappointing lack of diversity here: #YAMMM: 29 speakers, 4 women. Microbiome Drug Development Summit, 24-26 January 2017, Paris, France

General microbiome

An introduction to microbiome analysis for human biology applications – Katherine R. Amato – American Journal of Human Biology

Human oral microbiome

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

Human respiratory microbiome

Role of microbiome in the pathophysiology and disease course of asthma – Singanayagam A – Curr Opin Pulm Med

Human skin microbiome

Review: Topographical and physiological differences of the skin mycobiome in health and disease – Jay-Hyun Jo – Virulence

Human vaginal microbiome

A fruitful alliance: the synergy between Atopobium vaginae and Gardnerella vaginalis in bacterial vaginosis-associated biofilm – Liselotte Hardy – Sexually Transmitted Infections

Human gut microbiome

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

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

Review: Roles for Intestinal Bacteria, Viruses, and Fungi in Pathogenesis of Inflammatory Bowel Diseases and Therapeutic Approaches – R. Balfour Sartor – Gastroenterology

Review: The Microbiome and Human Disease Pathogenesis: How do you do what you do to me …? – Edward N. Janoff – Translational Research

Animal models

Evaluating the association between body weight and the intestinal microbiota of weaned piglets via 16S rRNA sequencing – Geon Goo Hana – Veterinary Microbiology

Alterations of the Host Microbiome Affect Behavioral Responses to Cocaine – Drew D. Kiraly – Scientific Reports

Animal microbiome

Developmental and ecological benefits of the maternally transmitted microbiota in a dung beetle – Daniel B. Schwab – The American Naturalist

Microbiome analysis shows enrichment for specific bacteria in separate anatomical regions of the deep-sea carnivorous sponge Chondrocladia grandis – Joost T.P. Verhoeven – FEMS Microbiology Ecology Letters

Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities – Jessica L. Ray – Molecular Ecology

Spatial Microbial Composition Along the Gastrointestinal Tract of Captive Attwater’s Prairie Chicken – Yan Zhang – Microbial Ecology

Plant, root, and soil microbiome

Nestedness in Arbuscular Mycorrhizal Fungal Communities along Soil pH Gradients in Early Primary Succession: Acid-Tolerant Fungi Are pH Generalists – Ai Kawahara – PLOS ONE

Review: Microbially Mediated Plant Salt Tolerance and Microbiome-based Solutions for Saline Agriculture – Yuan Qin – Biotechnology Advances

Water microbiome

Defining boundaries for the distribution of microbial communities beneath the sediment-buried, hydrothermally active seafloor – Katsunori Yanagawa – ISME J

More microbiology

Correspondence: Improving Microbiology Research: the Problems Are Less Statistical and More Biological – Dennis F. Lawler – mBio

What’s in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015 – Erik Munson – Journal of Clinical Microbiology

Microbes in the news

Tasmanian devil milk fights superbugs – BBC News
Tasmanian devil milk kills several deadly superbugs that are resistant to existing drugs – Science Alert

There’s a breast microbiome, and it’s different in women with breast cancer – Erin Blakemore – Washington Post

Research Highlight: A protective protozoan in mucosal infection – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Outbreak of Biofilm-Forming Achromobacter xylosoxidans Due to Environmental Transmission – Infection Control Today

The Emergent Microbiome: A Revolution for the Life Sciences – Part VII, The Microbiome and Immunotherapy I – Dilworth IP – Lexology

New science museum exhibit explores ‘the secret world’ inside us: N.C. Museum of Natural Sciences in downtown Raleigh opens a new special exhibit this weekend – WRAL.com

Vedanta Biosciences Granted First European Patent Broadly Covering Pharmaceutical Compositions for Microbiome Therapeutics Based on Bacterial Consortia – Business Wire

Science, publishing, and career

Married to the(ir) job: living with an academic. Scholars and their significant others share the good, the bad and the ugly – Times Higher Education

Investigation Finds Pathologist Guilty of Systemic Misconduct – Bob Grant – The Scientist

Women need to be seen and heard at conferences. A neuroscience initiative is boosting the number of female invited speakers at meetings. Other disciplines should do the same – Nature

The Bearded Lady Project . Q&A: Lexi Jamieson Marsh and Ellen Currano: Face to face – Alexandra Witze – Nature

October 14, 2016

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The pubic hair microbiome, lung transplant virome, IBS microbiome signature, coprolites, antibacterial molecules for babies the Tasmanian Devil pouch, Archaea in Mars simulation, white pudding, functional mapping pipeline,

Human oral microbiome

Clinical, Immune, and Microbiome Traits of Gingivitis and Peri-implant Mucositis – G.P. Schincaglia – Journal of Dental Research

The microbial community shifts of subgingival plaque in patients with generalized aggressive periodontitis following non-surgical periodontal therapy: a pilot study – Jing Hang – Oncotarget

Review: The Autoimmunity-Oral Microbiome Connection – N Nikitakis – Oral Diseases

Human respiratory microbiome

The Perioperative Lung Transplant Virome: Torque Teno Viruses are Elevated in Donor Lungs and Show Divergent Dynamics In Primary Graft Dysfunction – A. A. Abbas – American Journal of Transplantation

Composition and immunological significance of the upper respiratory tract microbiota – L. Patrick Schenck – FEBS Letters

Human skin and hair microbiome

Individualization of pubic hair bacterial communities and the effects of storage time and temperature – Diana W. Williams – Forensic Science International: Genetics

Gram-positive anaerobe cocci (GPAC) are underrepresented in the microbiome of filaggrin-deficient human skin – Patrick L.J.M. Zeeuwen – The Journal of Allergy and Clinical Immunology

Review: Microbiome in healthy skin, update for dermatologists – B. Dréno – Journal of the European Academy of Dermatology and Venereology

Human reproductive tract microbiome

Challenging dogma: the endometrium has a microbiome with functional consequences! – Linda C. Giudice – American Journal of Obstetics & Gynecology

Human gut microbiome

Intestinal microbiota in adult patients with Short Bowel Syndrome: Preliminary results from a pilot study – Stefania Boccia – Clinical Nutrition

Identification of an Intestinal Microbiota Signature Associated With Severity of Irritable Bowel Syndrome – Julien Tap – Gastroenterology

The dual role of Escherichia coli in the course of ulcerative colitis – Magdalena Pilarczyk-Zurek – BMC Gastroenterology

Review: The gut microbiota and gastrointestinal surgery – Kristina Guyton – Nature Reviews Gastroenterology & Hepatology

Review: Dysbiosis in the ICU: Microbiome science coming to the bedside – Georgios D Kitsios – Journal of Critical Care

Review: Parasites, microbiota and metabolic disease – Sonakshi Bhattacharjee – Parasite Immunology

Review: Metabolite and Microbiome Interplay in Cancer Immunotherapy – Caroline H. Johnson – Cancer Research

Review: Human Coprolites as a Source for Paleomicrobiology – Sandra Appelt – Microbiology Spectrum

Animal models

Behavioural and Neurochemical Consequences of Chronic Gut Microbiota Depletion during Adulthood in the Rat – A.E. Hoban – Neuroscience

Changes in the rumen microbiome and metabolites reveal the effect of host genetics on hybrid crosses – Zhipeng Li – Environmental Microbiology Reports

Microbial community mapping in intestinal tract of broiler chicken – Yingping Xiao – Poultry Science

Animal microbiome

Comparative Assessment of Mediterranean Gorgonian-Associated Microbial Communities Reveals Conserved Core and Locally Variant Bacteria – Jeroen A. J. M. van de Water – Microbial Ecology

Cathelicidins in the Tasmanian devil (Sarcophilus harrisii) – E. Peel – Scientific Reports

Plant, root, and soil microbiome

Ecology of the forest microbiome: Highlights of temperate and boreal ecosystems – S. Uroz – Soil Biology and Biochemistry

Forest plant community as a driver of soil biodiversity: experimental evidence from collembolan assemblages through large-scale and long-term removal of oak canopy trees Quercus petraea – Ludovic Henneron – Oikos

Microbiome and Exudates of the Root and Rhizosphere of Brachypodium distachyon, a Model for Wheat – Akitomo Kawasaki – PLOS ONE

Review: Recent Developments in Systems Biology and Metabolic Engineering of Plant–Microbe Interactions – Vishal Kumar – Frontiers in Plant Science

Water microbiome

Microbial eukaryote communities exhibit robust biogeographical patterns along a gradient of Patagonian and Antarctic lakes – M. Romina Schiaffino – Environmental Microbiology

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

Phylotype Dynamics of Bacterial P Utilization Genes in Microbialites and Bacterioplankton of a Monomictic Endorheic Lake – Patricia M. Valdespino-Castillo – Microbial Ecology

Consistent responses of the microbial community structure to organic farming along the middle and lower reaches of the Yangtze River – Wenhui Wang – Scientific Reports

Microbes in space

Survivability and Growth Kinetics of Methanogenic Archaea at various pHs and Pressures: Implications for Deep Subsurface Life on Mars – Navita Sinha – Planetary and Space Science

Food microbiology

The use of 16S rRNA gene metagenetic monitoring of refrigerated food products for understanding the kinetics of microbial subpopulations at different storage temperatures: The example of white pudding – Emilie Cauchie – International Journal of Food Microbiology

Microbial diversity in pitted sweet cherries (Prunus avium L.) as affected by high-hydrostatic pressure treatment – Julia Toledo del Árbol – Food Research International

Built environment microbiology

Bioaerosol assessment in the library of Istanbul University and fungal flora associated with paper deterioration – Duygu Göksay Kadaifciler – Aerobiologia

Techniques / Fungi

Accurate Estimation of Fungal Diversity and Abundance Through Improved Lineage-Specific Primers Optimized for Illumina Amplicon Sequencing – D. Lee Taylor – Applied and Environmental Microbiology

Bioinformatics and metagenomics

Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli – Minseung Kim – Nature Communications

FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies – Jiwoong Kim – BMC Bioinformatics

A critical evaluation of ecological indices for the comparative analysis of microbial communities based on molecular datasets – Rico Lucas – FEMS Microbiology Ecology

Microbes in the news

Extremophiles found in a lake, and this is great news for biotech – Colm Gorey – Silicon Republic

‘I want my teeth back’: Kids infected with jaw-eating bacteria after dental treatment – Katie Mettler – Sacramento Bee

Microbiome biotech joins Peter Thiel’s Breakout Labs project – Fierce Biotech

Science, publishing, and career

Book:  Fungible Life: Experiment in the Asian City of Life – Aihwa Ong – Amazon

September 29, 2016

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Two human skin microbiota papers, effects of eating chili powder, methanogens can tolerate Mars-like low pressure, gut microbiota signatures of longevity.

Human skin microbiome

Topical Decolonization Does Not Eradicate the Skin Microbiota of Community-Dwelling or Hospitalized Adults – Carey-Ann D. Burnham – Antimicrobial Agents and Chemotherapy

Evolutionary and Functional Implications of Hypervariable Loci Within the Skin Virome – Geoffrey D Hannigan – bioRxiv

Human gut microbiome

Healthy subjects differentially respond to dietary capsaicin correlating with the specific gut enterotypes – Chao Kang – Journal of Clinical Endocrinology & Metabolism

Gut microbiota signatures of longevity – Fanli Kong – Current Biology

Shifts in the fecal microbiota associated with adenomatous polyps – Vanessa L Hale – Cancer Epidemiology, Biomarkers & Prevention

When pathogenic bacteria meet the intestinal microbiota – Nathalie Rolhion – Philosophical Transactions of the Royal Society B

Review: From homeostasis to pathology: decrypting microbe–host symbiotic signals in the intestinal crypt – Thierry Pédron – Philosophical Transactions of the Royal Society B

Review: Human microbiome as therapeutic intervention target to reduce cardiovascular disease risk – Annefleur M. Koopen – Current Opinion in Lipidology

Review: The microbial epigenome in metabolic syndrome – Marlene Remely – Molecular Aspects of Medicine

Animal and in vitro models

Probiotic legacy effects on gut microbial assembly in tilapia larvae – Christos Giatsis – Scientific Reports

D-Tryptophan from probiotic bacteria influences the gut microbiome and allergic airway disease – Inge Kepert – The Journal of Allergy and Clinical Immunology

Expression of the aryl hydrocarbon receptor contributes to the establishment of intestinal microbial community structure in mice – Iain A. Murray – Scientific Reports

Animal microbiome

The chicken tracheal microbiome: unexpected preliminary data – Tim Johnson Lab

Contrasting diets reveal metabolic plasticity in the tree-killing beetle, Anoplophora glabripennis (Cerambycidae: Lamiinae) – Charles J. Mason – Scientific Reports

Plant, root, and soil microbiome

Structure, Variation, and Co-occurrence of Soil Microbial Communities in Abandoned Sites of a Rare Earth Elements Mine – Yuanqing Chao – Environmental Science & Technology

Fungal endophytes as priority colonizers initiating wood decomposition – Zewei Song – Functional Ecology

Water and extremophile microbiome

Culture-independent study of bacterial communities in tropical river sediment  –
Honglada Thoetkiattikul – Bioscience, Biotechnology, and Biochemistry

Oligotrophic lagoons of the South Pacific Ocean are home to a surprising number of novel eukaryotic microorganisms – Eunsoo Kim – Environmental Microbiology

Low Pressure Tolerance by Methanogens in an Aqueous Environment: Implications for Subsurface Life on Mars – R. L. Mickol – Origins of Life and Evolution of Biospheres

Microbes and robots

Did not quite grasp the abstract, but cool picture of a small robot: Bioinspired decision architectures containing host and microbiome processing units – K C Heyde – Bioinspiration & Biomimetics

Microbes in the news
Research Breakthrough Could Help Diagnose, Treat Biofilm Infections – Lorena Anderson – UC Merced

Profile: Dr. Bonnie Bassler, a pioneer who’s investigating how bacteria communicate – Joe Tyrrell – New Jersey Spotlight

World’s Largest MS Research Conference Highlights Advances in Progressive MS, Gut Microbiome, Managing Symptoms, and New Approaches to Restoring Function – National MS Society

Assembly Biosciences Announces Key Additions to Microbiome Team – Globe Newswire

Can’t lose weight? You might be able to blame it on your parents—and their gut bacteria – Akshat Rathi – Quartz
Are Your Genes Making It Hard To Get Into Your Jeans? – Julie Taylor – uBiome blog

Deadly Mud-Dwelling Bacteria Melioidosis Stirs In The Northern Territory – Cayla Dengate – Huffington Post Australia

 

Science, publishing, and career

Young researchers thrive in life after academia. Alternative career paths should be celebrated, not seen as a compromise. – Nature

September 22, 2016

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Jobs at Second Genome, endohyphal bacteria in fungi on tropical seeds and leaves, designing buildings to house our germs.

Jobs and events

Second Genome (San Francisco, CA) is hiring.

Southern California Microbiome Symposium – Connections to the Environment and Health – Sept 23, UC Irvine

Human gut microbiome

Review: Current Hypothesis for the Relationship between Dietary Rice Bran Intake, the Intestinal Microbiota and Colorectal Cancer Prevention – Winnie K. W. So – MDPI Nutrients

Animal models

Temporal Development of Gut Microbiota in Triclocarban Exposed Pregnant and Neonatal Rats – Rebekah C. Kennedy – Scientific Reports

Animal microbiome

Parasitic Infection by Pseudocapillaria tomentosa is Associated with a Longitudinal Restructuring of the Zebrafish Gut Microbiome – Christopher A Gaulke – bioRxiv

Biology, Pest Status, Microbiome and Control of Kudzu Bug (Hemiptera: Heteroptera: Plataspidae): A New Invasive Pest in the U.S. – Anirudh Dhammi – International Journal of Molecular Sciences

Plant, root, and soil microbiome

A Hardy Plant Facilitates Nitrogen Removal via Microbial Communities in Subsurface Flow Constructed Wetlands in Winter – Penghe Wang – Scientific Reports

Diversity, Specificity, and Phylogenetic Relationships of Endohyphal Bacteria in Fungi That Inhabit Tropical Seeds and Leaves – Justin P. Shaffer – Frontiers in Ecology and Evolution

More microbiology

Nuclear pore-like structures in a compartmentalized bacterium – Evgeny Sagulenko – bioRxiv

Review: Molecular microbiology methods for environmental diagnosis – T. Bouchez – Environmental Chemistry Letters

Self-healing cementitious materials based on bacteria and nutrients immobilized respectively – Huaicheng Chen – Construction and Building Materials

Techniques

An Enteric Micromotor Can Selectively Position and Spontaneously Propel in the Gastrointestinal Tract – Jinxing Li – ACS Nano

Microbes in the news

Black Slime Is Coating World Monuments—And That May Be Good – Michelle Z. Donahue – National Geographic

Designing Buildings to House Our Favorite Germs – Melissa Pandika – Ozy

Very cool talks: Lake Arrowhead Microbial Genomes #LAMG16: Day 3 – David Coil – MicroBEnet

Prairies Yield Clues for Antibiotic Resistance – AgResearch Magazine

Genetically Engineered Bacteria Can Grow Food, Forks on Mars – Jacqueline Ronson – Inverse.com

CosmoCrops! – The 2016 winners of the Nordic Mini-Jamboree! – Copenhagen University iGEM
UW Medical Center takes action after finding bacteria in medical devices – Coral Garnick – BizJournals

Gut bacteria explain insects’ tolerance to a toxic diet – Science Daily

A field guide to dangerous bacteria – Tabletopwhale

Science, publishing, and career

The natural selection of bad science – Paul E. Smaldino – Royal Society Open Science

Press: The Inevitable Evolution of Bad Science – Ed Yong – The Atlantic

Salaries: Reality check: A feeling that good performance is not adequately rewarded is pervading the research world – Chris Woolston – Nature Careers