Category Archives: Human respiratory

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 12, 2016

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Infants with bronchiolitis, vitamin D receptor GWAS study, long-term effects of stool transplants, genome reduction in insect endosymbionts, San Francisco Bay denitrifying communities, resistomes in metagenomic datasets, Picodroplet WGA for metagenomics.

Jobs and events

Scientist/Senior Scientist opening at WholeBiome

Upcoming mothur and R workshops – Pat Schloss – Mothur

Pregnancy and early life

Rapid change of fecal microbiome and disappearance of Clostridium difficile in a colonized infant after transition from breast milk to cow milk – Manli Y. Davis – Microbiome

Human general and multisite microbiome

Multi-Body-Site Microbiome and Culture Profiling of Military Trainees Suffering from Skin and Soft Tissue Infections at Fort Benning, Georgia – Jatinder Singh – mSphere

Review: The human gastrointestinal tract and oral microbiota in inflammatory bowel disease: a state of the science review – Rosario Lucas López – APMIS

Human oral microbiome

Does obesity influence the subgingival microbiota composition in periodontal health and disease? – Suellen da Silva Maciel – Journal of Clinical Periodontology

Human respiratory microbiome

Throat Swabs and Sputum Culture as Predictors of P. aeruginosa or S. aureus Lung Colonization in Adult Cystic Fibrosis Patients – Darius Seidler – PLOS ONE

Association of nasopharyngeal microbiota profiles with bronchiolitis severity in infants hospitalised for bronchiolitis – Kohei Hasegawa – European Respiratory Journal

Human urinary tract microbiome

Changes in Urinary Microbiome Populations Correlate in Kidney Transplants With Interstitial Fibrosis and Tubular Atrophy Documented in Early Surveillance Biopsies –
B. D. Modena – American Journal of Transplantation

Human reproductive tract microbiome

Evidence that the endometrial microbiota has an effect on implantation success or failure – Immaculada Moreno – American Journal of Obstetrics & Gynecology

Human gut microbiome

Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes – Anna Heintz-Buschart – Nature Microbiology

Genome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota – Jun Wang – Nature Genetics

A Pair of Identical Twins Discordant for Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Differ in Physiological Parameters and Gut Microbiome Composition – Ludovic Giloteaux – American Journal of Case Reports

Unique Features of Ethnic Mongolian Gut Microbiome revealed by metagenomic analysis – Wenjun Liu – Scientific Reports

Long-term effects on luminal and mucosal microbiota and commonly acquired taxa in faecal microbiota transplantation for recurrent Clostridium difficile infection – Jonna Jalanka – BMC Medicine

Press: Healing effect of fecal microbiota transplantation lasts for long – Science Daily

Integrity of the Human Faecal Microbiota following Long-Term Sample Storage – Elahe Kia – PLOS ONE

Review: Signals from the gut microbiota to distant organs in physiology and disease -Bjoern O Schroeder – Nature Medicine

Review: The Gut Microbiome as Therapeutic Target in Central Nervous System Diseases: Implications for Stroke – Katarzyna Winek – Neurotherapeutics

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

Commentary: Microbiome: Should we diversify from diversity? – Katerina V.-A. Johnson – Gut Microbes

Review: I-Cubed (Infection, Immunity, and Inflammation) and the Human Microbiome – David S. Younger – Neurologic Clinics

Animal models

Microbiota of the Small Intestine Is Selectively Engulfed by Phagocytes of the Lamina Propria and Peyer’s Patches – Masatoshi Morikawa – PLOS ONE

Spatial and Temporal Shifts in Bacterial Biogeography and Gland Occupation during the Development of a Chronic Infection – Daniela Keilberg – mBio

Altered gut microbiota in female mice with persistent low body weights following removal of post-weaning chronic dietary restriction – Jun Chen – Genome Medicine

Animal microbiome

Mosquitoes host communities of bacteria that are essential for development but vary greatly between local habitats – Kerri L. Coon – Molecular Ecology

Review: Dissecting genome reduction and trait loss in insect endosymbionts – Amparo Latorre – Annals of the New York Academy of Sciences

Review: Beneficial microorganisms for honey bees: problems and progresses – Daniele Alberoni – Applied Microbiology and Biotechnology

Plant, root, and soil microbiome

The interplay between soil structure, roots, and microbiota as a determinant of plant–soil feedback – Joana Bergmann – Ecology and Evolution

Soil type determines the distribution of nutrient mobilizing bacterial communities in the rhizosphere of beech trees – O. Nicolitch – Soil Biology and Biochemistry

Bacterial selection for biological control of plant disease: criterion determination and validation – Monalize Salete Mota – Brazilian Journal of Microbiology

Killing two birds with one stone: Natural rice rhizospheric microbes reduce arsenic uptake and blast infections in rice – Venkatachalam Laksmanan – Frontiers in Plant Science

Bioenergy cropping systems that incorporate native grasses stimulate growth of plant-associated soil microbes in the absence of nitrogen fertilization – Lawrence G. Oates – Agriculture, Ecosystems & Environment

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

Review: Chatting With a Tiny Belowground Member of the Holobiome: Communication Between Plants and Growth-Promoting Rhizobacteria – R. Sharifi – Advances in Botanical Research

Water and extremophile microbiome

Spatiotemporal Characterization of San Francisco Bay Denitrifying Communities: a Comparison of nirK and nirS Diversity and Abundance – Jessica A. Lee – Microbial Ecology

Molecular diversity of plankton in a tropical crater lake switching from hyposaline to subsaline conditions: Lake Oloidien, Kenya – Wei Luo – Hydrobiologia

Distinct biogeographical patterns of marine bacterial taxonomy and functional genes – John Matthew Haggerty – Global Ecology and Biogeography

Waste and pollution microbiology

The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system – Jiaojiao Niu – Scientific Reports

Comparison of the microbial community composition of pristine rock cores and technical influenced well fluids from the Ketzin pilot site for CO2 storage – Linda Pellizzari – Environmental Earth Sciences

Food microbiology

Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir – Aaron M. Walsh – mSystems

Spatial and compositional variation in the fungal communities of organic and conventionally grown apple fruit at the consumer point-of-purchase – Ahmed Abdelfattah – Horticulture Research

Bioinformatics and metagenomics

Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis – Maria Hammond – Microbiome

The structure and diversity of human, animal and environmental resistomes – Chandan Pal – Microbiome

 

TreeScaper: Visualizing and Extracting Phylogenetic Signal from Sets of Trees – Wen Huang – Molecular Biology and Evolution

 

Proteomics

Mining gut microbiome oligopeptides by functional metaproteome display – Jonas Zantow – Scientific Reports

More microbiology

Multiple Signals Govern Utilization of a Polysaccharide in the Gut Bacterium Bacteroides thetaiotaomicron – Nathan D. Schwalm III – mBio

Living together in biofilms: the microbial cell factory and its biotechnological implications – Mercedes Berlanga – Microbial Cell Factories

Microbes in the news

The Virus With Spider DNA. How did part of a black-widow venom gene end up in a virus that infects one of the world’s most successful bacteria? – Ed Yong – The Atlantic

The Human Microbiome – ASM Cultures microbiome special featuring top scientists and biotech companies

The superhero in your vagina – Kendall Powell – Mosaic Science

Legionella Bacteria Detected at 4 American Airlines Hangars – ABC News

Study Sees Link Between Allergies and the Infant Gut – Robert Lee Hotz – Wall Street Journal

Breasts have their own microbiome – and it could influence your cancer risk
Your breast has its own unique ecosystem – Bec Crew – Science Alert

Researchers restored a colony of microbes in the gut – Ian Graber-Stiehl – Popular Science

Microbes and money

Second Genome Partners with King’s College London to Evaluate the Influence of the Microbiome in Landmark EAT Study – PR Newswire

MicroBiome Therapeutics’ NM504 For Improving Blood Glucose Regulation Is First Microbiome Modulator to Receive U.S. Patent Allowance – PR Web

Seres’s pioneering microbiome drug fails mid-stage trial – Mark Ratner

Farmers Are Manipulating Microbiomes to Help Crops Grow – Sarah Zhang – Wired

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 23, 2016

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Microbial dysbiosis in familial Crohn’s Disease, probiotic treatment of captive Colorado Toads, microbiome forecasting in the ocean, a new r package for phylogenetic trees, and MacArthur winner Dianne Newman.

General microbiome

Classic Spotlight: 16S rRNA Redefines Microbiology – Igor B. Zhulin – Journal of Bacteriology

Human vaginal microbiome

Microbiome Composition and Function Drives Wound-Healing Impairment in the Female Genital Tract – Alexander S. Zevin – PLOS Pathogens

Human respiratory microbiome

Clinical implications of microbial biofilms in chronic rhinosinusitis and orbital cellulitis – Niranjan Nayak – BMC Ophthalmology

Human gut microbiome

Bacteriome and Mycobiome Interactions Underscore Microbial Dysbiosis in Familial Crohn’s Disease – G. Hoarau – mBio

Prebiotic Effects of Xylooligosaccharides on the Improvement of Microbiota Balance in Human Subjects – Shyh-Hsiang Lin – Gastroenterology Research and Practice

Metformin and the Gut Microbiome in Diabetes – Sridevi Devaraj – Clinical Chemistry

Classic Spotlight: Bacteroides thetaiotaomicron, Starch Utilization, and the Birth of the Microbiome Era – George A. O’Toole – Journal of Bacteriology

Review: The human microbiome and juvenile idiopathic arthritis – Anouk Verwoerd – Pediatric Rheumatology

Animal experiments

A secreted bacterial peptidoglycan hydrolase enhances tolerance to enteric pathogens – Kavita J. Rangan – Science

Animal microbiome

Probiotic treatment restores protection against lethal fungal infection lost during amphibian captivity – Jordan G. Kueneman – Proceedings of the Royal Society B

Press: Probiotic treatment protects endangered Colorado toads from lethal fungal infection – University of Colorado Boulder

Plant, root, and soil microbiome

Microbial nitrification in throughfall of a Japanese cedar associated with archaea from the tree canopy – Keiji Watanabe – Springer Plus

Spatial heterogeneity of physicochemical properties explains differences in microbial composition in arid soils from Cuatro Cienegas, Mexico – Silvia Pajares – PeerJ

Taxonomic resolution is a determinant of biodiversity effects in arbuscular mycorrhizal fungal communities – Haishui Yang – Journal of Ecology

Water microbiome

Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone – Stilianos Louca – PNAS

New model could point way to microbiome forecasting in the ocean – Science Daily

Built environment microbiome

Buzz Off! An Evaluation of Ultrasonic Acoustic Vibration for the Disruption of Marine Microorganisms on Sensor Housing Materials – Jonathan S. McQuillan – Letters in Applied Microbiology

Bioinformatics and metagenomics

MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples – Moreno Zolfo – Nucleic Acids Resarch

ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data – Guangchuang Yu – Methods in Ecology and Evolution

Techniques

This article is not about primer barcodes, but compares 16S rRNA V6 PCR/454 sequencing to V4 PCR/Illumina sequencing:
Choice of molecular barcode will affect species prevalence but not bacterial community composition – Karen Lebret – Marine Genomics

Webinar | Combating the “garbage-in-garbage-out” paradigm: The importance of library prep in next-gen sequencing workflows – Maura Costello – Science

Microbes in the news

Bacteria have sculpted the world we live in, and that’s why MacArthur winner Dianne Newman studies them – Deborah Netburn – LA Times

Book Review: “Let Them Eat Dirt: Saving Your Child from an Oversanitized World” provides suggestions for a microbially rich and healthy childhood – Anne Estes – Mostly Microbes

Professionally printed version of Gut Check:The Microbiome Game available for a limited time from MOBIO. See below for a chance to win a free copy! – Anne Estes – Mostly Microbes

New Research Collaboration Explores Microbiome of the Space Station – Astrobiology Magazine

Swarms of magnetic bacteria could be used to deliver drugs to tumors – Science Daily

How do antibiotic-resistant bacteria get into the environment? – Suzanne Young and Valerie Harwood – The Conversation

Using bacteria to clean up oil – Anmar Frangoul – CNBC

Penn: Plant-made Antimicrobial Peptide Targets Dental Plaque and Gum Tissues – Penn News

Bacteria Hysteria

Note: little science here other than a 1997 paper, but lots of promotion for a certain manufacturer of stainless steel coffee mugs. Proceed with caution:
You should be washing your coffee mug way more than you think – Melia Robinson – Business Insider

And this one quotes a study from 1994, which looked at plant-based, not plastic sponges that were deliberately inoculated with pathogens. Proceed with caution:
Loofahs Have More Bacteria Than You Think — In Fact, You Should Probably Throw Yours Out – Lily Feinn – Bustle

Science, publishing, and career

Mark Zuckerberg and Priscilla Chan announce $3 billion effort aimed at curing disease – Shayla Love – STAT News

With some of my tweets!
A future without women – no female Future Prize nominees – Carla Bleiker – Deutsche Welle

September 20, 2016

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A review of antibiotics’ effect on the human microbiome, the pig gut microbiome, microbiome of Green Design, expanding Unifrac, and GutCheck, the Microbiome Game.

General human microbiome

Review: Antibiotic use and microbiome function – Manuel Ferrer – Biochemical Pharmacology

Human respiratory microbiome

Taxa of the Nasal Microbiome Are Associated with Influenza-Specific IgA Response to Live Attenuated Influenza Vaccine – Hannah M. Salk – PLOS ONE

Changes in the bacterial microbiome of patients with chronic rhinosinusitis after endoscopic sinus surgery – Ravi Jain – International Forum of Allergy & Rhinology

Human gut microbiome

Gastric microbiota in the functional dyspepsia patients treated with probiotic yogurt – Hirohiko Nakae – BMJ Open Gastroenterology

Animal microbiome

A reference gene catalogue of the pig gut microbiome – Liang Xiao – Nature Microbiology

Press: Gut Microbial Genes Profiled in Pigs From Diverse Breeds, Locations – Genome Web

The Prevalence of Canine Oral Protozoa and Their Association with Periodontal Disease – Niran Patel – The Journal of Eukaryotic Microbiology

Functional diversity of ant-associated bacterial communities – A. A. Dymova – Biology Bulletin

Plant, root, and soil microbiome

Can inoculation with living soil standardize microbial communities in soilless potting substrates? – Petra Bukovská – Applied Soil Ecology

Effects of saline water irrigation and fertilization regimes on soil microbial metabolic activity – Li -Juan Chen – Journal of Soils and Sediments

More on the Centralia coal mine fire (see yesterday’s post): Diversity and mechanisms of arsenic resistance among soil bacteria impacted by the ongoing Centralia coal mine fire – Taylor K Dunivin – PeerJ Preprint

Water and extremophile microbiome

Metagenomics as a preliminary screen for antimicrobial bioprospecting – Soha Al-Amoudi – Gene

Built environment microbiome

The Microbiome of Green Design: Sustainable building practices may have unforeseen consequences for microbial communities and human health – Carolyn Beans – BioScience

More microbiology

Cat-Scratch Disease in the United States, 2005–2013 – Christina A. Nelson – Emerging Infectious Diseases

Press: Don’t Kiss That Kitty: Cat-Scratch Fever Is Making People Sicker – Erin Ross – NPR

Bioinformatics and proteomics

Strategies to improve usability and preserve accuracy in biological sequence databases – Johan Bengtsson-Palme – Proteomics

Expanding the UniFrac Toolbox – Ruth G. Wong – PLOS ONE

MetaStorm: A Public Resource for Customizable Metagenomics Annotation – Gustavo Arango-Argoty – PLOS ONE

Microbes in the news

Gut Check: The Microbiome Game – MoBio
Gut Check: The Microbiome Game now available for purchase – David Coil – MicroBEnet

Antibiotic Resistant Bacteria and the World’s Peril: The U.N. General Assembly is taking on a danger that threatens the health of our entire species – Laurie Garrett – Scientific American

Scientists uncover a clever ranking strategy bacteria use to fight off viruses – NewsWire Rockefeller

Oetzi Iceman Update: Bacteria Found In Mummy’s Stomach May Lead To Cancer Research – Janice Williams – International Business News

Stone Age mummy still revealing secrets, 25 years on – Simon Sturdee – Phys.org

Lake Arrowhead Microbial Genomics #LAMG16 Report: Day 1 – David Coil – MicroBEnet

September 19, 2016

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Effects of siblings on infants’ microbiotas, kids with end-stage renal disease, gut microbiota of 4 termite species.

Pregnancy and early life

Association of household siblings with nasal and fecal microbiota in infants – Kohei Hasegawa – Pediatrics International

Human respiratory microbiome

Review: Linking Microbiota and Respiratory Disease – Matthias Hauptmann – FEBS Letters

Human blood ‘microbiome’

Changes in blood microbiota profiles associated with liver fibrosis in obese patients: A pilot analysis – Benjamin Lelouvier – Hepatology

Human gut microbiome

Intestinal microbiota in pediatric patients with end stage renal disease: a Midwest Pediatric Nephrology Consortium study – Janice Crespo-Salgado – Microbiome

Review: Interaction between gut microbiota and toll-like receptor: from immunity to metabolism – Jensen H.C. Yiu – Journal of Molecular Medicine

Animal and in vitro experiments

An intestinal microbiota-farnesoid X receptor axis modulates metabolic disease – Frank J. Gonzalez – Gastroenterology

Review: Modeling infectious diseases and host-microbe interactions in gastrointestinal organoids – Sina Bartfeld – Developmental Biology

Animal microbiome

Comparative Gut Microbiomes of Four Species Representing the Higher and the Lower Termites – LiJuan Su – Journal of Insect Science

Plant, root, and soil microbiome

Rare taxa maintain microbial diversity and contribute to terrestrial community dynamics throughout bark beetle infestation – Kristin M. Mikkelson – Applied and Environmental Microbiology

More microbes

Microbial herd protection mediated by antagonistic interaction in polymicrobial communities – Megan Wong – Applied and Environmental Microbiology

Microbes in the news

Attack of the plastic eaters: Can mushrooms, bacteria and mealworms save the planet from pollution? – Diane Stopyra – Salon

Harnessing the amazing work of the 40 trillion chemists in your gut microbiome – Emily P. Balskus – STAT News

 

Microbiome Companies Attract Big Investments – Brian Gormley – The Wall Street Journal

Mud Pies: Superfood for the Microbiome? – John L. Marshall – MedScape

 

 

September 12, 2016

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Individual response of gut microbiota to diet (in mice), appendicitis, adaptive evolution of goose with its microbiome, fungi in rubber plantations.

Events

Storify of days 1-2 of the 6th ASM Beneficial Microbes Meeting, Sept 9-12, Seattle, WA.

Pregnancy and birth

Urinary Microbiota Associated with Preterm Birth: Results from the Conditions Affecting Neurocognitive Development and Learning in Early Childhood (CANDLE) Study – Nicholas J. Ollberding – PLOS ONE

Review: The role of the bacterial microbiota on reproductive and pregnancy health – Deborah B. Nelson – Anaerobe

Human skin microbiome

Skin microbiome prior to development of atopic dermatitis: early colonization with commensal staphylococci at 2 months is associated with a lower risk of atopic dermatitis at 1 year – Elizabeth A. Kennedy – Journal of Allergy and Clinical Immunology

Human respiratory microbiome (and Methods)

Note that 2 different amplification strategies were performed, so IMHO this is more reflection of primer differences than sequencing differences: Different next generation sequencing platforms produce different microbial profiles and diversity in cystic fibrosis sputum – Andrea Hahn – Journal of Microbiological Methods

Human gut microbiome

Evaluation of the microbiome in children’s appendicitis – Martin Salö – International Journal of Colorectal Disease

Review: Food: a new form of personalised (gut microbiome) medicine for chronic diseases? – Tess Pallister – Journal of the Royal Society of Medicine

Review: Linking the Microbiota, Chronic Disease, and the Immune System – Timothy W. Hand – Trends in Endocrinology & Metabolism

Animal and bioreactor experiments

From the Sonnenburg lab @Stanford: Individualized Responses of Gut Microbiota to Dietary Intervention Modeled in Humanized Mice – Samuel A. Smits – mSystems

An In Vitro Approach to Study Effects of Prebiotics and Probiotics on the Faecal Microbiota and Selected Immune Parameters Relevant to the Elderly – Yue Liu – PLOS ONE

Animal microbiome

Genome and metagenome analyses reveal adaptive evolution of the host and interaction with the gut microbiota in the goose – Guangliang Gao – Scientific Reports

Hold off on the orange oil: Characterization of Antibacterial Activities of Eastern Subterranean Termite, Reticulitermes flavipes, against Human Pathogens – Yuan Zeng – PLOS ONE

Use of MALDI-TOF MS and culturomics to identify mosquitoes and their midgut microbiota – Fatalmoudou Tandina – Parasites & Vectors

Plant, root, and soil microbiome

Drought history affects grassland plant and microbial carbon turnover during and after a subsequent drought event – Lucia Fuchslueger – Journal of Ecology

Effect of organic matter enrichment on the fungal community in limestone cave sediments – ELS Marques – Genetics and Molecular Research

Contrasting elevational diversity patterns for soil bacteria between
two ecosystems divided by the treeline – Guixiang Li – Science China Life Sciences

Review: Diversity and ecology of soil fungal communities in rubber plantations – Jutamart Monkai – Fungal Biology Reviews

Illumina sequencing reveals a rhizosphere bacterial community associated with foxtail millet smut disease suppression – Yansha Han – Plant and Soil

Water and extremophile microbiome

Viruses-to-mobile genetic elements skew in the deep Atlantis II brine pool sediments – Mustafa Adel – Scientific Reports

Built environment microbiome

Review: The Microbiome of the Built Environment and Human Behavior: Implications for Emotional Health and Well-Being in Postmodern Western Societies – C.E. Stamper – International Review of Neurobiology

Microbes in the news

The Bacteria on Your Skin Are Safer Than These Two Chemicals the FDA Just Banned From Your Soap – Jill Richardson – Truth Digg

DNA in London Grave May Help Solve Mysteries of the Great Plague – Roff Smith – National Geographic

Bik’s Non-Microbiology Picks

This paper was discussed on Twitter this weekend because of a conflict of interest of one of the authors (Deepak Chopra) and the design and interpretation of the study:

Identification of Altered Metabolomic Profiles Following a Panchakarma-based Ayurvedic Intervention in Healthy Subjects: The Self-Directed Biological Transformation Initiative (SBTI) – Christine Tara Peterson – Scientific Reports

September 10, 2016

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Bifidobacteria and ulcerative colitis, the pollen microbiome, busting the 5-second rule, resistance genes in 23,000 microbial genomes, and a cool video of evolution of bacterial resistance.

Events

Gut health, microbiota & probiotics throughout the lifespan – Metabolic & Brain function 2016 – Sept 15-16, Harvard Medical School, Boston, MA

Human oral microbiome

Deep sequencing reveals microbiota dysbiosis of tongue coat in patients with liver carcinoma – Haifeng Lu – Scientific Reports

Human respiratory microbiome

Review: The microbiome in asthma – Magali Noval Rivas – Current Opinion Pediatrics

Human gut microbiome

Elucidating the gut microbiome of ulcerative colitis: bifidobacteria as novel microbial biomarkers – Sabrina Duranti – FEMS Microbiology Ecology

Review: Gut Microbiota, Inflammation, and Colorectal Cancer – Caitlin A. Brennan – Annual Review of Microbiology

Review: Microbiota—myeloid cell crosstalk beyond the gut – Sayeh Gorjifard – Journal of Leukocyte Biology

Four reviews in Current Pharmaceutical Design in the category “Could the gut microbiota perhaps be involved in disease X?” – with 4 different X’s. 

Animal models

Antibiotic Treatment Induces Long-lasting Changes in the Fecal Microbiota that Protect Against Colitis – Naomi L. Ward – Inflammatory Bowel Diseases

Differences In CD8αα And Cecal Microbiome Community During Proliferation And Late Cytolytic Phases Of Marek’s Disease Virus (MDV) Infection Are Associated With Genetic Resistance To Marek’s Disease – Sudeep Perumbakkam – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Bacterial microbiota associated with flower pollen is influenced by pollination type, and shows a high degree of diversity and species-specificity – Binoy Ambika Manirajan – Environmental Microbiology

Land use intensification in the humid tropics increased both alpha and beta diversity of soil bacteria – Teotonio Soares de Carvalho – Ecology

Small-scale spatial heterogeneity of ecosystem properties, microbial community composition and microbial activities in a temperate mountain forest soil – Martina Štursová – FEMS Microbiology Ecology

Extremophile microbiome

Seasonal dynamics of extremely halophilic microbial communities in three Argentinian salterns – Leonardo Di Meglio – FEMS Microbiology Ecology

Built environment microbiome

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Christin Lola / Fotolia (via Science Direct)

Longer Contact Times Increase Cross-Contamination of Enterobacter aerogenes from Surfaces to Food – Robyn C. Miranda – Applied and Environmental Microbiology

Researchers debunk ‘five-second rule’: Eating food off the floor isn’t safe. Sometimes bacteria transfer in less than a second – Science Daily

Forget the ‘five-second rule’: Food dropped on the floor picks up bacteria in just ONE second – David Gardner – Daily Mail

Antimicrobial Chemicals Are Associated with Elevated Antibiotic Resistance Genes in the Indoor Dust Microbiome – Erica M. Hartmann – Environmental Science & Technology

Antibiotic Resistance Genes in Indoor Dust – Technology Networks

Metagenomics and bioinformatics

The transfer network of bacterial mobile resistome connecting animal and human microbiome – Yongfei Hu – Applied and Environmental Microbiology

Catalog of Mobile Antibiotic Resistance Genes Helps Explain Transfer to Human Pathogens – Genome Web

Chinese investigators characterize the world of resistance gene exchange among bacteria – Phys.org

Phages and viruses

Bacteriophages in clinical samples can interfere with microbiological diagnostic tools – Maryury Brown-Jaque – Scientific Reports

Techniques

Absolute quantification of microbial taxon abundances – Ruben Props – The ISME Journal

Microbes in the news

Jo Handelsman of White House Office of Science and Technology to Speak Monday – University of Tennessee

WATCH: Bacteria Invade Antibiotics And Transform Into Superbugs – Angus Chen – NPR
This might be the coolest visualization of evolution ever. Watch these bacteria evolve antibiotic resistance in just 12 days – Brian Resnick – Vox

These researchers would like you to mail them your gut bacteria – Katherine Lindemann – Research Gate Blog

Hepatitis A Outbreak Linked to Strawberries at Smoothie Chain – Daniel Victor – New York Times

Bacteria Hysteria

M&S becomes first supermarket to offer anti-bacterial shopping bags to banish bugs such as E. coli –  Katie Morley – The Telegraph

Bik’s non-microbiology Picks

Microbiome analysis, please! Giraffes aren’t just giraffes. Turns out there are four species – Rachel Feltman – Washington Post

Flatworm parasite named after Barack Obama: Is that a compliment? – Rowena Lindsay Christian Science Monitor

 

September 6, 2016

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Tongue diagnostics and bacterial communities, microbiome and ALS, flowers and bees sharing microbes, and CRISPR assembly.

Events

4th World Congress on Targeting Microbiota is organized at Institut Pasteur, Paris, France – October 17-19, 2016

How the Indoor Microbiome Influence Health, with Jack A. Gilbert – October 27, 2016 at British International School of Chicago – Lincoln Park in Chicago

Human oral microbiome

Bacillus as a potential diagnostic marker for yellow tongue coating – Juan Ye – Scientific Reports

Human skin microbiome

Redefining the Chronic-Wound Microbiome: Fungal Communities Are Prevalent, Dynamic, and Associated with Delayed Healing – Lindsay Kalan – mBio

Human respiratory tract microbiome

Review: Development of the respiratory tract microbiota in cystic fibrosis – Emma M. de Koff – Current Opinion in Pulmonary Medicine

Human urinary tract microbiome

Commentary: “Urinary tract infection” and the microbiome – Thomas E. Finucane – The American Journal of Medicine

Human gut microbiome

Pitfalls in Inferring Human Microbial Dynamics from Temporal Metagenomics Data – Hong-Tai Cao – bioRxiv

Evaluation of the microbial diversity in amyotrophic lateral sclerosis using high-throughput sequencing – Xin Fang – Frontiers in Microbiology

Review: Beyond 16S rRNA community profiling: intra-species diversity in the gut microbiota – Kirsten M. Ellegaard – Frontiers in Microbiology

Review: Epigenetic mechanisms in microbial members of the human microbiota: current knowledge and perspectives – Natacha Cureau – Future Medicine

Microbiology and immunology

Perspective: Autoimmunity and the microbiome: T-cell receptor mimicry of “self” and microbial antigens mediates self tolerance in holobionts – Robert Root-Bernstein – BioEssays

Animal models of microbiome research

Ketogenic diet modifies the gut microbiota in a murine model of autism spectrum disorder – Christopher Newell – Molecular Autism

Animal microbiome

Disentangling a holobiont – recent advances and perspectives in Nasonia wasps – Jessica Dittmer – Frontiers in Microbiology

Review: The terrestrial isopod microbiome: An all-in-one toolbox for animal-microbe interactions of ecological relevance – Didier Bouchon – Frontiers in Microbiology

Plant, root, and soil microbiome

Microbial communities in passive remediation systems at three abandoned coal mine sites in the United Kingdom – Carmen Falagán – Proceedings IMWA 2016, Freiberg

Primary Succession of Nitrogen Cycling Microbial Communities Along the Deglaciated Forelands of Tianshan Mountain, China – Jun Zeng – Frontiers in Microbiology

Flowers and Wild Megachilid Bees Share Microbes – Quinn S. McFrederick – Microbial Ecology

Triclosan Resistome from Metagenome Reveals Diverse Enoyl Acyl Carrier Protein Reductases and Selective Enrichment of Triclosan Resistance Genes – Raees Khan – Scientific Reports

Water and extremophile microbiome

Oligotrophic Lagoons of the South Pacific Ocean Are Home to a Surprising Number of Novel Eukaryotic Microorganisms – Eunsoo Kim – Environmental Microbiology

Upstream freshwater and terrestrial sources are differentially reflected in the bacterial community structure along a small Arctic river and its estuary – Aviaja L. Hauptmann – Frontiers in Microbiology

Built environment microbiology

Review: Emerging Investigators Series: Sewer surveillance for monitoring antibiotic use and prevalence of antibiotic resistance: urban sewer epidemiology – Nicole Fahrenfeld – Environmental Science: Water Research & Technology

Food microbiology

High-throughput identification of the microbial biodiversity of cocoa bean fermentation by MALDI-TOF MS – S. Miescher Schwenninger – Letters in Applied Microbiology

Bioinformatics and metagenomics

Assemble CRISPRs from metagenomic sequencing data – Jikai Lei – Bioinformatics

Contig annotation tool CAT robustly classifies assembled metagenomic contigs and long sequences – Diego D. Cambuy – bioRxiv

Techniques

High throughput sequencing of multiple amplicons for barcoding and integrative taxonomy – Perrine Cruaud – bioRxiv

Microbes in the news

Podcast (12 min) with Stephen Pointing: Protecting the Earth’s Microbiome – Jesse Mulligan – Radio NZ

Biochemists’ discovery could lead to vaccine against ‘flesh-eating’ bacteria – Science Daily

Enzyme from oral bacteria could be potential therapy for celiac disease – News Medical

Bik’s Non-Microbiology Picks

Bizarre ant colony discovered in an abandoned Polish nuclear weapons bunker – Annalee Newitz – ArsTechnica

September 1, 2016

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Bedouins, urban Saoudis and monkeys, a subglacial lake, and the oldest microbial fossils.

Events

Alfred P. Sloan Foundation Workshop on Viruses to be Held in Singapore, January 2017 – David Coil – MicroBEnet

Human respiratory microbiome

News: Does barnyard dust protect Amish children from asthma? – Bryant Furlow – The Lancet

Human gut microbiome

Gut microbiome and dietary patterns in different Saudi populations and monkeys – Emmanouil Angelakis – Scientific Reports

Fecal Microbiota Transplantation is Safe and Efficacious for Recurrent or Refractory Clostridium difficile Infection in Patients with Inflammatory Bowel Disease – Monika Fischer

Animal experiments

High fat diet drives obesity regardless the composition of gut microbiota in mice – Sylvie Rabot – Scientific Reports

Gut Microbiota Promote Angiotensin II–Induced Arterial Hypertension and Vascular Dysfunction – Susanne H. Karbach – Hypertension

Plant, root, and soil microbiome

Forest area and connectivity influence root-associated fungal communities in a fragmented landscape – Rachel L. Vannette – Ecology

Review: Comparative phylogenomics of symbiotic associations – Pierre-Marc Delaux – New Phytologist

Water and extremophile

Microbial Community Structure of Subglacial Lake Whillans, West Antarctica – Amanda M. Achberger – Frontiers in Microbiology

Dust microbiome

Poultry houses: DNA from dust: comparative genomics of large DNA viruses in field surveillance samples – Utsav Pandey – bioRxiv

Techniques

Direct 16S rRNA-seq from bacterial communities: a PCR-independent approach to simultaneously assess microbial diversity and functional activity potential of each taxon – Riccardo Rosselli – Scientific Reports

More microbiology

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Geological map and location of microbial structures

Rapid emergence of life shown by discovery of 3,700-million-year-old microbial structures – Allen P. Nutman – Nature

Press: Life thrived on young Earth: scientists discover 3.7-billion-year-old fossils – Science Daily
The World’s Oldest Fossils Are 3.7 Billion Years Old. The newly discovered rocks suggest that life arose very quickly after the Earth was formed – Ed Yong – The Atlantic

Microbes in the news

Microbial genomics and the future of food microbiology – Julie Wolf – American Society for Microbiology

Space Microbiome? Yes Please! and I’ll take a minION sequencer as well if you don’t mind – Ben Libberton – NPJ Biofilms Community

Multitalented microbiology student is highly lauded for her scholarship – Western Michigan University

Manuka honey makes bacteria less resistant to antibiotics – Rowena Jenkins – The Conversation

Changes in Gut microflora – early warning of Equine Metabolic Syndrome (EMS)? – Jackie Bellamy-Zions – Harness Link

uBiome Hires New Vice President of Research and Development: Dr. Audrey Goddard Joins from Genomic Health and Genentech – PR Web

Samorost 3’s fairy tale of microbiology is now on iPhone – Chris Priestman – Kill Screen

Science, publishing, and career

How to Motivate Your Employees: Give Them Compliments and Pizza – Melissa Dahl – New York Magazine

Opinion: Fixing Science’s Human Bias. It’s time to accelerate the conversation about why the research community is still not diverse – Edward Courchaine and Sarah Smaga – The Scientist

Thanks to the glass ceiling breakers – Yarrow Axford – Science

Peer review

HT: Tomer Altman: Stupid Patent of the Month: Elsevier Patents Online Peer Review – Electronic Frontier Foundation

Research Integrity

OMICS vs. The FTC: Plagiarism at a Predatory Publisher – Neuroskeptic – Discover