Category Archives: Water microbiome

October 15, 2016

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Bacteria in wounds, Oxalobacter and kidney stones, harbor seals, sables, leeches, response to afforestation, subglacial lake, polluted river water.

Human skin and wound microbiome

Bacterial Contribution in Chronicity of Wounds – Kashif Rahim – Microbial Ecology

Human gut microbiome

The fecal microbiota as a biomarker for disease activity in Crohn’s disease – Danyta. I. Tedjo – Scientific Reports

Review: Fungi in the healthy human gastrointestinal tract – Heather E. Hallen-Adams – Virulence

Animal and other experiments

Anti-obese effects of two lactobacilli and two bifidobacteria on ICR mice fed on a high fat diet – Zhipeng Li – Biochemical and Biophysical Research Communications

Skin microbiome promotes mast cell maturation by triggering stem cell factor (SCF) production in keratinocytes – Zhenping Wang – Journal of Allergy and Clinical Immunology

Diet-related gut bacterial dysbiosis correlates with impaired development, increased mortality and Nosema disease in the honeybee (Apis mellifera) – Patrick W. Maes – Molecular Ecology

Oxalobacter formigenes–Derived Bioactive Factors Stimulate Oxalate Transport by Intestinal Epithelial Cells – Donna Arvans – Journal of the American Society of Nephrology

Press: Factors secreted by gut bacteria may help combat kidney stones – Science Daily

Protein- and zinc-deficient diets modulate the murine microbiome and metabolic phenotype – Jordi Mayneris-Perxachs – The American Journal of Clinical Nutrition

Animal microbiome

Comparative analysis of the fecal bacterial community of five harbor seals (Phoca vitulina) – Daniela Numberger – MicrobiologyOpen

Comparison of the bacterial communities in feces from wild versus housed sables (Martes zibellina) by high-throughput sequence analysis of the bacterial 16S rRNA gene – Yu Guan – AMB Express

Host Matters: Medicinal Leech Digestive-Tract Symbionts and Their Pathogenic Potential – Jeremiah N. Marden – Frontiers in Microbiology

Plant, root, and soil microbiome

Interkingdom Responses to Bacterial Quorum Sensing Signals Regulate Frequency and Rate of Nodulation in Legume–Rhizobia Symbiosis – Andrew G. Palmer – ChemBioChem

Development of Soil Bacterial Communities in Volcanic Ash Microcosms in a Range of Climates – Dorsaf Kerfahi – Microbial Ecology

Response of soil microbial community to afforestation with pure and mixed species – Anna Gunina – Plant and Soil

Experimental Climate Change Modifies Degradative Succession in Boreal Peatland Fungal Communities – Asma Asemaninejad – Microbial Ecology

The role of arbuscular mycorrhizal fungi in grain production and nutrition of sorghum genotypes: Enhancing sustainability through plant-microbial partnership – Adam B. Cobb – Agriculture, Ecosystems & Environment

Arbuscular mycorrhizal fungal assemblages in biological crusts from a Neotropical savanna are not related to the dominant perennial Trachypogon – R.M. Hernández-Hernández – Science of the Total Environment

Review: Belowground nitrogen transfer from legumes to non-legumes under managed herbaceous cropping systems. A review – Malinda S. Thilakarathna – Agronomy for Sustainable Development

Water and extremophile microbiome

Virulence and biodegradation potential of dynamic microbial communities associated with decaying Cladophora in Great Lakes – Chan Lan Chun – Science of The Total Environment

A monotonically declining elevational pattern of bacterial diversity in freshwater lake sediments – Jin Zeng – Environmental Microbiology

Grazers structure the bacterial and algal diversity of aquatic metacommunities – Julia Birtel – Ecology

Changes of the bacterial abundance and communities in shallow ice cores from Dunde and Muztagata glaciers, Tibetan Plateau – Yong Chen – Frontiers in Microbiology

Physiological ecology of microorganisms in Subglacial Lake Whillans – Trista J. Vick-Majors – Frontiers in Microbiology

Built environment microbiome

Microorganisms in Confined Habitats: Microbial Monitoring and Control of Intensive Care Units, Operating Rooms, Cleanrooms and the International Space Station – Maximilian Mora – Frontiers in Microbiology

Waste and pollution microbiology

Environmental Drivers of Differences in Microbial Community Structure in Crude Oil Reservoirs across a Methanogenic Gradient – Jenna L. Shelton – Frontiers in 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

Response of Core Microbial Consortia to Chronic Hydrocarbon Contaminations in Coastal Sediment Habitats – Mathilde Jeanbille – Frontiers in Microbiology

Bioinformatics and metagenomics

Bacterial human virulence genes across diverse habitats as assessed by in silico analysis of environmental metagenomes – Ditte A. Søborg – Frontiers in Microbiology

Microbes in the news

Reflections on 1500 blog posts at #microbenet – David Coil – Microbe.net

Staff Pick: ‘I Contain Multitudes’ by Ed Yong – Publishers Weekly

Mapping the Subway’s Microbiome – Grégory Fléchet – CNRS News

Your child’s microbiome, and why its health matters – Jennifer Graham – Statesboro Herald

Enquiring About Tolerance (EAT) study: Second Genome, King’s College London study eczema, food allergies in infants – Healio

The ‘Swiss Agent’: Long-forgotten research unearths new mystery about Lyme disease – Charles Piller – STAT News

What radiation-resistant space fungus can do for drug discovery – Shayla Love – STAT News

3 New Vaccines Against ‘Black Death’ Plague Bacteria Show Promise – Rachael Rettner – Live Science

Scientists engineer ‘glow in the dark’ bacteria – to help spot the bugs that cause food poisoning – Lizzie Parry – The Sun

If you want to make bacteria glow, give it a virus – Ben Coxworth – New Atlas

How the Gut Microbiome May Help Us Prevent IBD – Science Blog

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 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 3, 2016

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Gut microbiota in a Belgian nursing home,  aspirin and antibiotics, and Enterococcus in fecal samples of wild marine species. Please note that the next couple of days won’t leave me much time to run literature searches after work-hours. I might publish less and shorter posts, but I hope to be back soon!

Pregnancy and birth

Review: Impact of Maternal Nutrition in Pregnancy and Lactation on Offspring Gut Microbial Composition and Function – Derrick M Chu – Gut Microbes

Human oral microbiome

Microbiome in the Apical Root Canal System of Teeth with Post-Treatment Apical Periodontitis – José F. Siqueira Jr, – PLOS ONE

Bacterial community of saliva in adults with and without periodontitis – Jianye Zhou – Int J Clin Exp Med

Human gut microbiome

Longitudinal survey of Clostridium difficile presence and gut microbiota composition in a Belgian nursing home – Cristina Rodriguez – BMC Microbiology

Dysbiosis of small intestinal microbiota in liver cirrhosis and its association with etiology – Yanfei Chen – Scientific Reports

Editorial: Disease-Associated Microbial Communities in Healthy Relatives: A Bacteria-Filled Crystal Ball? – Mark R. Frey – CMGH Cellular and Molecular Gastroenterology and Hepatology

Review: The association between the gut microbiota and the inflammatory bowel disease activity: a systematic review and meta-analysis – Michelle Prosberg – Scandinavian Journal of Gastroenterology

Animal models

Reduced metabolic activity of gut microbiota by antibiotics can potentiate the antithrombotic effect of aspirin – In Sook Kim – Biochemical Pharmacology

Bacterial Abscess Formation Is Controlled by the Stringent Stress Response and Can Be Targeted Therapeutically – Sarah C. Mansour – EBioMedicine

Press: New weapon for hard-to-treat bacterial infections – Science Daily

Animal microbiome

Enterococcus species diversity in fecal samples of wild marine species by real-time PCR – Aline Weber Medeiros – Canadian Journal of Microbiology

A Metabarcoding Survey on the Fungal Microbiota Associated to the Olive Fruit Fly – Antonino Malacrinò – Microbial Ecology
Drosophila Adaptation to Viral Infection through Defensive Symbiont Evolution – Vitor G. Faria – PLOS Genetics

Press: Evolution of a species also involves the bacteria it carries – Science Daily

Plant, root, and soil microbiome

Assemblages of fungi associated with cork oak forests in northwestern Tunisia – Mourad Ben Hassine Ben Ali – Nova Hedwigia

Nutrient enrichment induces dormancy and decreases diversity of active bacteria in salt marsh sediments – Patrick J. Kearns – Nature Communications

Book chapter: Plant Growth-Promoting Bacteria: A Good Source for Phytoremediation of Metal-Contaminated Soil – Iqra Munir – Phytoremediation

Water and extremophile microbiome

Differences in the Composition of Archaeal Communities in Sediments from Contrasting Zones of Lake Taihu – Xianfang Fan – Frontiers in Microbiology

Seasonal Variation in an Acid Mine Drainage Microbial Community – Ryan Richard Auld – Canadian Journal of Microbiology

Distribution and Diversity of Microbial Eukaryotes in Bathypelagic Waters of the South China Sea – Dapeng Xu – Journal of Eukaryotic Microbiology

Built environment microbiome

Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden) – Kessy Abarenkov – MycoKeys

Bioaerosols in the Barcelona subway system – X. Triadó-Margarit – Indoor Air

Metagenomics, metatranscriptomics, and bioinformatics

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics – Christian Rinke – PeerJ

SAMSA: a comprehensive metatranscriptome analysis pipeline – Samuel T. Westreich – BMC Bioinformatics

More microbiology

Resveratrol suppresses NTHi-induced inflammation via up-regulation of the negative regulator MyD88 short – Carla S. Andrews – Scientific Reports

Press: Does red wine have health benefits? – Tim Sandle – Digital Journal
Resveratrol can help to reduce inflammation, study finds – Medical Xpress

Microbes in the news

Does gum disease have a link to cancer, dementia, stroke? – Suzanne Allard Levingston – Washington Post

From smart socks for diabetes to hand rehab: Health 2.0’s most interesting startups. DayTwo seeks to use insights from evaluating users’ microbiome to guide their diet choices – Stephanie Baum – MedCityNews

Graceleigh, Inc. Recalls Sammy’s Milk Baby Food Because of Possible Health Risk – FDA

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 28, 2016

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Twins, body fat, and bacteria, dietary zinc and C. diff infections, honey inhibits biofilm formation, microbial life in a Great Lake sinkhole.

Pregnancy and early life

Review: The Eukaryotic Microbiome: Origins and Implications for Fetal and Neonatal Life -William B. Miller Jr. – Frontiers in Pediatrics

Human gut microbiome

Heritable components of the human fecal microbiome are associated with visceral fat – Michelle Beaumont – Genome Biology

Press: Body fat link to bacteria in faeces – BBC
How Gut Bacteria May Predict Belly Fat – Alice Park – Time

Characterisation of the faecal microbiota in Japanese patients with paediatric-onset primary sclerosing cholangitis – Kentaro Iwasawa – Gut

Commentary: Thinking with your stomach? Gut feelings on microbiome modulation of brain structure and function (Commentary on Luczynski et al.) – Anthony J. Hannan – European Journal of Neuroscience

Dietary zinc alters the microbiota and decreases resistance to Clostridium difficile infection – Joseph P Zackular – Nature Medicine

Editorial: Devil in the detail: A closer look at childhood obesity and the gut microbiota – Michael W. Taylor – Environmental Microbiology

News and views: Culturing: Looking it up in our gut – Clarisse Marotz – Nature Microbiology

Animal microbiome

Spatial Heterogeneity of Gut Microbial Composition along the Gastrointestinal Tract in Natural Populations of House Mice – Taichi A. Suzuki – PLOS ONE

Plant, root, and soil microbiome

Using a Control to Better Understand Phyllosphere Microbiota – Andrea R. Ottesen – PLOS ONE

Caves: Microbial contributions to subterranean methane sinks – J. T. Lennon – Geobiology

Diatom blooms and associated vegetation shifts in a subarctic peatland: responses to distant volcanic eruptions? – U. Kokfelt – Journal of Quaternary Science

The Green Tetrahymena utriculariae n. sp. (Ciliophora, Oligohymenophorea) with Its Endosymbiotic Algae (Micractinium sp.), Living in Traps of a Carnivorous Aquatic Plant – Gianna Pitsch – The Journal of Eukaryotic Microbiology

Differential Communications between Fungi and Host Plants Revealed by Secretome Analysis of Phylogenetically Related Endophytic and Pathogenic Fungi – Xihui Xu – PLOS ONE

Fungal Endophytes as a Metabolic Fine-Tuning Regulator for Wine Grape – Ming-Zhi Yang – PLOS ONE

Water and extremophile microbiome

Groundwater shapes sediment biogeochemistry and microbial diversity in a submerged Great Lake sinkhole – L. E. Kinsman-Costello – Geobiology

Nutrient enrichment induces dormancy and decreases diversity of active bacteria in salt marsh sediments – Patrick J. Kearns – Nature Communications

Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes – Jan-Hendrik Hehemann – Nature Communications

Proteomics

The impact of sequence database choice on metaproteomic results in gut microbiota studies – Alessandro Tanca – Microbiome

More microbiology

Diluted honey inhibits biofilm formation: potential application in urinary catheter management? – Somadina Emineke – Journal of Clinical Pathology

Press: Manuka honey may help prevent life-threatening urinary infections – Simon Hendel – The Conversation
Honey May Be a Natural Way to Beat Bacteria – Alexandra Sifferlin – Time

Personalized therapeutic cocktail of wild environmental phages rescues mice from A. baumannii wound infections – James M. Regeimbal – Antimicrobial Agents and Chemotherapy

Press: A Cocktail Of Wild Viruses Treats Bacterial Wound Infections In Mice – Alex Berezow – American Council on Science and Health

Microbes in the news

Chicago Shedd Aquarium Studies Microbes’ Effect on Sea Life – Illumina

The 3 Robs: NIH Funds Research to See if Gut Microbiomes of Hispanics/Latinos Influence Their Diabetes Risk – Albert Einstein College of Medicine

Antibiotic resistance can occur naturally in soil bacteria – Science Daily

Science, publishing, and career / Peer review

Author affiliation can bias peer review: Single-blind vs Double-blind Peer Review in the Setting of Author Prestige – Kanu Okike – JAMA

September 27, 2016

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Pediatric multiple sclerosis,  Hydra as a microbiome model, species from bat feces, textile wastewater, and sample preparation for metabolomics.

Events

HIV Microbiome Workshop 2016, November 17-18, 2016, NIH Campus, Bethesda, MD. Here is the program

Pregnancy and early life

Association of Chorioamnionitis with Aberrant Neonatal Gut Colonization and Adverse Clinical Outcomes – Kriti Puri – PLOS ONE

Human respiratory microbiome

Translational Aspects of the Human Respiratory Virome – Alicia B Mitchell – American Journal of Respiratory and Critical Care Medicine

Human skin and gut microbiome

The role of skin and gut microbiota in the development of atopic eczema – T. Marrs – British Journal of Dermatology

Associations between the gut microbiota and host immune markers in pediatric multiple sclerosis and controls – Helen Tremlett – BMC Neurology

Intestinal Dysbiosis and Yeast Isolation in Stool of Subjects with Autism Spectrum Disorders – Maria Rosaria Iovene – Mycopathologia

Interactions between Obesity Status and Dietary Intake of Monounsaturated and Polyunsaturated Oils on Human Gut Microbiome Profiles in the Canola Oil Multicenter Intervention Trial (COMIT) – Shuaihua Pu – Frontiers in Microbiology

Review: Diet Influence on the Gut Microbiota and Dysbiosis related to Nutritional Disorders – Maryam Tidjani Alou – Human Microbiome Journal

Review: Role of the Intestinal Microbiota in Host Responses to Stressor Exposure – A.R. Mackos – International Review of Neurobiology

Review: Exploring relationships between host genome and microbiome: new insights from genome-wide association studies – Muslihudeen A. Abdul-Aziz – Frontiers in Microbiology

Animal models

Vitamin D and allergic airway disease shape the murine lung microbiome in a sex-specific manner – Michael Roggenbuck – Respiratory Research

Perspective: Transitioning from microbiome composition to microbial community interactions: the potential of the metaorganism Hydra as an experimental model – Peter Deines – Frontiers in Microbiology

Animal microbiome

Bats: Species From Feces: Order-Wide Identification of Chiroptera From Guano and Other Non-Invasive Genetic Samples – Faith M. Walker – PLOS ONE

Symbionts modify interactions between insects and natural enemies in the field – Jan Hrček – Journal of Animal Ecology

Plant, root, and soil microbiome

Cultivated Sub-Populations of Soil Microbiomes Retain Early Flowering Plant Trait – Kevin Panke-Buisse – Microbial Ecology

Effects of Artificial Soil Aeration Volume and Frequency on Soil Enzyme Activity and Microbial Abundance when Cultivating Greenhouse Tomato – Yuan Li – Soil Science Society of America Journal

Water and pollution microbiome

Degradation of crude oil in a contaminated tidal flat area and the resilience of bacterial community – Jaejin Lee – Marine Pollution Bulletin

Assessing the composition of microbial communities in textile wastewater treatment plants in comparison with municipal wastewater treatment plants – Ken Meerbergen – MicrobiologyOpen

Metabolomics

Sample preparation procedures utilized in microbial metabolomics: an overview – Małgorzata Patejko – Journal of Chromatography B

More microbiology

The quest for the minimal bacterial genome – Esteban Martínez-García – Current Opinion in Biotechnology

Microbes in the news

Inaugural lecture will explore some microbes’ invisible war on humans – University of Kansas

 

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 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