Category Archives: Food Microbiology

October 18, 2016

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Vaginal probiotics, forensic analysis of skin bacteria on fabrics, Wolbachia in nematodes, ivy phyllosphere, microbial life in two polar extremes, how to improve the indoor environment, and mass spec analysis of human habitat molecules.

Pregnancy and early life

Vaginal Probiotic Administration in the Management of Preterm Premature Rupture of Membranes – Daskalakis G.J. – Fetal Diagnosis and Therapy

General human microbiome

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

Human respiratory microbiome

Review: Host–Bacterial Crosstalk Determines Staphylococcus aureus Nasal Colonization – Michelle E. Mulcahy – Trends in Microbiology

Human skin and tissue microbiome

Forensic analysis using microbial community between skin bacteria and fabrics – So-Yeon Lee – Toxicology and Environmental Health Sciences

Not a word about extraction controls, so proceed with caution: Bacterial Communities Associated with Atherosclerotic Plaques from Russian Individuals with Atherosclerosis – Elvira E. Ziganshina – PLOS ONE

Human gut microbiome

Construction and Analysis of Functional Networks in the Gut Microbiome of Type 2 Diabetes Patients – Lianshuo Li – Genomics, Proteomics & Bioinformatics

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

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

Review: Gut Microbiota and Risk of Developing Celiac Disease – Cenit, Maria C. – Journal of Clinical Gastroenterology

Editorial: What’s in Your GI Microbiome? – Martin H. Floch – Journal of Clinical Gastroenterology

Animal and in vitro models

Study of the Ability of Bifidobacteria of Human Origin to Prevent and Treat Rotavirus Infection Using Colonic Cell and Mouse Models – Mélanie Gagnon – PLOS ONE

Farnesoid X Receptor Signaling Shapes the Gut Microbiota and Controls Hepatic Lipid Metabolism – Limin Zhang – mSystems

A mixture of milk and vegetable lipids in infant formula changes gut digestion, mucosal immunity and microbiota composition in neonatal piglets – Isabelle Le Huërou-Luron – European Journal of Nutrition

An Advanced In Vitro Technology Platform to Study the Mechanism of Action of Prebiotics and Probiotics in the Gastrointestinal Tract – Marzorati, Massimo – Journal of Clinical Gastroenterology

Animal microbiome

Sea lions: Protein and RNA extraction from mucosal swabs: a minimally invasive source of ecological data for studies of natural populations – W Espinosa-de Aquino – Methods in Ecology and Evolution

Mycobacteria in aquarium fish: results of a 3-year survey indicate caution required in handling pet-shop fish – D Kušar – Journal of Fish Diseases

Genomic evidence for plant-parasitic nematodes as the earliest Wolbachia hosts – Amanda M. V. Brown – Scientific Reports

Plant, root, and soil microbiome

Disentangling interactions between microbial communities and roots in deep subsoil – Martina I. Gocke – Science of the Total Environment

Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock – Alexandre Bagnoud – Nature Communications

Diversity and hydrocarbon-degrading potential of epiphytic microbial communities on Platanus x acerifolia leaves in an urban area – Isabella Gandolfi – Environmental Pollution

Response of soil bacterial communities to lead and zinc pollution revealed by Illumina MiSeq sequencing investigation – Xihui Xu – Environmental Science and Pollution Research

Impact of urban land use on the bacterial phyllosphere of ivy (Hedera sp.) – Wenke Smets – Atmospheric Environment

Water and extremophile microbiome

Periodic change in coastal microbial community structure associated with submarine groundwater discharge and tidal fluctuation – Eunhee Lee – Limnology and Oceanography

Microbial Community Dynamics in Two Polar Extremes: The Lakes of the McMurdo Dry Valleys and the West Antarctic Peninsula Marine Ecosystem – Jeff S. Bowman – BioScience

Diversity and physiological and biochemical properties of heterotrophic bacteria isolated from Lake Baikal neuston – A. D. Galach’yants – Microbiology

Phylogenetic and functional prokaryotic diversity in the Hoito-Gol mesothermal mineral spring (Eastern Sayan Mountains, Buryat Republic) – E.S. Kashkak – Microbiology

Metagenomic Insights into Effects of Chemical Pollutants on Microbial Community Composition and Function in Estuarine Sediments Receiving Polluted River Water – Xiao-Ming Lu – Microbial Ecology

Built environment microbiome

How do we make indoor environments and healthcare settings healthier? – Jack A. Gilbert – Microbial Biotechnology

Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats – Daniel Petras – Analytical Chemistry

Food microbiology

Raw Ready-to-Eat Seafood Safety: Microbiological Quality of the Various Seafood Species Available at Fishery, Hyper, and Online Market – H.W. Kim – Letters in Applied Microbiology

Bioinformatics and metagenomics

MIxS-HCR: a MIxS extension defining a minimal information standard for sequence data from environments pertaining to hydrocarbon resources – Nicolas Tsesmetzis – Standards in Genomic Sciences

IMG/M: integrated genome and metagenome comparative data analysis system
I-Min A. Chen – Nucleic Acids Research

Review: The present and future of de novo whole-genome assembly – Jang-il Sohn – Briefings in Bioinformatics

Microbes in the news

Soaking A Bunch Of Toads In Their Own Bacteria Could Save Their Lives – Krista Langlois – Five Thirty Eight

Bacteria Hysteria

Why your office could be making you sick: Keyboards ‘contain 20,000 MORE bacteria than a toilet bowl’– Stephen Matthews – Daily Mail

How to clean and disinfect your keyboard and mouse – Ed Rhee – CNET

Science, publishing, and career

A Tale of Two Women and Their Careers in Science – Anna Katie – YouTube

Promoting Responsible Scientific Research – American Society for Microbiology

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

October 13, 2016

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Ethics and microbiome research, oversimplifying microbiome studies, viruses destroy archaea in the deep seafloor, Clostridium difficile in patients sharing hospital beds.

General microbiome

Perspective: Ethical issues in microbiome research and medicine – Rosamond Rhodes – BMC Medicine

Interview: Science communication: the dangers of oversimplifying microbiome studies – Interview with Lauren Freeman and Saray Ayala – Ben Johnson – NPJ Biofilms Community

Human gut microbiome

Preview: Making It Stick: A Compelling Case for Precision Microbiome Reconstitution – David Berry – Cell Host & Microbe

Preview: A Commensal Protozoan Strikes a Balance in the Gut – P’ng Loke – Cell Host & Microbe

Animal models

Intestinal microbiota could transfer host Gut characteristics from pigs to mice – H. Diao – BMC Microbiology

Plant, root, and soil microbiome

Review: How lichens impact on terrestrial community and ecosystem properties – Johan Asplund – Biological Reviews

Water (and coral) microbiology

Virus-mediated archaeal hecatomb in the deep seafloor – Roberto Danovaro – Science Advances

Press: Deep-Sea Viruses Destroy Archaea. Viruses are responsible for the majority of archaea deaths on the deep ocean floors, scientists show – Ruth Williams – The Scientist

Multifaceted impacts of the stony coral Porites astreoides on picoplankton abundance and community composition – Sean P. McNally – Limnology and Oceanography

Food microbiology

Ultrasound improves chemical reduction of natural contaminant microbiota and Salmonella enterica subsp. enterica on strawberries – Denes Kaic Alves do Rosário – International Journal of Food Microbiology

Techniques

Greater than X kb: a quantitative assessment of preservation conditions on genomic DNA quality, and a proposed standard for genome-quality DNA – Daniel G. Mulcahy – PeerJ

Metagenomics

Diverse Intestinal Bacteria Contain Putative Zwitterionic Capsular Polysaccharides with Anti-inflammatory Properties – C. Preston Neff – Cell Host & Microbe

Other microbiology

Division of labour in microorganisms: an evolutionary perspective – Stuart A. West – Nature Reviews Microbiology

Receipt of Antibiotics in Hospitalized Patients and Risk for Clostridium difficile Infection in Subsequent Patients Who Occupy the Same Bed – Daniel E. Freedberg – JAMA

Press: Antibiotics Encourage Spread of C.diff To Subsequent Patients Who Occupy the Same Bed and Haven’t Received Antibiotics: Interview with Daniel Freedberg – Medical Research

Microbes in the news

The Conversation Gut Series:

RI Hospital receives $500,000 CDC grant to research new approach for combating antibiotic resistance. Microbiome research will help prevent ongoing spread of multi-drug resistant bacteria – EurekAlert

Science, publishing, and career

How Are Scientists Using Social Media in the Workplace? – Kimberley Collins – PLOS ONE

5 retractions and a sack for Pfizer lead cancer researcher Min-Jean Yin – Leonid Schneider – For Better Science
Pfizer fires employee, requests five retractions – Alison McCook – Retraction Watch

Bik’s non-microbiology Picks

Genomics is failing on diversity – Alice B. Popejoy & Stephanie M. Fullerton – Nature
The Simons Genome Diversity Project: 300 genomes from 142 diverse populations – Swapan Mallick – Nature

October 10, 2016

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A Mostly Male Microbiome meeting, host genetics and microbiota in IBD, dysbiosis in dogs and humans, airport door handles, and surfing the world for microbes. I’m back!

Events

I wish I could recommend this, but it has only 2 of the 27 invited speakers are women. This is so sad. See Jonathan Eisen’s blog post about this. Second Annual Human Microbiome Congress in San Diego / North American Microbiome Congress – 24/25 January 2017 – San Diego.

Human gut microbiome

Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease – Floris Imhann – Gut

Effect of dietary interventions on the intestinal microbiota of Mongolian hosts – Jing Li – Science Bulletin

Animal models

Dog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networks – Yoshiki Vázquez-Baeza – Nature Microbiology

Acute Infectious Gastroenteritis Potentiates a Crohn’s Disease Pathobiont to Fuel Ongoing Inflammation in the Post-Infectious Period – Cherrie L. Small – PLOS Pathogens

Press: Diarrhea-Causing Bacteria Promote Growth of Crohn’s-Linked Microbe in Mice – ET Healthworld

Neonatal androgen exposure causes persistent gut microbiota dysbiosis related to metabolic disease in adult female rats – Isabel Moreno-Indias – Endocrinology

Exposure to the Functional Bacterial Amyloid Protein Curli Enhances Alpha-Synuclein Aggregation in Aged Fischer 344 Rats and Caenorhabditis elegans – Shu G. Chen – Scientific Reports

Press: Gut microbiota may have role in neurodegenerative diseases: study – CTV News

Plant, root, and soil microbiome

Review: Too much or not enough: Reflection on two contrasting perspectives on soil biodiversity – Philippe C. Baveye – Soil Biology and Biochemistry

Built environment microbiology

Airport door handles and the global spread of antimicrobial-resistant bacteria: a cross sectional study – Frieder Schaumburg – Clinical Microbiology and Infection

Press: Are Airport Bathrooms Spreading Antibiotic-Resistant Bacteria Globally? – Alex Berezow – American Council on Science and Health

Food microbiology

Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria – Kevin S. Bonham – bioRxiv

Does fingerprinting truly represent the diversity of wine yeasts? A case study with interdelta genotyping of S. cerevisiae strains – Walter P. Pfliegler – Letters in Applied Microbiology

Microbes in the news

This Surfer/PhD Student Is Scraping Bacteria off Surfers Around the World for Science – Dylan Heyden – The Inertia
Surfing the world for microbes – Erika Johnson, UC San Diego – University of California

Weethinking the role of bacteria in incontinence. Researchers look at the role of bacteria in incontinence – EurekAlert

The Unseen Cloud Makers From The Ocean – Jennifer – The Microbial Menagerie

Marine bacteria are the climate’s wild card – ScienceNordic

Researchers Hunt for a Link Between Microbiome and Autism – KQED

The natural wonder that holds the key to the origins of life – and warns of its destruction – Michael Slezak – The Guardian

Did his artificial hips put him at risk of infection when he saw the dentist? – David Lindley – Washington Post

Millions of craft paint units recalled over bacteria concerns – Morgan Maria Pawl – KDVR

Science, publishing, and career

Scientific Misconduct: The Elephant in the Lab. A Response to Parker et al. – Timothy D. Clark – Trends in Ecology & Evolution

Bik’s non-microbiology Picks

As DNA reveals its secrets, scientists are assembling a new picture of humanity – Carl Zimmer

October 1, 2016

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Microbiome of tonsils in kidney disease, poisonous salamanders,  Kruger National Park, drought tolerance of plants, and human milk microbiota.

Pregnancy and birth

Distinct patterns in human milk microbiota and fatty acid profiles across specific geographic locations – Himanshu Kumar – Frontiers in Microbiology

Review: Systematic Review of the Human Milk Microbiota – John L. Fitzstevens – Nutrition in Clinical Practice

Human respiratory microbiome

Comprehensive microbiome analysis of tonsillar crypts in IgA nephropathy – Hirofumi Watanabe – Nephrology Dialysis Transplantation

Human skin microbiome

Microbiota is a primary cause of pathogenesis of chronic wounds – R. Wolcott – Journal of Wound Care

Animal and in vitro models

Transient and Prolonged Response of Chicken Cecum Mucosa to Colonization with Different Gut Microbiota – Jiri Volf – PLOS ONE

Effect of flow and peristaltic mixing on bacterial growth in a gut-like channel – Jonas Cremer – PNAS

Animal microbiome

Cutaneous Bacterial Communities of a Poisonous Salamander: a Perspective from Life Stages, Body Parts and Environmental Conditions – Eugenia Sanchez – Microbial Ecology

Characterization of the Cutaneous Bacterial Communities of Two Giant Salamander Subspecies – Obed Hernández-Gómez – Microbial Ecology

Host-specific functional significance of Caenorhabditis gut commensals – Maureen Berg – Frontiers in Microbiology

Sexual variation of bacterial microbiota of Dendroctonus valens guts and frass in relation to verbenone production – Letian Xu – Journal of Insect Physiology

Plant, root, and soil microbiome

Comparative Metagenomics Reveal Phylum Level Temporal and Spatial Changes in Mycobiome of Belowground Parts of Crocus sativus – Sheetal Ambardar – PLOS ONE

Community composition and abundance of nitrifiers and total bacterial and archaeal populations in savanna soils on contrasting bedrock material in Kruger National Park, South Africa – Saskia Rughoeft – Frontiers in Microbiology

Microbial Mat Compositional and Functional Sensitivity to Environmental Disturbance – Eva C. Preisner – Frontiers in Microbiology

Plant Drought Tolerance Enhancement by Trehalose Production of Desiccation-Tolerant Microorganisms – Juan I. Vílchez – Frontiers in Microbiology

Associations between an Invasive Plant (Taeniatherum caput-medusae, Medusahead) and Soil Microbial Communities – Elise S. Gornish – PLOS ONE

Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input – Alacia Armstrong – Scientific Reports

Annual Removal of Aboveground Plant Biomass Alters Soil Microbial Responses to Warming – Kai Xue – mBio

Impact of Cropping Systems, Soil Inoculum, and Plant Species Identity on Soil Bacterial Community Structure – Suzanne L. Ishaq – Microbial Ecology

Extremophiles

Metagenomics of Thermophiles with a Focus on Discovery of Novel Thermozymes – María-Eugenia DeCastro – Frontiers in Microbiology

Food microbiology

Kimchi and Other Widely Consumed Traditional Fermented Foods of Korea: A Review – Jayanta Kumar Patra – Frontiers in Microbiology

Biofilms

Fungal Super Glue: The Biofilm Matrix and Its Composition, Assembly, and Functions – Kaitlin F. Mitchell – PLOS Pathogens

Microbes in the news

Dr. Rob Knight, co-founder of American Gut, Discusses the Microbiota and Microbiota testing – Dr Ruscio

Flesh-Eating Bacteria Like It Hot – Hannah Gavin – Discover Magazine

September 30, 2016

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When does a probiotic stick around, microbial diversity in 12 French cheese varieties, effects of field conditions on fecal microbiota.

Events

Microbiome Drug Development Summit Europe – 24-26 January 2017, Paris, France

Human oral microbiome

Changes in the oral ecosystem induced by the use of 8% arginine toothpaste – Jessica E. Koopman – Archives of Oral Biology

Review: Role of oral microbiome on oral cancers, a review – Pourya Gholizadeh – Biomedicine & Pharmatherapy

Human skin microbiome

Novel volatiles of skin-borne bacteria inhibit the growth of Gram-positive bacteria and affect quorum-sensing controlled phenotypes of Gram-negative bacteria – Marie Chantal Lemfack – Systematic and Applied Microbiology

Human gut microbiome

Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome – María X. Maldonado-Gómez – Cell Host & Microbe

Press: A Probiotic That Actually Lasts. The bacteria in yogurts have largely failed to live up to their hyped health benefits, but there are other microbes that might – Ed Yong – The Atlantic

Animal microbiome

Consequences of coinfection with protective symbionts on the host phenotype and symbiont titres in the pea aphid system – Mélanie Leclair – Insect Science

Corals: Bacterial community diversity of the deep-sea octocoral Paramuricea placomus – Christina A. Kellogg – PeerJ

Plant, root, and soil microbiome

Effects of slope exposure on soil physico-chemical and microbiological properties along an altitudinal climosequence in the Italian Alps – Tommaso Bardelli – Science of the Total Environment

Food microbiology

Highlighting the microbial diversity of 12 French cheese varieties – Eric Dugat-Bony – International Journal of Food Microbiology

Microbial ecology and more microbiology

Macroecology for microbiology – Jay T Lennon – PeerJ Preprint

Review: Fungal Super Glue: The Biofilm Matrix and Its Composition, Assembly, and Functions – Kaitlin F. Mitchell – PLOS Pathogens

Techniques

Effects of field conditions on fecal microbiota – Vanessa L. Hale – Journal of Microbiological Methods

A cost-efficient and simple protocol to enrich prey DNA from extractions of predatory arthropods for large-scale gut content analysis by Illumina sequencing – Henrik Krehenwinkel – Methods in Ecology and Evolution

Microbes in the news

The cost of cheap drugs? Toxic Indian lake is ‘superbug hotspot’ – Zeba Siddiqui – Reuters

Effects of maternal stress on newborn health: An Interview with Dr. Connie Mulligan of the University of Florida – DNA Genotek

Gene-engineered gut bacteria successfully treat sick mice — and could treat humans someday – Leah Samuel – STAT News

Microbiology retreat showcases research – Anamika Veeramani – Yale Daily News

Science, publishing, and career

Working life: Doing science while black – Edward J. Smith – Science

September 24, 2016

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Eye microbiome, malnutrition and rotavirus, edible insects, vineyard management, and drones.

Human eye / skin microbiome

Impact of Microbiota on Resistance to Ocular Pseudomonas aeruginosa-Induced Keratitis – Abirami Kugadas – PLOS Pathogens

Press (scroll to halfway the page to read this item): Lab chat: Eye bacteria and contact lenses  – Megan Thielking – STAT News

Human gut microbiome

Malnutrition Is Associated with Protection from Rotavirus Diarrhea: Evidence from a Longitudinal Birth Cohort Study in Bangladesh – Hans Verkerke – Journal of Clinical Microbiology

Animal models

Immunosuppression, peripheral inflammation and invasive infection from endogenous gut microbiota activate retinal microglia in mouse models – Victoria Maneu – Microbiology and Immunology

Animal microbiome

Phenological asynchrony between host plant and gypsy moth reduces insect gut microbiota and susceptibility to Bacillus thuringiensis – Vyacheslav V. Martemyanov – Ecology and Evolution

Plant, root, and soil microbiome

Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by vineyard management – Kayla N. Burns – Soil Biology and Biochemistry

Fungal community composition in soils subjected to long-term chemical fertilization is most influenced by the type of organic matter – Ruibo Sun – Environmental Microbiology

Change in soil fungal community structure driven by a decline in ectomycorrhizal fungi following a mountain pine beetle (Dendroctonus ponderosae) outbreak – Gregory J. Pec – New Phytologist

Water microbiome

Dense water plumes modulate richness and productivity of deep sea microbes – Gian Marco Luna – Environmental Microbiology

Food microbiology

The microbiota of marketed processed edible insects as revealed by high-throughput sequencing – Cristiana Garofalo – Food Microbiology

Metagenomics reveals flavour metabolic network of cereal vinegar microbiota – Linhuan Wu – Food Microbiology

Techniques

Detection of food and skin pathogen microbiota by means of an electronic nose based on metal oxide chemiresistors – Estefanía Núñez Carmona – Sensors and Actuators B: Chemical

A one-step matrix application method for MALDI mass spectrometry imaging of bacterial colony biofilms – Bin Li – Journal of Mass Spectrometry

Microbial ecology

The biogeography of kin discrimination across microbial neighbourhoods – Susanne A. Kraemer – Molecular Ecology

More microbiology

Microbes can fly: Drone Transport of Microbes in Blood and Sputum Laboratory Specimens – Timothy K. Amukele – Journal of Clinical Microbiology

Microbes in the news

New CDC Report Shows One Quarter of Contact Lens-related Eye Infections Due to Improper Use, Modifiable Factors – PR Web

Extremely rare US leprosy case found in California elementary school student – Andrew Dalton – STAT News

How Can Science Benefit from Microbes on the ISS? – Jessica F – Nature World News

New Research Indicates Alzheimer’s and Other Neurodegenerative Diseases Are Contagious – PR Newswire

Deadly Viruses and Bacteria Mistakenly Shipped 21 Times – R. Jeffrey Smith – The Daily Beast

Science, publishing, and career

Meet the world’s top peer reviewer: Jonas Ranstam – Ivan Oransky and Adam Marcus – STAT News

September 8, 2016

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Geese in wintering areas, Hirschsprung’s disease, and extreme metagenomics.

Jobs and Events

Assistant Professor in Microbiome Research – University of Maryland Baltimore County

Virtual Conference: Microbiology & Immunology 2016 interactive online conference, latest Research on Microscopic Organisms and How They Impact the Human Body – September 7-8, 2016

EPA Webinar and Discussion: What Have We Learned about the Microbiomes of Indoor Environments? – Brent Stephens – September 22, 2016

SMi’s 6th annual Pharmaceutical Microbiology conference – January 18-19, London, UK

Human gut microbiome

screen-shot-2016-09-08-at-7-35-07-amCharacterization of Intestinal Microbiomes of Hirschsprung’s Disease Patients with or without Enterocolitis Using Illumina-MiSeq High-Throughput Sequencing – Yuqing Li – PLOS ONE

Preview: Harnessing Genes and Diet to Fine-Tune the Gut Microbial Fitness – Patrice D. Cani – Cell Metabolism

Animal microbiome

Geese: Characterising the interspecific variations and convergence of gut microbiota in Anseriformes herbivores at wintering areas – Yuzhan Yang – Scientific Report

Water and extremophile microbiome

Extreme metagenomics using nanopore DNA sequencing: a field report from Svalbard, 78 N – Arwyn Edwards – bioRxiv

Bacterial community succession in a high altitude sub-arctic glacier foreland is a three-stage process – Sina Kazemi – Molecular Ecology

Communities that thrive in extreme conditions captured from a freshwater lake – Etienne Low-Décarie – Biology Letters

Review: Substratum-Associated Microbiota – Paula C. Furey – Water Environment Research

Food microbiology

Mungo bean sprout microbiome and changes associated with culture based enrichment protocols used in detection of Gram-negative foodborne pathogens – Heike Margot – Microbiome

Bioinformatics and metagenomes

De novo extraction of microbial strains from metagenomes reveals intra-species niche partitioning – Christopher Quince – bioRxiv

Microbes in the news

Captive Komodo Dragons Share Their Teeming Microbiome with Their Environment, Just Like Us – Naomi Shavin – Smithsonian Magazine

OSTP call to action on saving soil – Jonathan Eisen – MicroBEnet

IIT-Bombay team finds bacteria responsible for neonatal deaths – Priyanka Sahoo – The Indian Express

Scientists discover link between bacteria and supposedly non-infectious diseases – BBSRC

Life on Mars? Martian Meteorites, Martian Microbes – Julie Taylor – uBiome blog

New website (with a link to my blog, so it’s all good): The Microbiome, sponsored by Era7 Bioinformatics Inc.

Science integrity

Macchiarini scandal is a valuable lesson for the Karolinska Institute – Nature

September 7, 2016

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Events

International Human Microbiome Consortium, November 9-11, 2016, Houston Texas.

Human gut microbiome

Review: The Role of the Microbiota in Shaping Infectious Immunity – Timothy W. Hand – Trends in Immunology

Animal microbiome

Effects of host genetics and environment on egg-associated microbiotas in brown trout (Salmo trutta) – Laetitia G. E. Wilkins – Molecular Ecology

Food microbiology

Multiplex 16S rRNA-derived geno-biochip for detection of 16 bacterial pathogens from contaminated foods – Hwa Hui Shin – Biotechnology Journal

More microbiology

Acute induction of anomalous and amyloidogenic blood clotting by molecular amplification of highly substoichiometric levels of bacterial lipopolysaccharide – Etheresia Pretorius – Journal of the Royal Society Interface

Extrapolated interpretation? Bacteria lurking in blood could be culprit in countless diseases – Debora MacKenzie – New Scientist

Microbes in the news

FDA Bans Antiseptics: One Small Step for Bacteria and Humankind – Anne Estes – Mostly Microbes

How bad for you is a boring diet? – Tim Spector – BBC

Flowers critical link to bacteria transmission in wild bees – Science Daily

Doughnut in a cage holds the key to bacteria’s survival – Science Daily

Fungi contribute to delayed healing of chronic wounds – EurekAlert

Microbe tenants help – and hinder – your immune system – Dyani Lewis – Cosmos Magazine

Microbes and money

Monsanto Collaborates with Second Genome to Use Microbiome Technology Platform to Accelerate Protein Discovery – Business Wire

BioMed X Announces the Start of New Research Team on Oral Biofilm Disruption through Continued Collaboration with Johnson & Johnson Innovation – PharmaVoice

BioMed X to collaborate with Johnson & Johnson on oral biofilm research – Drug Target Review

Science, publishing, and career

Why women leave academia and why universities should be worried – Curt Rice – The Guardian

 

 

August 29b, 2016

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Male grey cockatiel, Wikipedia

Factors that shape early life microbiome, pet birds, robust ambient temperature storage of stool samples, antibacterial activity of wasabi.

Pregnancy and birth

Joint effects of pregnancy, sociocultural, and environmental factors on early life gut microbiome structure and diversity – Albert M. Levin – Scientific Reports

Human gut microbiome

Theoretical Review: The shift work and health research agenda: Considering changes in gut microbiota as a pathway linking shift work, sleep loss and circadian misalignment, and metabolic disease – Amy C. Reynolds – Sleep Medicine Reviews

Review: Mechanisms of inflammation-driven bacterial dysbiosis in the gut – M Y Zeng – Mucosal Immunology

Animal experiments

Review: Experimental Models to Study the Role of Microbes in Host-Parasite Interactions – Megan A. Hahn – Frontiers in Microbiology

Animal microbiome

Comprehensive Molecular Characterization of Bacterial Communities in Feces of Pet Birds Using 16S Marker Sequencing – Jose F. Garcia-Mazcorro – Microbial Ecology

Effects of environment, dietary regime and ageing on the dengue vector microbiota: evidence of a core microbiota throughout Aedes aegypti lifespan – Mariana Rocha David – Memórias do Instituto Oswaldo Cruz

Plants, roots, and soil microbiome

Visual Comparative Omics of Fungi for Plant Biomass Deconstruction – Shingo Miyauchi – Frontiers in Microbiology

Bacterial Abilities and Adaptation Toward the Rhizosphere Colonization – Lucas D. Lopes – Frontiers in Microbiology

Review: Advances in research on Epichloë endophytes in Chinese native grasses – Hui Song – Frontiers in Microbiology

Water microbiome

Phytoplankton-associated bacterial community composition and succession during toxic diatom bloom and non-bloom events – Marilou P. Sison-Mangus – Frontiers in Microbiology

Distinct distribution patterns of prokaryotes between sediment and water in the Yellow River estuary – Guangshan Wei – Applied Microbiology and Biotechnology

Waste and pollution microbiome

Evaluating robustness of a diesel-degrading bacterial consortium isolated from contaminated soil – Mateusz Sydow – New Biotechnology

Metagenomic analysis of an ecological wastewater treatment plant’s microbial communities and their potential to metabolize pharmaceuticals – Ian N. Balcom – F1000 Research Preprint

Food microbiology

Review: Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing – J. Ronholm – Clinical Microbiology Reviews

Techniques

A robust ambient temperature collection and stabilization strategy: Enabling worldwide functional studies of the human microbiome – Ericka L. Anderson – Scientific Reports

Press: DNA Genotek’s OMNIgene®Ÿ GUT Kit is Proposed as Standardized Test for Worldwide Studies of the Human Microbiome – Globe NewsWire

More microbiology

Antibacterial activities of wasabi against Escherichia coli O157:H7 and Staphylococcus aureus – Zhongjing Lu – Frontiers in Microbiology

Resource Availability Modulates the Cooperative and Competitive Nature of a Microbial Cross-Feeding Mutualism – Tim A. Hoek – PLOS Biology

Microbes in the news

The women who discovered India’s first HIV cases – Geeta Pandey – BBC News

Captivity Makes Monkey Microbiomes More Human-Like – Ed Yong – The Atlantic

Interview with author of The Germ Files – Jason Tetro – Ben Libberton – Nature Microbiology Community

UGent researchers create bacteria that turns organic waste into plastic – Toon Lambrechts – Flanders Today

First DNA Sequencing in Space a Game Changer – NASA

UCSD alumna first to sequence DNA in space – Gary Robbins – San Diego Union Tribune