Category Archives: Human reproductive or urinary

September 21, 2016

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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 18, 2016

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Gut fermentation bubbles might promote decompression sickness in divers, corals of the Tropical Eastern Pacific, and a new microbiome book: Let Them Eat Dirt.

General microbiome

Review: Transitioning From Descriptive to Mechanistic Understanding of the Microbiome: The Need for a Prospective Longitudinal Approach to Predicting Disease – Victoria J. Martin – The Journal of Pediatrics

Pregnancy and early life

Shifts in Lachnospira and Clostridium sp. in the 3-month stool microbiome are associated with preschool-age asthma – Leah Stiemsma – Clinical Science

Human oral microbiome

Review: The role of bacteriophages in periodontal health and disease – Graça Pinto – Future Medicine

Human urinary tract microbiome

A diverse virome in kidney transplant patients contains multiple viral subtypes with distinct polymorphisms – Asha Rani – Scientific Reports

Human vaginal microbiome

Neither vaginal nor buccal administration of 800 μg misoprostol alters mucosal and systemic immune activation or the cervicovaginal microbiome: a pilot study – Spyros A. Kalams – The European Journal of Contraception & Reproductive Health Care

Human gut microbiome

Gut fermentation seems to promote decompression sickness in humans – Sébastien de Maistre – Journal of Applied Physiology

Review: Role of gut microbiota and nutrients in amyloid formation and pathogenesis of Alzheimer disease – Francesca Pistollato – Nutrition Reviews

Review: Enteric immunity, the gut microbiome, and sepsis: Rethinking the germ theory of disease – Javier Cabrera-Perez – Experimental Biology and Medicine

Review: Probiotic supplementation can positively affect anxiety and depressive symptoms: a systematic review of randomized controlled trials – Meysam Pirbaglou – Nutrition Research

Animal experiments

Structural modulation of the gut microbiota and the relationship with body weight: compared evaluation of liraglutide and saxagliptin treatment – Lin Wang – Scientific Reports

Microbial antigen mimics activate diabetogenic CD8 T cells in NOD mice – Ningwen Tai – Journal of Experimental Medicine

Press: Yale study shows that gut microbes could trigger type 1 diabetes – Jack Woodfield – Diabetes.co.uk

Intestinal immune maturation is accompanied by temporal changes in the composition of the microbiota – G. Den Hartog – Beneficial Microbes

Animal microbiome

First deep screening of bacterial assemblages associated with corals of the Tropical Eastern Pacific – Joicye Hernández-Zulueta – FEMS Microbiology Ecology

Bioinformatics

Reference point insensitive molecular data analysis – M. Altenbuchinger – Bioinformatics

Microbes in the news
New book: Let Them Eat Dirt – B. Brett Finlay and Marie-Claire Arrieta

September 16, 2016

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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

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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 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

August 29, 2016

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Breast milk protects against GBS colonization, niche segregation in the gut, drug detection and effects in streams, reconstruction of metabolic networks.

Pregnancy and birth

Role of human milk oligosaccharides in Group B Streptococcus colonisation – Nicholas J Andreas – Clinical & Translational Immunology

Press: Breast Milk Sugar May Protect Newborns Against Deadly Bacterial Infection – Dianne Depra – Tech Times

Human skin microbiome

News and Views: Microbiome: Ecology of eczema – Ian D. Odell – Nature Microbiology

Human respiratory microbiome

Changes in the prevalence and biofilm formation of Haemophilus influenzae and Haemophilus parainfluenzae from the respiratory microbiota of patients with sarcoidosis – Urszula Kosikowska – BMC Infectious Diseases

Human vaginal microbiome

The cervico-vaginal microbiota in women notified for Chlamydia trachomatis infection: A case-control study at the STI outpatient clinic in Amsterdam, the Netherlands – C van der Veer – Clinical Infectious Diseases

Human gut microbiome

Transcriptional interactions suggest niche segregation among microorganisms in the human gut – Damian Rafal Plichta – Nature Microbiology

Review: Alzheimer’s disease and gut microbiota – Xu Hu – Science China Life Sciences

Review: In Sickness and in Health: The Relationships Between Bacteria and Bile in the Human Gut – A.J. Hay – Advances in Applied Microbiology

Animal experiments

Enterococcus faecalis readily colonizes the entire gastrointestinal tract and forms biofilms in a germ-free mouse model – Aaron M.T. Barnes – Virulence

Animal microbiome

Distinct Bacterial Microbiomes in Sexual and Asexual Potamopyrgus antipodarum, a New Zealand Freshwater Snail – Cristina Takacs-Vesbach – PLOS ONE

Water and extremophile microbiome

Occurrence and Potential Biological Effects of Amphetamine on Stream Communities – Sylvia S. Lee – Environmental Science & Technology

Press: Ecological consequences of amphetamine pollution in urban streams – Cary Institute
Your drain on drugs: Amphetamines seep into Baltimore’s streams – Jen Christensen – CNN
Comment from PubMed Commons by Daniel Himmelstein 

Diversity of culturable bacteria recovered from Pico Bolívar’s glacial and subglacial environments, at 4950 m, in Venezuelan tropical Andes – Johnma Rondón – Canadian Journal of Microbiology

Metabolomics

Efficient Reconstruction of Predictive Consensus Metabolic Network Models – Ruben G. A. van Heck – PLOS Computational Biology

Bioinformatics and Metagenomics

Review: Toward Accurate and Quantitative Comparative Metagenomics – Stephen Nayfach – Cell

Techniques

Thousands of primer-free, high-quality, full-length SSU rRNA sequences from all domains of life – Soeren M Karst – bioRxiv

A method for assessing efficiency of bacterial cell disruption and DNA release – Olle M. de Bruin – BMC Microbiology

Microbes in the news

Findings from the American Physiological Society’s Inflammation, Immunity and Cardiovascular Disease conference: Targeting gut bacteria to reduce weight gain – Science Daily

Microbes at work in your Kimchi – Jennifer – The Microbial Menagerie

Artist’s 46-year-old loo paper to be studied: Billy Apple’s decades-old lavatory paper is now part of a scientific study at Auckland University – Jamie Morton – NZ Herald

BacteriaHysteria: The ultimate embodiment of modern day germophobia: Squix – Jonathan Eisen – MicroBEnet

Science misconduct

Leading scientist suspended amid misconduct claims: Robert Ryan, award-winning Scottish microbiologist now under investigation – Victoria Weldon – Herald Scotland

August 13, 2016

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Fracking, floating islands and a multivariate statistical framework.

Human respiratory microbiome

Editorial: Another piece in the ‘research mosaic’ that describes the role of the lung microbiome in COPD – Gary B Huffnagle – Thorax

Review: Toward revision of antimicrobial therapies in hematopoietic stem cell transplantation: target the pathogens, but protect the indigenous microbiota – Alexander Khoruts – Translational Research

Human urinary tract microbiome

Note: no mention of extraction controls. Does the Urinary Microbiome Play a Role in Urgency Urinary Incontinence and Its Severity? – Lisa Karstens – Frontiers in Cellular Infection Microbiology

Human gut microbiome

Review: Gut Microbiota: Modulation of Host Physiology in Obesity – Vandana Nehra – Physiology

Close encounters of the type‐six kind: injected bacterial toxins modulate gut microbial composition – Martina Sassone‐Corsi – EMBO Reports

Plant, root, and soil microbiome

Floating islands: Metagenomic approach to characterize soil microbial diversity of Phumdi at Loktak Lake – Sampada Puranik – Water Science & Technology

Hydraulic fracturing offers view of microbial life in the deep terrestrial subsurface – Paula J. Mouser – FEMS Microbiology Ecology

Isolation studies reveal a shift in the cultivable microbiome of oak affected with Acute Oak Decline – Sandra Denman – Systematic and Applied Microbiology

Arbuscular mycorrhizal fungal communities in forest plant roots are simultaneously shaped by host characteristics and canopy-mediated light availability – Kadri Koorem – Plant and Soil

Soil and plant components ecological stoichiometry in four steppe communities in the Loess Plateau of China – Quanchao Zeng – CATENA

Effect of cobalt and silver nanoparticles and ions on Lumbricus rubellus health and on microbial community of earthworm faeces and soil – Livia Vittori Antisari – Applied Soil Ecology

Bioreactor microbiology

Engineering artificial communities for enhanced FTOH degradation – Matthew Lewis – Science of the Total Environment

Metagenomics, phages and viruses, bioinformatics

Metagenomic recovery of phage genomes of uncultured freshwater actinobacteria – Rohit Ghai – The ISME Journal

MixMC: A Multivariate Statistical Framework to Gain Insight into Microbial Communities – Kim-Anh Lê Cao – PLOS ONE

Book: Algorithms in Bioinformatics. 16th International Workshop, WABI 2016, Aarhus, Denmark, August 22-24, 2016. Proceedings
Better Identification of Repeats in Metagenomic Scaffolding – Jay Ghurye –
Compact Universal k-mer Hitting Sets – Yaron Orenstein

Proteomics

Review: Environmental Microbial Community Proteomics: Status, Challenges and Perspectives – Da-Zhi Wang – Int J Mol Sci

Microbes in the news

Saving antibiotics for when they are really needed: the Dutch example – Tony Sheldon – BMJ

Could friendly bacteria be used to treat cancer? – Paul Dyson – The Conversation

August 11, 2016

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Association between gut microbiome and cardiovascular disease risk, Arctic glacial surface habitats.

Human oral microbiome

Review: Discuss the role of microorganisms in the aetiology and pathogenesis of periapical disease – Vincent Aw – Australian Endodontic Journal

Human respiratory microbiome

Environmental and mucosal microbiota and their role in childhood asthma – Lena T. Birzele – Allergy

FUT2 genotype influences lung function, exacerbation frequency and airway microbiota in non-CF bronchiectasis – Steven L Taylor – Thorax

Human vaginal microbiome

Review: Vaginal Microbiota and Lubricant Use During Labor. Implications for Nursing Research, Practice, and Policy – Katie G. McElroy – SAGE Open Nursing

Human gut microbiome

Gut Microbiome Associates With Lifetime Cardiovascular Disease Risk Profile Among Bogalusa Heart Study Participants – Tanika N Kelly – Circulation Research

Association of Intestinal Microbiota with Metabolic Markers and Dietary Habits in Patients with Type 2 Diabetes – Yamaguchi Y. – Digestion

Cardiorespiratory fitness as a predictor of intestinal microbial diversity and distinct metagenomic functions – Mehrbod Estaki – Microbiome

Bacterial invasion of the pancreas revealed after analyses of the pancreatic cyst fluids – Vilvapathy Narayanan – bioRxiv

Review: Insights into human evolution from ancient and contemporary microbiome studies – Stephanie L Schnorr – Current Opinion in Genetics & Development

http://www.sciencedirect.com/science/article/pii/S0959437X1630096X

Review: An overview of the bacterial contribution to Crohn disease pathogenesis – Moftah H Alhagamhmad – Journal of Medical Microbiology

Animal experiments

Intestinal Microbial Metabolites Are Linked to Severity of Myocardial Infarction in Rats – Vy Lam – PLOS ONE

Gut Microbial Metabolites Fuel Host Antibody Responses – Myunghoo Kim – Cell Host & Microbe

Fap2 Mediates Fusobacterium nucleatum Colorectal Adenocarcinoma Enrichment by Binding to Tumor-Expressed Gal-GalNAc – Jawad Abed – Cell Host & Microbe

Editorial: When Mr. Fap Meets the Gals – Santosh K. Ghosh – Cell Host & Microbe

Plant, root, and soil microbiome

Comparative metagenomic analysis reveals mechanisms for stress response in hypoliths from extreme hyperarid deserts – Phuong Thi Le – Genome Biology and Evolution

Review: Recent advances in actinorhizal symbiosis signaling – Emilie Froussart – Plant Molecular Biology

Water and extremophile microbiome

Marine and giant viruses as indicators of a marine microbial community in a riverine system – Lisa M. Dann – Microbiology Open

Linking microbial diversity and functionality of Arctic glacial surface habitats – Stefanie Lutz – Environmental Microbiology

More microbiology

Microbiology, philosophy and education – Maureen A. O’Malley – Microbiology Letters

Local adaptation of a bacterium is as important as its presence in structuring a natural microbial community – Pedro Gómez – Nature Communications

Review: Biofilms: an emergent form of bacterial life – Hans-Curt Flemming – Nature Reviews Microbiology

 

Microbes in the news

Mental Health, Free Will, and Your Microbiome – Maria Popova – BrainPickings

A grimy, black biofilm is starting to cover the Jefferson Memorial, and it can’t be killed – Michael E. Ruane – The Washington Post
NPS ready to battle grimy biofilm coating on Jefferson Memorial – Nick Iannelli – WTOP
The Jefferson Memorialome? The Jeffersonome? The Jefferson Microbiome? A biofilm by any other name … – Jonathan Eisen – MicroBEnet

Young Inventors Work On Secret Proteins To Thwart Antibiotic-Resistant Bacteria – Joe Palca – NPR Shots

DRDO developing bacteria from Antarctica to aid setting up of bio-toilets in India – India TV News

How the world’s tiniest organisms explain our evolution, our health, and our eventual demise: Interview with Ed Yong about Leeuwenhoek and microbes – Julia Belluz

Could Earth Bacteria Survive on Mars? LSU MARSLIFE Researcher Noelle Bryan Recovers Bacteria from the Stratosphere – Paige Brown Jarreau – Vimeo

Microbiology: Mob rule – Adrian Woolfson examines four books on the microbiological universe that churns within us – Nature

The social network in your gut – Wudan Yan – New Yorker

Bik’s non-microbiology Picks

Exoskeletons and economics: indoor arthropod diversity increases in affluent neighbourhoods – Misha Leong – Biology Letters

Research Highlight: Insect mix high in rich areas – Nature

Ancient DNA: Muddy messages about American migration – Suzanne McGowan – Nature

Science, publishing, and career

NIH sets new postdoc stipend levels – Maggie Kuo – Science

Kudos for female Antarctic researchers: to inspire the roughly 60% of early-career polar scientists who are women – Jan Strugnell – Nature

Nominate influential female Antarctic researchers and those involved in supporting research, both past and present, to potentially be included in Wikibomb event

August 9, 2016

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Climate change and increasing Vibrio species in North Atlantic, microbiome of the aging mouth, Antarctic soil around Little Auk colony.

Events

5th Exploring Human Host-Microbiome Interactions in Health and Disease – Welcome Genome Campus, Cambridge, UK, 7-9 September 2016

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

Hot topics in microbiology: Campden BRI conference – Campden BRI, Chipping Campden, Gloucestershire, UK, October 13-14

Today & tomorrow – live webcast – Standards for Microbiome Measurements @NIST – Jonathan Eisen – MicroBEnet

General microbiome

Note: includes 16S rRNA gene studies as well, so not metagenomic sensu stricto: An overview of major metagenomic studies on human microbiomes in health and disease – Hongfei Cui – Quantitative Biology

Brazil: A Step Forward to Empower Global Microbiome Research Through Local Leadership – Victor S. Pylro – Trends in Microbiology

Human oral microbiome

Distinct interacting core taxa in co-occurrence networks enable discrimination of polymicrobial oral diseases with similar symptoms – Takahiko Shiba – Scientific Reports

Oral microbial community typing of caries and pigment in primary dentition – Yanhui Li – BMC Genomics

Review: The subgingival periodontal microbiota of the aging mouth – Magda Feres – Periodonotology 2000

Human respiratory microbiome

Review: The microbiome in chronic inflammatory airway disease: A threatened species – Robin John Green – The South African Medical Journal

Review: Lung microbiome in human immunodeficiency virus infection – Homer L. Twigg IIIa – Translational Research

Human vaginal microbiome

Evaluation of the vaginal flora in pregnant women receiving opioid maintenance therapy: a matched case-control study – Alex Farr – BMC Pregnancy Childbirth

Human gut microbiome

Microbial Factors Associated with Postoperative Crohn’s Disease Recurrence – Emily K. Wright – Journal of Crohn’s and Colitis

The mucosal microbiota in a young child with severe non-Helicobacter gastritis – Geoffrey A. Preidis – Therapeutic Advances in Gastroenterology

Profile of Gut Microbiota Associated With the Presence of Hepatocellular Cancer in Patients With Liver Cirrhosis – M. Grąt – Transplantation Proceedings

Comparison of the gut microbial community between obese and lean peoples using 16S gene sequencing in a Japanese population – Akira Andoh – Journal of Clinical Biochemistry and Nutrition

Book Chapter: The Second Brain and Possible Interactions with the Heart – Rosa Sollazzo – Psychotherapy for Ischemic Heart Disease

Infection microbiology

Comparison of methods for the identification of microorganisms isolated from blood cultures – Aydir Cecília Marinho Monteiro – Annals of Clinical Microbiology and Antimicrobials

Animal experiments

Disturbance in the Mucosa-Associated Commensal Bacteria Is Associated with the Exacerbation of Chronic Colitis by Repeated Psychological Stress; Is That the New Target of Probiotics? – Sohei Arase – PLOS ONE

Role of the Gut Microbiome in Modulating Arthritis Progression in Mice – Xiaofei Liu – Scientific Reports

Salmonella Typhimurium utilizes a T6SS-mediated antibacterial weapon to establish in the host gut – Thibault G. Sana – PNAS

Animal microbiome

Does adaptive radiation of a host lineage promote ecological diversity of its bacterial communities? A test using gut microbiota of Anolis lizards – Tiantian Ren – Molecular Ecology

The gut microbiota of the pine weevil is similar across Europe and resembles that of other conifer-feeding beetles – Aileen Berasategui – Molecular Ecology

Plant, root, and soil microbiome

The Arctic soil bacterial communities in the vicinity of a little auk colony – Sylwia Zielinska – Frontiers in Microbiology

Soil Fungal:Bacterial Ratios Are Linked to Altered Carbon Cycling – Ashish A. Malik – Frontiers in Microbiology

Ancient landscapes and the relationship with microbial nitrification – Sasha N. Jenkins – Scientific Reports

Long-term antibiotic exposure in soil is associated with changes in microbial community structure and prevalence of class 1 integrons – David W. Cleary – FEMS Microbiology Ecology

Are Epiphytic Microbial Communities in the Carposphere of Ripening Grape Clusters (Vitis vinifera L.) Different between Conventional, Organic, and Biodynamic Grapes? – Elizabeth Kecskeméti – PLOS ONE

Bacterial communities in Antarctic lichens – Chae Haeng Park – Antarctic Science

Water and extremophile microbiome

Climate influence on Vibrio and associated human diseases during the past half-century in the coastal North Atlantic – Luigi Vezzulli – PNAS

Press: We’re trashing the oceans — and they’re returning the favor by making us sick – Chris Mooney – The Washington Post
Deadly Bacteria Spread across Oceans as Water Temperatures Rise. Cholera bacteria and others arise in more places and in greater abundance – Umair Irfan – Scientific American
Warming seas linked to rise in cholera bacteria in Europe and US – Brian Owens – New Scientist

Microbial community structure in hypolentic zones of a brine lake in a desert plateau, China – Wenzhen Yuan – Environmental Earth Sciences

Microbial diversity in sediment ecosystems (evaporites domes, microbial mats and crusts) of hypersaline Laguna Tebenquiche, Salar de Atacama, Chile – Ana B. Fernandez – Frontiers in Microbiology

Bioreactor microbiome

The full-scale anaerobic digestion microbiome is represented by specific marker populations – Jo De Vrieze – Water Research

Viruses and phages

Challenges in the analysis of viral metagenomes – Rebecca Rose – Virus Evolution

Metagenomics and bioinformatics

Bipartite graph analyses reveal inter-domain LGT involving ultrasmall prokaryotes and their divergent, membrane-related proteins – Alexander L. Jaffe – Environmental Microbiology

FARAO – The Flexible All-Round Annotation Organizer – Rickard Hammarén – Bioinformatics

Identifying wrong assemblies in de novo short read primary sequence assembly contigs – Vandna Chawla – Journal of Biosciences

A Bayesian Framework for the Classification of Microbial Gene Activity States – Craig Disselkoen – Frontiers in Microbiology

Techniques

Evaluation of 16S rRNA gene primer pairs for monitoring microbial community structures showed high reproducibility within and low comparability between datasets generated with multiple archaeal and bacterial primer pairs – Martin A. Fischer – Frontiers in Microbiology

More microbiology

Editorial: New insights into microbial ecology through subtle nucleotide variation – A M. Eren – Frontiers in Microbiology

Neisseria meningitides Can Survive in Corpses for At Least Eleven Days – Antonio Osculati – Frontiers in Cellular and Infection Microbiology

Microbes in the news

List of papers about bias in microbiome techniques: The unbearable madness of microbiome – Mick Watson – Opiniomics

Book Review: Follow your gut – The Enormous Impact of Tiny Microbes – Daniel K. Morais – Frontiers in Microbiology

Brito went to Fiji to study mobile genes in human microbiome – Tom Fleischman – Cornell Chronicle

MSU graduate awarded NSF fellowship to study disease affecting world’s citrus crops – Denise Hoepfner – Montana State University

Bacteria Could Aid Search for Creatures On Other Planets – Elizabeth Howell – Astrobiology Magazine

U.Va. scientists make important discovery about dangerous bacteria strains
Researchers pinpoint mechanisms of C. difficile strains – Daisy Xu – Cavalier Daily

Did farming practices in China create an antibiotic resistant bacteria that’s spreading around the world? – Alanna Shaikh – United Nations Dispatch

Science, publishing, and career

Dog eat dog: is a troubled expedition to Kenya causing the Smithsonian to devour its young?
A star scientist stands accused of misconduct, but colleagues say he’s being railroaded
– Michael Balter – The Verge

A “Scientific Diversity” Intervention to Reduce Gender Bias in a Sample of Life Scientists – Corinne A. Moss-Racusin – CBE Life Sciences Education

Bik’s non-microbiology Picks

Innate Immunity and Asthma Risk in Amish and Hutterite Farm Children – Michelle M. Stein – New England Journal of Medicine

August 8, 2016

Posted on by

Sutures, preterm birth, and vaginal dysbiosis, captive Komodo Dragons, and stochastic assembly of microbial communities.

Jobs

Assistant Professor of Biology (Microbiology): background in microbiome research, molecular mechanisms of microbial pathogenesis, virulence and/or quorum sensing, or host-pathogen interactions – California State University, East Bay

Human vaginal microbiome

Relationship between vaginal microbial dysbiosis, inflammation, and pregnancy outcomes in cervical cerclage – Lindsay M. Kindinger – Science Translational Medicine

Press: Pregnancy procedure may be associated with increased risk of premature birth and neonatal loss – Science Daily
Braided Cervical Cerclage May Raise Risk for Preterm Birth – Lara C. Pullen – MedScape

Human gut microbiome

Addendum (reanalysis of published data): Partial recovery of microbiomes after antibiotic treatment – Frédéric Raymond – Gut Microbes

Review: Microbiota and chronic inflammatory arthritis: an interwoven link – Andrea Picchianti Diamanti – Journal of Translational Medicine

Review: Microbiomic and Posttranslational Modifications as Preludes to Autoimmune Diseases – Ghislain Opdenakker – Trends in Molecular Medicine

Animal microbiome

The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat – Embriette R. Hyde – mSystems

Press: What Captive Komodo Dragons Might Tell Us About Our Own Microbiomes – UC San Diego Health

Dysbiosis of the Fecal Microbiota in Cattle Infected with Mycobacterium avium subsp. paratuberculosis – Marie-Eve Fecteau – PLOS ONE

Microbiome Composition and Diversity of the Ice-Dwelling Sea Anemone, Edwardsiella andrillae – Alison E. Murray – Integrative & Comparative Biology

Microbiota from Rhabditis regina may alter nematode entomopathogenicity – Jesús Guillermo Jiménez-Cortés – Parasitology Research

Plant, root, and soil microbiome

Soil contamination with olive mill wastes negatively affects microbial communities, invertebrates and plants – Olfa Hentati – Ecotoxicology

Arbuscular mycorrhizal fungi-assisted phytoremediation of a lead-contaminated site – Jerusa Schneider – Science of the Total Environment

Ecology of microbial communities

Effects of dispersal and selection on stochastic assembly in microbial communities – Sarah Evans – The ISME Journal

Microbes in the news

Microbes have no morals – Ed Yong – Aeon

A California City Is Fending Off Zika by Releasing 40,000 Mosquitoes Every Week – Sarah Zhang – Wired

New therapy could help treat skin infections without turning them into superbugs – Chelsea Harvey – Mashable

Getting down and dirty is good for us – Tim Krohn – Mankato Free Press

UNC researchers link gut bacteria to infant brain development – Stephen Ginley – The News & Observer

Hey Bear! Can I Sample Your Microbiota? – Scott Chimileski – American Society For Microbiology