Category Archives: Water microbiome

September 24, 2016

Posted on by

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

Posted on by

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 21, 2016

Posted on by

Secretor status of mother affects infant’s gut microbiota development, differences between lean and obese kids, effect of ozone levels on plant microbiomes.

Pregnancy and early life

Mothers Secretor Status Affects Development of Childrens Microbiota Composition and Function: A Pilot Study – Paula Smith-Brown – PLOS ONE

Press: Research reveals importance of breast milk gene for toddler gut bacteria – University of Queensland

Human vaginal microbiome

Evaluation of Lysis Methods for the Extraction of Bacterial DNA for Analysis of the Vaginal Microbiota – Christina Gill – PLOS ONE

Human urinary tract microbiome

Review: Urinary incontinence: Making sense of the urinary microbiota in clinical urology – Gregor Reid – Nature Reviews Urology

Human gut microbiome

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

Role of Gut Microbiota and Short Chain Fatty Acids in Modulating Energy Harvest and Fat Partitioning in Youth – Martina Goffredo – Journal of Clinical Endocrinology & Metabolism

Press: Gut bacteria differ between obese and lean youth – MedicalXpress
Fat Flora? Gut Bacteria Differ in Obese Kids – Christopher Wanjek – LiveScience

Conference poster: Unique Gut Microbiome Triggers Ankylosing Spondylitis, Research Hints – Nancy A. Melville – Medscape

Review: The Microbiome: a Revolution in Treatment for Rheumatic Diseases? – James T. Rosenbaum – Current Rheumatology Reports

Review: Gut Instincts: microbiota as a key regulator of brain development, ageing and neurodegeneration – Timothy G. Dinan – The Journal of Physiology

Animal models

Interleukin-15 promotes intestinal dysbiosis with butyrate deficiency associated with increased susceptibility to colitis – Marlies Meisel – The ISME Journal

Animal microbiome

In situ visualization of bacterial populations in coral tissues: pitfalls and solutions – Naohisa Wada – PeerJ

Plant, root, and soil microbiome

Effects of Elevated Tropospheric Ozone Concentration on the Bacterial Community in the Phyllosphere and Rhizoplane of Rice – Yoshiaki Ueda – PLOS ONE

Rhizospheric Bacterial Community of Endemic Rhododendron arboreum Sm. Ssp. delavayi along Eastern Himalayan Slope in Tawang – Rajal Debnath – Frontiers in Plant Science

Does cryptic microbiota mitigate pine resistance to an invasive beetle-fungus complex? Implications for invasion potential – Chihang Cheng – Scientific Reports

Microbial Community Dynamics and Response to Plant Growth-Promoting Microorganisms in the Rhizosphere of Four Common Food Crops Cultivated in Hydroponics – C. Sheridan – Microbial Ecology

Review: The Plant Microbiota: Systems-Level Insights and Perspectives – Daniel B. Müller – Annual Review of Genetics

Water microbiome

Revealing the relationship between microbial community structure in natural biofilms and the pollution level in urban rivers: a case study in the Qinhuai River basin, Yangtze River Delta – Wei Cai – Wter Science & Technology

Metagenomics and bioinformatics

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

TreeScaper: visualizing and extracting phylogenetic signal from sets of trees – Wen Huang – Molecular Biology and Evolution

Techniques

Microbial community analysis using MiSeq sequencing in a novel configuration fluidized bed reactor for effective denitrification – Phatchariya Rungkitwatananukul – Bioresource Technology

A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq – Catherine M. Burke – PeerJ

More microbiology

A Comprehensive Study of Cyanobacterial Morphological and Ecological Evolutionary Dynamics through Deep Geologic Time – Josef C. Uyeda – PLOS ONE

Microbes in the news

The Perks of Manipulating the Microbiome: Probiotics, poop pills and … – Lynne Peeples – Gastroenterology & Endoscopy News

About paper that came out in June: The Breast Has Its Own Microbiome—and the Mix of Bacteria could Prevent or Encourage Cancer – Knvul Sheikh – Scientific American

Plants take it all in to deal with bacteria – Science Daily

Purdue scientists have bright idea for detecting harmful bacteria in food products – Purdue University

UCR professor discovers bacterial connection between wild bees and flowers – Som Chaturvedi – The Highlander (belongs to this paper)

Microbes and money

Skin Microbiome Company Mother Dirt Launches First-Ever Biome-Friendly Moisturizer
AOBiome’s consumer division expands skin product line to complement signature AO+Mist – PR Newswire

Science, publishing, and career

Sad outcome of survey: “Although the majority of department chairs value educational scholarship, only a minority perceive value in faculty blogging effort”. Does Academic Blogging Enhance Promotion and Tenure? A Survey of US and Canadian Medicine and Pediatric Department Chairs – Christian Blake Cameron

September 17, 2016

Posted on by

Metabolic interactions between a 4-species community, captive and wild red-crowned cranes, microbial life around a coal mine fire that’s been burning for over 50 years.

Pregnancy and early life

Associations between EBV and CMV Seropositivity, Early Exposures, and Gut Microbiota in a Prospective Birth Cohort: A 10-Year Follow-up – Claudia Carvalho-Queiroz – Frontiers in Pediatrics

Human oral microbiome

The Oral Microbiome of Children: Development, Disease, and Implications Beyond Oral Health – Andres Gomez – Microbial Ecology

Human gut microbiome

Gut microbiota, metabolome and immune signatures in patients with uncomplicated diverticular disease – Giovanni Barbara – Gut

Faecal Concentrations of Short-chain Fatty Acids and Selected Bacteria in Healthy and Celiac Children – Maša Primec – International Journal of Celiac Disease

Animal and in vitro experiments

Impact of Gluten-Friendly Bread on the Metabolism and Function of In Vitro Gut Microbiota in Healthy Human and Coeliac Subjects – Antonio Bevilacqua – PLOS ONE

Protocol: Intestinal Organoids as a Novel Tool to Study Microbes–Epithelium Interactions – Giulia Nigro – Methods in Molecular Biology

The Contribution of High-Order Metabolic Interactions to the Global Activity of a Four-Species Microbial Community – Xiaokan Guo – PLOS Computational Biology

Animal microbiome

Effects of captivity and artificial breeding on microbiota in feces of the red-crowned crane (Grus japonensis) – Yuwei Xie – Scientific Reports

Compartmentalization of microbial communities that inhabit the hindguts of millipedes – James B. Nardi – Arthropod Structure & Development

Plant, root, and soil microbiome

Seasonal and altitudinal changes of culturable bacterial and yeast diversity in Alpine forest soils – Luís França – Extremophiles

Niche filtering of bacteria in soil and rock habitats of the Colorado Plateau Desert, Utah, USA – Kevin Lee – Frontiers in Microbiology

The Centralia, PA, coal mine fire has been burning since 1962. Stochastic extremes but convergent recovery of bacterial and archaeal soil communities to an ongoing subterranean coal mine fire – Sang-Hoon Lee – PeerJ Preprint

Water and extremophile microbiome

Functional ecology of soil microbial communities along a glacier forefield in Tierra de Fuego (Chile) – Miguel Angel Fernández-Martínez – Frontiers in Microbiology

Riverine Bacterial Communities Reveal Environmental Disturbance Signatures within the Betaproteobacteria and Verrucomicrobia – John Paul Balmonte – Frontiers in Microbiology

Shifts in Microbial Community Structure and Activity in the Ultra-Oligotrophic Eastern Mediterranean Sea Driven by the Deposition of Saharan Dust and European Aerosols – Cui Guo- Frontiers in Marine Science

Phylogenetic Characterization of Marine Benthic Archaea in Organic-Poor Sediments of the Eastern Equatorial Pacific Ocean (ODP Site 1225) – Antje Lauer – Microorganisms

Built environment microbiome

Occurrence and diversity of both bacterial and fungal communities in dental unit waterlines subjected to disinfectants – Damien Costa – Pathogens and Disease

Techniques

Stable Isotope Techniques for the Assessment of Host and Microbiota Response During Gastrointestinal Dysfunction – Butler, Ross N. – Journal of Pediatric Gastroenterology and Nutrition

Microbes in the news

Get Your Children Good and Dirty – B. Brett Finlay and Marie-Claire Arrieta – Wall Street Journal

NASA Space Biology Fellowships to Study the Microbiome of the ISS as a Built Environment Research Announcement – SpaceRef

Intercontinental Plant Microbiome Research Earns UBiome Grant – Haverford.edu

Scientific research shows how corrugated stops bacteria – Packaging World

Bacterial Predators Surprise Scientists with Hidden Diversity – Jennifer Frazer – Scientific American

Bacteria Hysteria

Fear-mongering story sponsored by industry, performed by microbiology professor: Petri dishes you can wear: UA researchers study the bacteria on the bottoms of your shoes – Courtney Gallant – The Daily Wildcat

September 16, 2016

Posted on by

Hadza fecal metabolome, phyllosphere of indoor plants, decoupling function and taxonomy in the ocean, and winners of the 2016 MoBio Microbiome Awards.

Events

The Swarm Inside: Making Sense of the Microbiome – September 27, 2016 – Kavli Conversations

Human oral microbiome / proteomics

Metaproteomics of saliva identifies human protein markers specific for individuals with periodontitis and dental caries compared to orally healthy controls – Daniel Belstrøm – PeerJ

Human reproductive tract microbiome

Inflammation, Microbiota, and Prostate Cancer – Martin Puhr – European Urology Focus

Human gut microbiome / metabolome

Fecal metabolome of the Hadza hunter-gatherers: a host-microbiome integrative view – Silvia Turroni – Scientific Reports

Association of brain amyloidosis with pro-inflammatory gut bacterial taxa and peripheral inflammation markers in cognitively impaired elderly – Annamaria Cattaneo – Neurobiology of Aging

Minireview: Correlations of Host Genetics and Gut Microbiome Composition – Krystyna Dąbrowska – Frontiers in Microbiology

Animal and bioreactor experiments

Normalizing Microbiota-Induced Retinoic Acid Deficiency Stimulates Protective CD8+ T Cell-Mediated Immunity in Colorectal Cancer – Nupur Bhattacharya – Immunity

In vitro analysis of partially hydrolyzed guar gum fermentation on identified gut microbiotaIn vitro analysis of partially hydrolyzed guar gum fermentation on identified gut microbiota – Justin Carlsona – Anaerobe

Plant, root, and soil microbiome

The plant is crucial: specific composition and function of the phyllosphere microbiome of indoor ornamentals – Rocel Amor Ortega – FEMS Microbiology Ecology

Water microbiome

Decoupling function and taxonomy in the global ocean microbiome – Stilianos Louca – Science

Phages and viruses

The Expanding Virosphere – Edward C. Holmes – Cell Host & Microbe

From oil spills to barley growth – oil-degrading soil bacteria and their promoting effects – Annett Mikolasch – Journal of Basic Microbiology

More microbiology

Minimal Tool Set for a Prokaryotic Circadian Clock – Nicolas Schmelling – bioRxiv

Microbes in the news

I was in the jury! 2016 MoBio Microbiome Award Winners Announced – MoBio 

Oral infection outbreak appears linked to an Anaheim dental office, officials say – LA Times

Hundreds Of Children May Have Been Exposed To Infectious Bacteria At O.C. Dentist’s Office – CBSlocal.com

Transforming the Microbiology Laboratory to Address the Triple Aim in Healthcare – Irene Dusich – Health System Management

CSU professors hope to break ground in microbiology through RNA research – Allec Brust – Collegian

Increase in antibiotic-resistant bacteria hinders treatment of kidney infections– Phil Hampton – UCLA Newsroom

Bacteria Hysteria

Your water bottle has as much bacteria as your toilet – AOL

Science, publishing, and career

Universities failing to make best use of Twitter, researchers say – Chris Havergal – Times Higher Education

Science, a Deathbed Promise, and a Mother’s Gift – Jonathan Foley – The Macroscope

September 13, 2016

Posted on by

Infant gut microbiome and allergy risk, gut microbiome in mice and susceptibility to Plasmodium, microbiome of a stranded striped dolphin, cadavers in Canada, rRNA operon copy numbers.

Events

(repeat posting) 4th Microbiome R&D Business collaboration Forum & Probiotics Congress, October 3-4, 2016, La Jolla,San Diego, USA. Use discount code: ALLONG for a special rate of $399.

Pregnancy and birth

Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation – Kei E Fujimura – Nature Medicine

Press: Infant gut microbiome appears to shape allergy risk by altering immune responses – EurekAlert
Newborn gut microbiome predicts later allergy and asthma, study finds. Microbial byproducts link particular early-life gut microbes to immune dysfunction – Science Daily
Clues in microbiome of infants point to future allergies and asthma – Yvette Brazier – Medical News Today
Neonatal Gut Bacteria Might Promote Asthma. Byproducts of gut microbes in some 1-month–old babies trigger inflammation that is linked to later asthma development, researchers find. – Anna Azvolinsky – The Scientist

Human urinary tract microbiome

Urinary microbiome of kidney transplant patients reveals dysbiosis with potential for antibiotic resistance – Asha Rani – Translational Research

Human gut microbiome

Gut bacterial microbiota in psoriasis: A case control study – Doaa Masallat – African Journal of Microbiology Research

Review: Cognitive Function and the Microbiome – M.G. Gareau – International Review of Neurobiology

Review: Advances in Gut Microbiome Research and Relevance to Pediatric Diseases – Lindsey Albenberg – The Journal of Pediatrics

Animal experiments

Monitoring perinatal gut microbiota in mouse models by mass spectrometry approaches: parental genetic background and breastfeeding effects – Stefano Levi Mortera – Frontiers in Microbiology

Functional characteristics of the gut microbiome in C57BL/6 mice differentially susceptible to Plasmodium yoelii – Joshua M. Stough – Frontiers in Microbiology

Modulation of the bifidobacterial communities of the dog microbiota by zeolite – Alberto Sabbioni – Frontiers in Microbiology

Animal microbiome

The microbiome of a striped dolphin (Stenella coeruleoalba) stranded in Portugal – Filipa Godoy-Vitorino – Research in Microbiology

Book Chapter: Microbial Interactions on Coral Surfaces and Within the Coral Holobiont – Max Teplitski – The Cnidaria, Past, Present and Future

Book Chapter: Association of Coral-Microbes, and the Ecological Roles of Microbial Symbionts in Corals – Wei Sun – The Cnidaria, Past, Present and Future

Human Lice in Paleoentomology and Paleomicrobiology – Rezak Drali – ASM Microbiology Spectrum

Plant, root, and soil microbiome

Resource partitioning between bacteria, fungi and protists in the detritusphere of an agricultural soil – Susanne Kramer – Frontiers in Microbiology

Composition and activity of soil microbial communities in different types of temperate forests – Marcin Chodak – Biology and Fertility of Soils

The effect of the Falcon 460 EC fungicide on soil microbial communities, enzyme activities and plant growth – Małgorzata Baćmaga – Ecotoxicology

Review: Plant microbe interactions in post genomic era: perspectives and applications – Jahangir Imam – Frontiers in Microbiology

Water microbiome

Quantification of viral and prokaryotic production rates in benthic ecosystems: a methods comparison – Eugenio Rastelli – Frontiers in Microbiology

Microbiome of death

Cadavers in Canada: Book Chapter: Changes in Soil Microbial Activity Following Cadaver Decomposition During Spring and Summer Months in Southern Ontario – Heloise A. Breton – Soil in Criminal and Environmental Forensics

Wastewater and pollution microbiology

Poster: MiDAS: A curated database for the microorganisms of activated sludge and anaerobic digesters – Simon Jon McIlroy – Water Engineering and Biofilm IWA Specialist Conference, 2016

Probiotics

Layer-by-Layer Encapsulation of Probiotics for Delivery to the Microbiome – Aaron C. Anselmo – Advanced Materials

Food microbiology

Book: Functional Nucleic Acids Detection in Food Safety: Theories and Applications – Wentao Xu – Springer

Microbial ecology

Aligning the Measurement of Microbial Diversity with Macroecological Theory – James C. Stegen – Frontiers in Microbiology

Editorial: Insights into microbe-microbe interactions in human microbial ecosystems: strategies to be competitive – Nuria Salazar – Frontiers in Microbiology

Bioinformatics and metagenomics

Exploiting rRNA operon copy number to investigate bacterial reproductive strategies – Benjamin R.K. Roller – Nature Microbiology

Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers – Michelle Davison – PLOS ONE

SnpFilt: A pipeline for reference-free assembly-based identification of SNPs in bacterial genomes – Carmen H.S. Chan – Computational Biology and Chemistry

Review: Advances in biodiversity: metagenomics and the unveiling of biological dark matter – Robert J. Robbins – Standards in Genomic Sciences

Microbes in the news

What we have in common with corals and their unexplored microbial world – Alejandra Hernandez – The Conversation

September 12, 2016

Posted on by

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 8, 2016

Posted on by

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

Jobs and Events

Assistant Professor in Microbiome Research – University of Maryland Baltimore County

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

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

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

Human gut microbiome

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

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

Animal microbiome

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

Water and extremophile microbiome

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

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

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

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

Food microbiology

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

Bioinformatics and metagenomes

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

Microbes in the news

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

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

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

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

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

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

Science integrity

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

September 6, 2016

Posted on by

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 5, 2016

Posted on by

A microbial ecosystem created by fracking.

Human gut microbiome

Note: “All 34 PD patients were on dopaminergic drugs” Short chain fatty acids and gut microbiota differ between patients with Parkinson’s disease and age-matched controls – Marcus M. Unger – Parkisonism & Related Diseases

Effects of Proton Pump Inhibitors on the Gastric Mucosa-Associated Microbiota in Dyspeptic Patients – Francesco Paroni Sterbini – Applied and Environmental Microbiology

Upcoming study: Influence of habitual dietary fibre intake on the responsiveness of the gut microbiota to a prebiotic: protocol for a randomised, double-blind, placebo-controlled, cross-over, single-centre study – Genelle Healey – BMJ Open

Plants, roots, and soil microbiome

Screen Shot 2016-09-05 at 2.12.43 PMMicrobial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales – Rebecca A. Daly – Nature Microbiology

Press: New genus of bacteria found living inside hydraulic fracturing wells – ‘Frackibacter’ one of dozens of microbes forming sustainable ecosystems there, study finds – EurekAlert

Air microbiology

Aerobiology of the built environment: Synergy between Legionella and fungi – Absar Alum – American Journal of Infection Control

Generic aspects of the airborne spread of human pathogens indoors and emerging air decontamination technologies – M. Khalid Ijaz – American Journal of Infection Control

Water treatment microbiology

A modified weighted mixture model for the interpretation of spatial and temporal changes in the microbial communities in drinking water reservoirs using compositional phospholipid fatty acid data – I. Stanimirova – Talanta

Point-of-use Unit Based on Gravity Ultrafiltration Removes Waterborne Gastrointestinal Pathogens from Untreated Water Sources in Rural Communities – Cristóbal Chaidez – Wilderness & Environmental Medicine

Bioinformatics

MMinte: an application for predicting metabolic interactions among the microbial species in a community – Helena Mendes-Soares – BMC Bioinformatics

Microbes in the news

Chickenpox Cases In The US Down Since 2-Dose Vaccine Program Began – Dianne Depra – Tech Times

Study shows that more people carry meningitis bacteria than previously thought – Meningitis Research Foundation

Respect the old but seek out the new: Direct 16S rRNA-seq from bacterial communities – Kelle Freel – The Molecular Ecology

Bacterial Leaf Streak, a new corn disease hitting Kansas – Vincent Marshall – Dodge City Daily Globe

Manuka proves best bacteria fighter – Rush and Mills, Whangaroa College students, investigated manuka (tea tree) oil, won a top prize at the recent Top Energy Far North Science and Technology Fair.– Stuff.co.nz

Fears CSIRO staff exposed to ‘low risk’ toxic bacteria at Canberra lab – ABC Australia

Microbes and you: a partnership millions of years old – Dyani LewisCosmos Magazine