Category Archives: Events and jobs

April 12, 2016, part 1

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Too many alerts to go through after taking one day off, so here is part one. An updated tree of life, acute appendicitis, rhizosphere of a living fossil plant, Antarctic surface snow, and effects of Superstorm Sandy on creek water.

Jobs and events

Senior Scientist with significant track record in microbiome research – The National Institute for Biological Standards and Control, South Mimms, UK

General microbiome

A new view of the tree of life – Laura A. Hug – Nature Microbiology

Pregnancy and birth

The Gestational Vaginal Microbiome and Spontaneous Preterm Birth among Nulliparous African American Women – Deborah B. Nelson – American Journal of Perinatology

Early colonization of functional groups of microbes in the infant gut – Van T. Pham – Environmental Microbiology

The gut resistome is highly dynamic during the first months of life – Christian JH von Wintersdorff – Future Medicine

Human skin microbiome

Review: Skin Biomes – N. Fyhrquist – Current Allergy and Asthma Reports

Human respiratory microbiome

Review: Next Generation Sequencing and the Microbiome of Chronic Rhinosinusitis – A Primer for Clinicians and Review of Current Research, Its Limitations, and Future Directions – Jake Jervis Bardy – Ann Otol Rhinol Laryngol

Human oral microbiome

The salivary microbiome for differentiating individuals: proof of principle – Sarah L. Leake – Microbes and Infection

Concordance of HOMIM and HOMINGS technologies in the microbiome analysis of clinical samples – Jean-Luc C. Mougeot – Journal of Oral Microbiology

Human gut microbiome

There are no Enterotypes: Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle – Anastassia Gorvitovskaia – Microbiome

Experiment with n=1: Understanding the Impact of Omega-3 Rich Diet on the Gut Microbiota – Blanca S. Noriega – Case Reports in Medicine

First Occurrence of Severe Extraintestinal Manifestations of Crohn’s Disease Following Faecal Microbiota Transplantation – Niels Teich – Journal of Crohn’s and Colitis

Acute appendicitis in children is associated with a local expansion of Fusobacteria – Matthew B. Rogers – Clinical Infectious Diseases

Hypothesis: Gut Microbiota Diversity and Human Diseases: Should We Reintroduce Key Predators in Our Ecosystem? – Alexis Mosca – Frontiers in Microbiology

Not endorsing, because highly controversial and not well founded: Bread and Other Edible Agents of Mental Disease – Paola Bressan and Peter Kramer – Frontiers in Human Neuroscience

Review: The human gut microbiome in health: establishment and resilience of microbiota over a lifetime – Kacy Greenhalgh – Environmental Microbiology

Review: Cytotoxicity of Nanoparticles Contained in Food on Intestinal Cells and the Gut Microbiota – Esther E. Fröhlich – MDPI International Journal of Molecular Sciences

Review: The Role of the Gut Microbiota in Childhood Obesity – Pihl Andreas Friis – Childhood Obesity

Animal models

Gnotobiotic Rodents: An In Vivo Model for the Study of Microbe–Microbe Interactions – Rebeca Martín – Frontiers in Microbiology

Depletion of Cultivatable Gut Microbiota by Broad-Spectrum Antibiotic Pretreatment Worsens Outcome After Murine Stroke – Katarzyna Winek – Stroke

Plant, root, and soil microbiome

Common mycorrhizal networks and their effect on the bargaining power of the fungal partner in the arbuscular mycorrhizal symbiosis – Heike Bückinga – Communicative & Integrative Biology

Rhizosphere Microbiomes of European + Seagrasses Are Selected by the Plant, But Are Not Species Specific – Catarina Cúcio – Frontiers in Microbiology

Specific Microbial Communities Associate with the Rhizosphere of Welwitschia mirabilis, a Living Fossil – Angel Valverde – PLOS ONE

Impact of alien pines on local arbuscular mycorrhizal fungal communities – evidence from two continents – Antonio Gazol – FEMS Microbiology Ecology

Differences in stability of seed-associated microbial assemblages in response to invasion by phytopathogenic microorganisms – Samir Rezki – PeerJ

Using Ancient Traits to Convert Soil Health into Crop Yield: Impact of Selection on Maize Root and Rhizosphere Function – Jennifer E. Schmidt – Frontiers in Plant Science

Partitioning of Functional and Taxonomic Diversity in Surface-Associated Microbial Communities – Alexandra J. Roth-Schulze – Environmental Microbiology

Temporal dynamics of sediment bacterial communities in monospecific stands of Juncus maritimus and Spartina maritima – Daniel F R Cleary – Plant Biology

Thorough high-throughput sequencing analyses unravels huge diversities of soil parasitic protists – Stefan Geisen – Environmental Microbiology

Water and extremophile microbiome

Temporal and Spatial Dynamics of Archaeal Communities in Two Freshwater Lakes at Different Trophic Status – Yuyin Yang – Frontiers in Microbiology

Metagenomic Analysis of Bacterial Communities of Antarctic Surface Snow – Anna Lopatina – Frontiers in Microbiology

Partitioning of Functional and Taxonomic Diversity in Surface-Associated Microbial Communities – Alexandra J. Roth-Schulze – Environmental Microbiology

Impact of an intense water column mixing (0-1500m) on prokaryotic diversity and activities during an open-ocean convection event in the NW Mediterranean Sea – T. Severin – Environmental Microbiology

Aquatic bacterial community is restructured by hydric dynamics associated with Superstorm Sandy – Nikea Ulrich – Applied and Environmental Microbiology

Metagenomic analysis of lacustrine viral diversity along a latitudinal transect of the Antarctic Peninsula – Daniel Aguirre de Cárcer – FEMS Microbiology Ecology

Response of bacterial communities from California coastal waters to alginate particles and an alginolytic Alteromonas macleodii strain – Maximilian Mitulla – Environmental Microbiology

Waste and pollution microbiology

Partitioning of Viruses in Wastewater Systems and Potential for Aerosolization – Mari Titcombe Lee – Environmental Science & Technology Letters

Seasonality of antibiotic prescriptions for outpatients and resistance genes in sewers and wastewater treatment plant outflow – Serena Caucci – FEMS Microbiology Ecology

Spatial and temporal variability of bacterial communities within a combined sewer system – Henriette Stokbro Jensen – MicrobiologyOpen

Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters – Rasmus Hansen Kirkegaard – The ISME Journal

Bioinformatics

Not endorsing: Motif-Based Text Mining of Microbial Metagenome Redundancy Profiling Data for Disease Classification – Yin Wang – BioMed Research International

More microbiology

Host-Derived Sialic Acids Are an Important Nutrient Source Required for Optimal Bacterial Fitness In Vivo – Nathan D. McDonald – mBio

Review: Network-based metabolic analysis and microbial community modeling – Cesar Cardona – Current Opinion in Microbiology

Review: DNA-sensing inflammasomes: regulation of bacterial host defense and the gut microbiota – Si Ming Man – Pathogens and Disease

Microbes in the news

Most of the Tree of Life is a Complete Mystery. We know certain branches exist, but we have never seen the organisms that perch there – Ed Yong – The Atlantic

Wealth of unsuspected new microbes expands tree of life – Science Daily

Can more fiber restore microbiome diversity? – Science Daily

Science, publishing, and career

Research Funding: the Case for a Modified Lottery – Ferric C. Fang and Arturo Casadevall – mBio

 

April 7, 2016

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Biases and challenges with microbiome data, metabolic syndrome, stem cell transplants, ammonia-eating bacteria in fish gills, and a distinct pilus in the gut microbiome.

Events

Webinar: Cancer and the Oral Microbiome: A Metagenomics Approach – Scott Kelley, April 25

General microbiome

Good read about biases: Commentary: Challenges for Case-Control Studies with Microbiome Data – J. Paul Brooks – Annals of Epidemiology

Review: The importance of the microbiome in epidemiologic research – Blake M. Hanson – Annals of Epidemiology

Perspective: Microbiome and Anticancer Immunosurveillance – Laurence Zitvogel – Cell

Human oral microbiome

Effects of triclosan on host response and microbial biomarkers during experimental gingivitis – Brooke A. Pancer – Journal of Clinical Periodontology

Human skin microbiome

Review: New insights into acne pathogenesis: Exploring the role of acne-associated microbial populations – Bipul Kumar – Dermatologica Sinica

Human respiratory microbiome

Respiratory syncytial virus and rhinovirus severe bronchiolitis are associated with distinct nasopharyngeal microbiota – Jonathan M. Mansbach – Journal of Allergy and Clinical Immunology

Review: The respiratory microbiome: An underappreciated player in the human response to inhaled pollutants? – Sara D. Adar – Annals of Epidemiology

Human gut microbiome

The effect of heritability and host genetics on the gut microbiota and metabolic syndrome – Mi Young Lim – Gut

Functional changes in gut microbiota during haematopoietic stem cell transplantation for severe combined immunodeficiency – Jonathan P. Lane – Journal of Allergy and Clinical Immunology

Interplay between bile acid metabolism and microbiota in irritable bowel syndrome – M. Dior – Neurogastroenterology & Motility

Review: The Intestinal Microbiota in Metabolic Disease – Anni Woting – MDPI Nutrients

Animal models

The absence of microbiota delays the inflammatory response to Cryptococcus gattii – Marliete Carvalho Costa – International Journal of Medical Microbiology

Brain injury induces specific changes in the caecal microbiota of mice via altered autonomic activity and mucoprotein production – A. Houlden – Brain, Behavior, and Immunity

Animal microbiome

Branchial nitrogen cycle symbionts can remove ammonia in fish gills – Maartje A.H.J. van Kessel – Environmental Microbiology Reports

Bovine teat microbiome analysis revealed reduced alpha diversity and significant changes in taxonomic profiles in quarters with a history of mastitis – Helene Falentin – Frontiers in Microbiology

Plant, root, and soil microbiome

Could The Martian science heck work? Evolution of soil on Mars – Shannon Bohle – Astronomy & Geophysics

Enhanced Degradation of Diesel in the Rhizosphere of Lupinus luteus after Inoculation with Diesel-Degrading and Plant Growth-Promoting Bacterial Strains – María Balseiro-Romero – Journal of Environmental Quality

Amplicon-based metabarcoding reveals temporal response of soil microbial community to fumigation-derived products – Feng Wei – Applied Soil Ecology

Water microbiome

Identification of bacterial communities in sediments of Poyang Lake, the largest freshwater lake in China – Wenbo Kou – SpringerPlus

Influence of selected environmental factors on the abundance of aerobic anoxygenic phototrophs in peat-bog lakes – Sylwia Lew – Environmental Science and Pollution Research

Other microbiology

From Bacteroidia: A Distinct Type of Pilus from the Human Microbiome – Qingping Xu – Cell

Identification of new drug candidates against Borrelia burgdorferi using high-throughput screening – Venkata Raveendra Pothineni – Drug Design, Development and Therapy

Microbes and art

Another report on this beautiful art: Microbiome Art by Joana Ricou – Alex Alexiev – MicroBEnet

Students paint bacteria in cross campus learning Science Meets Art is a part of the SciCom initiative which is intended to help science students communicate their work and research – Connie Beltran – Texas Christian University

Microbes in the news

“Evolution of Soil on Mars”… where fiction becomes fact – David Coil – MicroBEnet

Gut Microbiota Altered in First-Episode Schizophrenia – Liam Davenport – Medscape

Gut Microbiome May Play Role in Myelination Disorders Including Multiple Sclerosis – interview with John Cryan – Medical Research

New type of symbiosis: Bacteria eat ammonia in fish gills – Science Daily

Elucidating the Microbiome of Acne Pathogenesis – Clincical Microbiomics

Biofilm oscillations: Excellent Paper on Metabolism dynamics + a video – Ben Libberton – NPJ Biofilms Community

California Strains of Lyme Bacteria May Survive Antibiotic Treatment According to Study – PR NewsWire

 

April 6, 2016

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C-section and gut colonization, N. flavescens in celiac patients, Lactobacillus in the gut, bird or whiskey, bacteria attached to phytodetritus, microbiology in the classroom, and CRISPR to decipher and shape bacterial diversity. And a bad article about women in space.

Event

Microbiome: How Commensal Bacteria Can Be Our Friends – A Talk by Dr. Deepshika Ramanan – April 14, Genspace Brooklyn, NY, Genspace

Organizing 2017 Microbes of the Built Environment conference, call for community input – Lynn Schriml – MicroBEnet

Pregnancy and birth

Cesarean section changes neonatal gut colonization – Jakob Stokholm – Journal of Allergy and Clinical Immunology

Human respiratory microbiome

Bacterial–viral load and the immune response in stable and exacerbated COPD: significance and therapeutic prospects – Silvestro Ennio D’Anna – International Journal of Chronic Obstructive Pulmonary Disease

Human gut microbiome

Metagenomics Reveals Dysbiosis and a Potentially Pathogenic N. flavescens Strain in Duodenum of Adult Celiac Patients – Valeria D’Argenio – American Journal of Gastroenterology

Th17 responses and natural IgM antibodies are related to gut microbiota composition in systemic lupus erythematosus patients – Patricia López – Scientific Reports

Mining metagenomic whole genome sequences revealed subdominant but constant Lactobacillus population in the human gut microbiota – Maddalena Rossi – Environmental Microbiology Reports

Diminution of the gut resistome after a gut microbiota-targeted dietary intervention in obese children – Guojun Wu – Scientific Reports

DGGE: The Effect of Probiotic Treatment on Patients Infected with the H7N9 Influenza Virus – Xinjun Hu – PLOS ONE

Review: Use your antibiotics wisely. Consequences to the intestinal microbiome – Jorge Cervantes – FEMS Microbiology Letters

Review: Diet, Microbiota, Obesity, and NAFLD: A Dangerous Quartet – Mariana Verdelho Machado – MDPI International Journal of Molecular Sciences

Animal models

Airway bacteria drive a progressive COPD-like phenotype in mice with polymeric immunoglobulin receptor deficiency – Bradley W. Richmond – Nature Communications

Reproduction and Growth in a Murine Model of Early Life-Onset Inflammatory Bowel Disease – Eniko Nagy – PLOS ONE

Intake of Meat Proteins Substantially Increased the Relative Abundance of Genus Lactobacillus in Rat Feces – Yingying Zhu – PLOS ONE

Colitis susceptibility in p47 phox−/− mice is mediated by the microbiome – E. Liana Falcone – Microbiome

Review: Multiscale analysis of the murine intestine for modeling human diseases – Jesse Lyons – Integrative Biology

Animal microbiome

The bird, not the whiskey: Activity of urealytic microorganisms in the gastrointestinal tract of the black grouse Lyrurus tetrix – M. V. Vecherskii – Doklady Biological Sciences

Plant, root, and soil microbiome

Zinc treatment increases the titre of ‘Candidatus Liberibacter asiaticus’ in huanglongbing-affected citrus plants while affecting the bacterial microbiomes – M.Q. Zhang – Journal of Applied Microbiology

Species Specificity of Bacteria Associated to the Brown Seaweeds Lobophora (Dictyotales, Phaeophyceae) and Their Potential for Induction of Rapid Coral Bleaching in Acropora muricata – Christophe Vieira – Frontiers in Microbiology

Water and extremophile microbiome

Aerobic Vinyl Chloride Metabolism in Groundwater Microcosms by Methanotrophic and Etheneotrophic Bacteria – Margaret Findlay – Environmental Science & Technology

Pyrosequencing analysis of bacterial communities in Lake Bosten, a large brackish inland lake in the arid northwest of China – Lei Zhang – Canadian Journal of Microbiology

Dynamic of bacterial communities attached to lightened phytodetritus – Morgan Petit – Environmental Science and Pollution Research

Waste and pollution microbiology

Detection of the Antimicrobial Triclosan in Environmental Samples by Immunoassay – Ki Chang Ahn – Environmental Science & Technology

Lactic acid fermentation from food waste with indigenous microbiota: Effects of pH, temperature and high OLR – Jialing Tang – Waste Management

Use of PCR-DGGE based molecular methods to assessment of microbial diversity during anaerobic treatment of antibiotic combinations – Sevcan Aydin – Bioresource Technology

Microbial Ecology

Host behaviour–parasite feedback: an essential link between animal behaviour and disease ecology – Vanessa O. Ezenwa – Proceedings of the Royal Society B

Myxococcus xanthus: Positively Frequency-Dependent Interference Competition Maintains Diversity and Pervades a Natural Population of Cooperative Microbes – Olaya Rendueles – Current Biology

Review: Deciphering and shaping bacterial diversity through CRISPR – Alexandra E Briner – Current Opinion in Microbiology

Microbes and education

Nice set of papers in ASM’s Journal of Microbiology and Biology Education:

Microbes in the news

The Scary Thing About a Virus That Kills Farmed Fish – Ed Yong – The Atlantic

Seres Therapeutics: All You Need To Know About What Will Be The First Prescription Microbiome Company – Seeking Alpha

Type IV pili: Appendages Help Microbes Survive Harsh Conditions – Charles Q. Choi – Astrobiology

Not endorsing this article. Microbiotas of men and women are not that different, not much published data on effects of space flight on gut microbiome, and I did not like the suggestion that women will get sick more often. Also, antibiotics ain’t gonna help if women have breast cancer.
Gender generates biological challenges for long duration spaceflight – Evan Gough

So long lithium, hello bacteria batteries? – ScienMag (not to be confused with Science)

Microbes in the news

Targeting the gut microbiome to fight heart disease – American Society for Microbiology

Science, publishing, and career

The Immoral Landscape? Scientists Are Associated with Violations of Morality – Bastiaan T. Rutjens – PLOS ONE

April 5, 2016

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Differences in myelination and gene expression in prefrontal cortex between GF and conventional mice, migratory passerines, metagenomics of probiotics, and megaviromes.

Events

NAS Meeting: Microbiomes of the Built Environment: From Research to Application – David Coil – MicroBEnet

Human oral microbiome

Impact of age and sex on the composition and abundance of the intestinal microbiota in individuals with and without enteric infections – Pallavi Singh – Annals of Epidemiology

Review [PDF]: Oral Microbial Shift: Factors affecting the Microbiome and Prevention of Oral Disease – Namrata Dagli – Journal of Contemporary Dental Practice

Human reproductive tract microbiome

Review: Incorporating microbiota data into epidemiological models: Examples from vaginal microbiota research – Janneke van de Wijgert – Annals of Epidemiology

Combined effect of diet and cervical microbiome on the risk of cervical intraepithelial neoplasia – Sang-Soo Seo – Clinical Nutrition

Human gut microbiome

Diversified mcr-1-Harbouring Plasmid Reservoirs Confer Resistance to Colistin in Human Gut Microbiota – Huiyan Ye – mBio

Animal models

Regulation of prefrontal cortex myelination by the microbiota – AE Hoban – Translational Psychiatry

Responses of fecal bacterial communities to resistant starch intervention in diabetic rats – Zhongkai Zhou – Starch

Resveratrol Attenuates Trimethylamine-N-Oxide (TMAO)-Induced Atherosclerosis by Regulating TMAO Synthesis and Bile Acid Metabolism via Remodeling of the Gut Microbiota – Ming-liang Chen – mBio

Commentary: Policing of gut microbiota by the adaptive immune system – Laurent Dollé – BMC Medicine

Animal microbiome

Sample processing impacts the viability and cultivability of the sponge microbiome – Ana I. Esteves – Frontiers in Microbiology

Characterization of the gut microbiota of migratory passerines during stopover along the northern coast of the Gulf of Mexico – William B. Lewis – Journal of Avian Biology

Highlight: Microbes matter: herbivore gut endosymbionts play a role in breakdown of host plant toxins – Franziska Beran – Environmental Microbiology

Selective feeding by the giant barrel sponge enhances foraging efficiency – Steven E. McMurray – Limnology and Oceanography

PhD Thesis: Molecular investigation of Australian termites and their gut symbionts – Nurdyana Abdul Rahman – University of Queensland

Plant, root, and soil microbiome

Distance-dependent effects of pathogenic fungi on seedlings of a legume tree: impaired nodule formation and identification of antagonistic rhizosphere bacteria –  Lan Liu – Journal of Ecology

Bacterial community dynamics during ensiling of perennial ryegrass at two compaction levels monitored by terminal restriction fragment length polymorphism – K. Graf – Journal of Applied Microbiology

Microsite differentiation drives the abundance of soil ammonia oxidizing bacteria along aridity gradients – Manuel Delgado-Baquerizo – Frontiers in Microbiology

Not exactly microbes but sounded interesting: Do tropical rain forest soils have greater nematode diversity than High Arctic tundra? A metagenetic comparison of Malaysia and Svalbard – Dorsaf Kerfahi – Global Ecology and Biogeography

Use of two spatially separated plant species alters microbial community function in horizontal subsurface flow constructed wetlands – Mark Button – Ecological Engineering

Water microbiome

Spatio-temporal interdependence of bacteria and phytoplankton during a Baltic Sea spring bloom – Carina Bunse – Frontiers in Microbiology

Protist-bacteria associations: Gammaproteobacteria and Alphaproteobacteria are prevalent as digestion-resistant bacteria in ciliated protozoa – Jun Gong – Frontiers in Microbiology

Particulate matter stoichiometry driven by microplankton community structure in summer in the Indian sector of the Southern Ocean – M. Rembauville – Limnology and Oceanography

Waste and pollution microbiome

Functional Metagenomics of a Biostimulated Petroleum-Contaminated Soil Reveals an Extraordinary Diversity of Extradiol Dioxygenases – Laura Terrón-González – Applied and Environmental Microbiology

Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community – Christopher L. Hemme – mBio

Built environment microbiome

A novel, optical, on-line bacteria sensor for monitoring drinking water quality – Bo Højris – Scientific Reports

Food and probiotics microbiology

Culture-Independent Metagenomic Surveillance of Commercially Available Probiotics with High-Throughput Next-Generation Sequencing – Jennifer N. Patro – mSphere

Unravelling the effect of clostridia spores and lysozyme on microbiota dynamics in Grana Padano cheese: A metaproteomics approach – Alessio Soggiu – Journal of Proteomics

Viruses and phages / metagenomics

VIP: an integrated pipeline for metagenomics of virus identification and discovery – Yang Li – Scientific Reports

Antibiotic Resistome: Improving Detection and Quantification Accuracy for Comparative Metagenomics – Ali H. A. Elbehery – OMICS

Themed Issue of Current Opinion in Microbiology: Environmental microbiology/Megaviromes
Review: Giants among larges: how gigantism impacts giant virus entry into amoebae – Rodrigo Araújo Lima Rodrigues – Current Opinion in Microbiology
Review: Updating strategies for isolating and discovering giant viruses – Jacques Yaacoub Bou Khalil
Review, but not sure about what: Persistent virus and addiction modules: an engine of symbiosis – Luis P Villarreal

Metabolomics

In silico methods for linking genes and secondary metabolites: The way forward – Shradha Khater – Synthetic and Systems Biotechnology

Techniques and bioinformatics

It’s all relative: analyzing microbiome data as compositions – Gregory B. Gloor – Annals of Epidemiology

Not metagenomics but about a not-clearly defined 16S rRNA gene amplification pipeline. Not a good paper: Snapshot on a pilot metagenomic study for the appraisal of gut microbial diversity in mice, cat and men – Coline Plé – Gastroenterology Research and Practice

More microbiology

Expression of arsenic resistance genes in the obligate anaerobe Bacteroides vulgatus ATCC 8482, a gut microbiome bacterium – Jiajiao Li – Anaerobe

Cholesterol Analogs with Degradation-resistant Alkyl Side Chains Are Effective Mycobacterium tuberculosis Growth Inhibitors – Daniel J. Frank – The Journal of Biological Chemistry

Microbiology and art

This Artist Paints With Bacteria, And It’s Strangely Beautiful – Jacqueline Howard – Huffington Post

Microbes in the news

With a quote from me! Gut bacteria regulate nerve fibre insulation – Mo Costandi – The Guardian

Europe’s Microbiology Society’s Annual Conference 2016: the Twitter story – Microbepost

Antibiotic soap can alter a baby’s gut bacteria – Tim Sandle – Digital Journal

The fridge that detects bacteria in your food – NZ Herald

About COPD: Take a deep breath – your lung microbiome will appreciate it – GSK

Microbiome and the modern environment: a global drift toward dysbiosis? – Susan Prescott and Alan Logan – BioMed Central blog

Biofilm researcher: New Faces: Boo Shan Tseng: This Life Sciences professor is all about communities – University of Nevada, Las Vegas

Study by the University of Kaiserslautern: Viruses cause bacteria to produce pink pigments – AlphaGalileo

Promising new method inhibits TB–causing bacteria – Phys.org

Bacteria Hysteria

Do you know how clean your lean workout is? The DEADLY bacteria found in your gym mat – Kat Romero – Express

Bik’s Picks

Cellular telephone use during free-living walking significantly reduces average walking speed – Jacob E. Barkley – BMC Research Notes

So cool: The Cemetery as Archive: A 177-year-old cemetery is preparing to digitize millions of records that shed light on New York City’s shifting demographics – Jessica Leigh Hester

March 30, 2016

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Microbiome and mood, bone marrow transplantation, archaea in kangaroos, tardigrade genome contamination.

Events

UC Berkeley Event: Archaea and the Three Domains: Classification of Life for Middle School

Microbiome expert to speak at UB –  Martin Blaser is a former president of the Infectious Diseases Society of America, April 6-7 – Charlotte Hsu – University of Buffalo

Pregnancy and birth

Microbiome: Antibiotics and the infant microflora – Kristen Meyer & Kjersti Aagaard – Nature Microbiology

Human mouth microbiome

Accuracy of commercial kits and published primer pairs for the detection of periodontopathogens – Elisabeth Santigli – Clinical Oral Investigations

Human gut microbiome

Gut microbes in correlation with mood: case study in a closed experimental human life support system – L. Li – Neurogastroenterology & Motility

Anti-TNF Therapy Response in Patients with Ulcerative Colitis Is Associated with Colonic Antimicrobial Peptide Expression and Microbiota Composition – Maria K. Magnusson – Journal of Crohn’s and Colitis

Gut microbiota profiling of pediatric NAFLD and obese patients unveiled by an integrated meta-omics based approach – Federica Del Chierico – Hepatology

Commentary: Role of gut flora after bone marrow transplantation – Jonathan U. Peled – Nature Microbiology

Animal microbiome

Differences down-under: alcohol-fueled methanogenesis by archaea present in Australian macropodids – Emily C Hoedt – The ISME Journal

Mussel biofiltration effects on attached bacteria and unicellular eukaryotes in fish-rearing seawater – Eleni Voudanta – PeerJ

Plant, root, and soil microbiome

Tobacco, Microbes, and Carcinogens: Correlation Between Tobacco Cure Conditions, Tobacco-Specific Nitrosamine Content, and Cured Leaf Microbial Community – Audrey D. Law – Microbial Ecology

Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland – Noriko A. Cassman – Scientific Reports

Drinking water microbiome

Flow cytometric examination of bacterial growth in a local drinking water network –
Sam Van Nevel – Water and Environment Journal

Animal microbiome

Breakdown of coevolution between symbiotic bacteria Wolbachia and their filarial hosts – Emilie Lefoulon – PeerJ

Built environment microbiome

Review (but did not make much sense to me): Toward a microbial Neolithic revolution in buildings – David S. Thaler – Microbiome

Bioreactor microbiome

Functional maintenance and structural flexibility of microbial communities perturbed by simulated intense rainfall in a pilot-scale membrane bioreactor – Yuya Sato – Applied Microbiology and Biotechnology

Fungi

News: Microbiology: Fungus produces a toxic surprise – Aaron P. Mitchell – Nature

Candidalysin is a fungal peptide toxin critical for mucosal infection – David L. Moyes – Nature

Biofilms

Spatio-temporal assembly of functional mineral scaffolds within microbial biofilms – Yaara Oppenheimer-Shaanan – NPJ Biofilms

Metagenomics and bioinformatics

Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies – Tom O Delmont – PeerJ

myPhyloDB: a local web server for the storage and analysis of metagenomic data – Daniel K. Manter – Database

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning – Brian Cleary – Nature Biotechnology

Metabolomics

Optimization of metabolomics of defined in vitro gut microbial ecosystems – Dirk K. Wissenbach – International Journal of Medical Microbiology

Microbial ecology

Review: Challenges in microbial ecology: building predictive understanding of community function and dynamics – Stefanie Widder – The ISME Journal

Microbes in the news

Another reason to break the habit: Smoking alters bacterial balance in mouth – EurekAlert

Pseudomonas aeruginosa in shampoos and shower gels made by Gilchrist and Soames – FDA warning letter

Acne bacteria and hot dog cookers: Science projects take center stage at regional fair – Matt Barney – The Joplin Globe

Cave bacteria could control superbugs – News24

The 8-Bit Game That Makes Statistics Addictive – Ed Yong – The Atlantic

Microbes and art

“World’s First” Bacteria-Grown Book Combines Science and Culture – Nathaniel Ainley – The Creators Project

WTF

Polish company to brew beer from Czech model’s vagina bacteria – Ben Hooper – UPI

First Vaginal Beer: Bottled Instinct – Wojciech Mann – IndieGoGo
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March 22, 2016

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Eye microbiota and contact lenses, leaf-cutter ant dumps, bacteria help with platinum transformation, metagenomics from a Swedish cave, extreme habitats at home, bacteria on board the ISS, a special issue on Megaviromes, and a recipe for Poop Peeps.

Jobs

Lecturership in Human Microbiome Studies – University of Reading, UK

Pregnancy and birth

Effect of Infant Formula Containing a Low Dose of the Probiotic Bifidobacterium lactis CNCM I-3446 on Immune and Gut Functions in C-Section Delivered Babies: A Pilot Study – L. Baglatzi – Clinical Medicine Insights: Pediatrics

Infection, immunology, and transplantion microbiology

Metagenomic analysis of bloodstream infections in patients with acute leukemia and therapy-induced neutropenia – P. Gyarmati – Scientific Reports

Rifaximin preserves intestinal microbiota balance in patients undergoing allogeneic stem cell transplantation – D Weber – Bone Marrow Transplantation

Gut microbiome–derived metabolites modulate intestinal epithelial cell damage and mitigate graft-versus-host disease – Nathan D Mathewson – Nature Immunology

Crosstalk between microbiota, pathogens and the innate immune responses – Claudia Günther – International Journal of Medical Microbiology

Human oral microbiome

Commentary: Microbiota-derived metabolites modulate tissue homeostasis: relevance to the oral cavity? – Hervé Le Moual – Oral Diseases

Human eye and skin microbiome

Changes in the Eye Microbiota Associated with Contact Lens Wearing – Hakdong Shin – mBio

Human vaginal microbiome

Improvement and automation of a real-time PCR assay for vaginal fluids – E. De Vittori – Forensic Science International

Human gut microbiome

Conference report: Talking about cross-talk: the immune system and the microbiome: A report on the first EMBO conference entitled “Next Gen Immunology—From Host Genome to the Microbiome: Immunity in the Genomic Era”, Feb 2016 – David Zeevi – Genome Biology

Review: An (Anti)-Inflammatory Microbiota: Defining the Role in Inflammatory Bowel Disease? – Burman S. – Digestive Diseases

Review: Gut Microbiota: The Brain Peacekeeper – Chunlong Mu – Frontiers in Microbiology

Review [PDF]: The intestinal microbiota and its role in human health and
disease – Keiko Kataoka – The Journal of Medical Investigation

Editorial: The microbiome as a possible target to prevent celiac disease – Maureen M Leonard – Expert Review of Gastroenterology & Hepatology

Animal models

Mice: Arthritis-induced alveolar bone loss is associated with changes in the composition of oral microbiota – Jôice Dias Corrêa – Anaerobe

Chickens: Dietary High Fluorine Alters Intestinal Microbiota in Broiler Chickens – Qin Luo – Biological Trace Element Research

Tilapia: Abrupt suspension of probiotics administration may increase host pathogen susceptibility by inducing gut dysbiosis – Zhi Liu – Scientific Reports

Animal microbiome

Cellulose-Enriched Microbial Communities from Leaf-Cutter Ant (Atta colombica) Refuse Dumps Vary in Taxonomic Composition and Degradation Ability – Gina R. Lewin – PLOS ONE

Plant, root, and soil microbiome

Relic DNA is abundant in soil and obscures estimates of soil microbial diversity – Paul Carini – bioRxiv

Biological role in the transformation of platinum-group mineral grains – Frank Reith – Nature Geoscience

Associations between ectomycorrhizal fungi and bacterial needle endophytes in Pinus radiata: implications for biotic selection of microbial communities – Megan A. Rúa – Frontiers in Microbiology

Functional composition of plant communities determines the spatial and temporal stability of soil microbial properties in a long-term plant diversity experiment – Tanja Strecker – Oikos

No synergistic effects of water and nitrogen addition on soil microbial communities and soil respiration in a temperate desert – Yan Gui Su – CATENA

The role of phosphorus, magnesium and potassium availability in soil fungal exploration of mineral nutrient sources in Norway spruce forests – Nicholas P. Rosenstock – New Phytologist

Climate and edaphic controllers influence rhizosphere community assembly for a wild annual grass – Erin E. Nuccio – Ecology

Temporal distance decay of similarity of ectomycorrhizal fungal community composition in a subtropical evergreen forest in Japan – Shunsuke Matsuoka – FEMS Microbiology Ecology

Review: The Functioning of Rhizosphere Biota in Wetlands – a Review – Amir Neori – Wetlands

Water and extremophile microbiome

Experimental evidence that microbial activity lowers the albedo of glaciers – M. Musilova – Geochemical Perspectives Letters

Transcriptional analysis of sulfate reducing and chemolithoautotrophic sulfur oxidizing bacteria in the deep subseafloor – William D. Orsi – Environmental Microbiology Reports

Cave microbiome

Metagenomic Analysis from the Interior of a Speleothem in Tjuv-Ante’s Cave, Northern Sweden – Marie Lisandra Zepeda Mendoza – PLOS ONE

Built environment microbiology

Microbial diversity of extreme habitats in human homes – Amy M. Savage – PeerJ preprint

Growth of 48 built environment bacterial isolates on board the International Space Station (ISS) – David A. Coil – PeerJ

Food microbiology

Isolation and identification of biocellulose-producing bacterial strains from Malaysian acidic fruits – Wen Yi W. V – Letters in Applied Microbiology

Bioinformatics, techniques, and metagenomics

Strain-level microbial epidemiology and population genomics from shotgun metagenomics – Matthias Scholz – Nature Methods

Improving the microbial community reconstruction at the genus level by multiple 16S rRNA regions – Shengqin Wang – Journal of Theoretical Biology

A framework for inferring biological communities from environmental DNA – Andrew Olaf Shelton – Ecological Applications

Review: Next-generation sequencing (NGS) in the microbiological world: How to make the most of your money – Antony T. Vincent – Journal of Microbiological Methods

Metagenomics and viruses

A Next-Generation Sequencing Data Analysis Pipeline for Detecting Unknown Pathogens from Mixed Clinical Samples and Revealing Their Genetic Diversity – Yu-Nong Gong – PLOS ONE

Exploring the virome of cattle with non-suppurative encephalitis of unknown etiology by metagenomics – Daniel Wüthrich – Virology

The Intestinal Eukaryotic Virome in Healthy and Diarrhoeic Neonatal Piglets – Oskar E. Karlsson – PLOS ONE

Special issue of Current Opinion in Microbiology: Megaviromes
Review: Giant viruses come of age – Matthias G Fischer
Review: Giant viruses and the origin of modern eukaryotes – Patrick Forterre

To be or not to be alive: How recent discoveries challenge the traditional definitions of viruses and life – Patrick Forterre – Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences

More microbiology

The mystery of plague in medieval Iceland – Chris Callow – Journal of Medieval History

Microbes in the news

HT: Tomer Altman: Poop Peeps: Today we’re going to make Poop Peeps. Marshmallow Peeps that are shaped like the poop emoji.– Matthew Cetta – Nomageddon

Elizabethkingia, the rare and deadly bacteria that’s sickening people in the Midwest, explained – Julia Belluz – Vox

Forest resilience; can microbes help combat climate change issues faster than genetic adaptations? – Armand Séguin

Controversial New Push to Tie Microbes to Alzheimer’s Disease. A journal article says herpes virus and Lyme disease bacteria are behind the mind-robbing illness, but not all researchers are convinced – Melinda Wenner Moyer – Scientific American

Bacteria Are Revolutionizing Biotech–Here’s Why We Need To Talk About It – Catherine Feuillet – Forbes

Contact Lenses Fill Your Eyes With Bacteria – Mandy Oaklander – Time

Killing Bacteria With Gold Nanodisks And Light – Jennifer Hicks – Forbes

Space gives bacteria room to grow – Dan Satherley – NewsHub

Uncovering bacterial role in platinum formation – University of Adelaide

Top Science Fair Projects Put Stream Data, Bacteria to Work – Dan Swanson – News Channel Nebraska

The Daily Startup: Startups Look to ‘New Frontier’ of Microbiomes to Fight Disease – Wall Street Journal

The Human Microbiome Handbook – Edited by Jason Tetro, Emma Allen-Vercoe

New Bioinformatic Approach Enables Strain-Level Microbial Profiling From Metagenomic Data – Genome Web

Ulcerative Colitis Improves in Multidonor Fecal Transplant Trial – Damian McNamara – MedScape

Blog posts by me:

New papers, March 22, 2016 – Elisabeth Bik – MicroBEnet

Extreme environments at home – Elisabeth Bik – MicroBEnet

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March 16, 2016

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Events

Strategies & Techniques for Analyzing Microbial Population Structures (STAMPS) Course 8/3-8/13 – MicroBEnet

Human skin microbiome

An in Vitro Model for the Human Cutaneous Microbial Ecosystem – Danique A. van der Krieken – Acta Dermato-Venereologica

Human oral microbiome

Interactions between Streptococcus oralis, Actinomyces oris, and Candida albicans in the development of multispecies oral microbial biofilms on salivary pellicle – I.M.G. Cavalcanti – Molecular Oral Microbiology

Human respiratory tract microbiome

High genetic diversity of Staphylococcus aureus strains colonising the nasopharynx of Gambian villagers before widespread use of pneumococcal conjugate vaccines – Chinelo Ebruke – BMC Microbiology

Human gut microbiome

Note: data segregate according to study: Gene expression profiling gut microbiota in different races of humans – Lei Chen – Scientific Reports

Review: A healthy gastrointestinal microbiome is dependent on dietary diversity – Mark L. Heiman

Review: Gut Microbiota and Obesity: Potential Therapeutic Targets and Probiotic 
Nicole D. White – American Journal of Life Sciences

Animal models

Fuzhuan tea consumption imparts hepatoprotective effects and alters intestinal microbiota in high saturated fat diet-fed rats – Michelle T. Foster – Molecular Nutrition & Food Research

Long-term effects of early life microbiota disturbance on adaptive immunity in laying 
K. Simon – Poultry Science

Rapid evolution of microbe-mediated protection against pathogens in a worm host –
Kayla C King – ISME Journal

Impact of 4-epi-oxytetracycline on the gut microbiota and blood metabolomics of Wistar rats
Hongxing Han – Scientific Reports

Animal microbiome

Genomic Analysis of Companion Rabbit Staphylococcus aureus – Mark A. Holmes – PLOS ONE

Plant, root, and soil microbiome

Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants – Tao Ding – PLOS ONE

Water and extremophile microbiome

Ecosystem function decays by fungal outbreaks in Antarctic microbial mats – David Velázquez – Scientific Reports

Multi-laboratory survey of qPCR enterococci analysis method performance in U.S. coastal and inland surface waters – Richard A. Haugland – Journal of Microbiological Methods

Built environment microbiome

Potentially harmful secondary metabolites produced by indoor Chaetomium species on artificially and naturally contaminated building materials – I. Došen – Indoor AIr

Food microbiology

Helicobacter pylori in bottled mineral water: genotyping and antimicrobial resistance properties – Reza Ranjbar – BMC Microbiology

Effects of Temperature on Bacterial Communities and Metabolites during Fermentation of Myeolchi-Aekjeot, a Traditional Korean Fermented Anchovy Sauce – Ji Young Jung – PLOS ONE

Viruses and phages

The Formulation of Bacteriophage in a Semi Solid Preparation for Control of Propionibacterium acnes Growth – Teagan L. Brown – PLOS ONE

News & Views: Microbial oceanography: Viral strategies at sea – T. Frede Thingstad – Nature

Lytic to temperate switching of viral communities – B. Knowles – Nature

Microbial Ecology

Closely coupled evolutionary history of ecto- and endosymbionts from two distantly related animal phyla – Judith Zimmerman – Molecular Ecology

Bioinformatics

RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to 
Yanming Zhang – Nucleic Acids Research

Techniques

The US Culture Collection Network lays the foundation for progress in preservation of valuable microbial resources – Kevin McCluskey – Phytopathology

Assessing the impact of long term frozen storage of faecal samples on protein concentration and protease activity – Laura S. Morris – Journal of Microbiological Methods

A modified micro chamber agar spot slide culture technique for microscopic examination of filamentous fungi – Peralam Yegneswaran Prakash – Journal of Microbiological Methods

Microbes in the news

uBiome is World’s First Company to Appoint Citizen-Scientist-in-Residence – PR Web

Incredible images reveal bacteria motor parts in unprecedented detail – Science Codex

Ancient Bacteria With Photosynthesis Were Much More Common Than Previously Thought, Study Finds – Catherine Griffin – HNGN

Viral Remnants Help Regulate Human Immunity: Endogenous retroviruses in the human genome can regulate genes involved in innate immune responses – Jyoti Madhusoodanan – The Scientist

Plastic That Mimics Insect Wings Kills Bacteria, University of California, Irvine Study – Biospace

Early heavy metal exposure can cause permanent changes to gut microbiome and cause a host of diseases – Dave Mihalovic – SOTT

Slice of PLOS: Bacteria’s Social Media – Lauren Richardson – PLOS ONE

“Unsurprisingly, Perlmutter has his critics.” Neurologist David Perlmutter gets to the guts of brain health with surprising advice – SMH.com

Opinion: A Mother’s Microbes: On “vaginal seeding” and the challenge of evidence-based parenting – Rob Knight and Jack Gilbert – The Scientist

Australian Scientists Discover How Gut Bacteria May Prevent Stomach Cancer – MSN

Reduction in dietary diversity impacts richness of human gut microbiota – Science Codex
http://www.nature.com/articles/srep23075

Press might be overinterpreting Mouse seminal microbiome study:
Scientists discover microbiome that may be responsible for male reproductive disorders – EurekAlert

Seminal work. How unruly data led MU scientists to discover a new microbiome – Roger Meissen – Decoding Science

Microbiome: This Type Of Bacteria May Increase Risk Of Reproductive Disorders – Kathleen Lees – HNGN

Science, publishing, and career

Handful of Biologists Went Rogue and Published Directly to Internet – Amy Harmon

Peer-Led Team Learning Helps Minority Students Succeed – Julia J. Snyder – PLOS Biology

Video parody: PloS ANNA VS ELSAvier – For The First Time – Luisa Hugerth -YouTube

Bik’s Picks

A Month in Mammoth. Two sleep researchers braved the subterranean environment of a Kentucky cave to see if they could train their bodies to abandon the cyclical rhythms of the 24-hour day – The Scientist

Night Night, Flipper – Watch underwater footage of a dolphin sleeping in the wild – The Scientist

Scientists Find That Getting Multiple Tattoos Strengthens Your Immune System – Kelly Tatera – Science Explorer

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February 28, 2016

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Viral sequences in cancers, COPD, and EDGE, an easy online tool for metagenomics analysis.

Jobs

Researcher for a project on the effect of gut microbiome in human behavior – Radboud UMC Nijmegen, The Netherlands

General microbiome

Opinion: Manipulating Bacterial Communities by in situ Microbiome Engineering – Ravi U. Sheth – Trends in Genetics

Pregnancy and birth

Effect of Saccharomyces boulardii and Mode of Delivery on the Early Development of the Gut Microbial Community in Preterm Infants – Natalia Zeber-Lubecka – PLOS ONE

Human respiratory microbiome

Lung microbiome dynamics in chronic obstructive pulmonary disease exacerbations – Zhang Wang – European Respiratory Journal

Human gut microbiome

Presence of Porphyromonas gingivalis in esophagus and its association with the clinicopathological characteristics and survival in patients with esophageal cancer – Shegan Gao – BMC Infectious Agents and Cancer

Human colorectal mucosal microbiota correlates with its host niche physiology revealed by endomicroscopy – Ai-Hua Wang – Scientific Reports

Review: Gut Microbiota of Nonalcoholic Fatty Liver Disease – Reham M. Abdou – Digestive Diseases and Sciences

Review: Microbes and the Mind: Emerging Hallmarks of the Gut Microbiota-Brain Axis – Kylynda C. Bauer – Cellular Microbiology

Review: Beyond the gut bacterial microbiota: The gut virome – Paola Columpsi – Journal of Medical Virology

Human tissues and infection

Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers – Jens Friis-Nielsen – MDPI Viruses

Models of microbiome research

Maternal Weaning Modulates Emotional Behavior and Regulates the Gut-Brain – Pamela Farshim – Scientific Reports

Rats: Correlations of Fecal Metabonomic and Microbiomic Changes Induced by High-fat Diet in the Pre-Obesity State – Hong Lin – Scientific Reports

Animal microbiome

18S rRNA V9 metabarcoding for diet characterization: a critical evaluation with two sympatric zooplanktivorous fish species – Aitor Albaina – Ecology and Evolution

Plant, root and soil microbiome

Tundra soil carbon is vulnerable to rapid microbial decomposition under climate warming – Kai Xue – Nature Climate Change

Online Springer Book: Microbial Inoculants in Sustainable Agricultural Productivity – Springer

Book chapter: Soil Effects of Genetically Modified Trees (GMTs) – Fernando Gallardo – Biosafety of Forest Transgenic Trees

Borderline Products between Bio-fertilizers/ Bio-effectors and Plant Protectants: The Role of Microbial Consortia – Marco Nuti – David Publishing Company

Differences in substrate use efficiency: impacts of microbial community composition, land use management, and substrate complexity – Tobias Bölscher – Biology and Fertility of Soils

Comparing how land use change impacts soil microbial catabolic respiration in Southwestern Amazon – Andre Mancebo Mazzetto – Brazilian Journal of Microbiology

Bacterial community dissimilarity between the surface and subsurface soils equals horizontal differences over several kilometers in the western Tibetan Plateau – Haiyan Chu – Environmental Microbiology

Soil and tree species traits both shape soil microbial communities during early growth of Chinese subtropical forests – Zhiqin Pei – Soil Biology and Biochemistry

Water and extremophile microbiome

Functional interactions of archaea, bacteria, and viruses in a hypersaline endolithic community – Alexander Crits-Christoph – Environmental Microbiology

Ecological succession leads to chemosynthesis in mats colonizing wood in sea water – Dimitri Kalenitchenko – The ISME Journal

Chapter One – Geomicrobiology and Metagenomics of Terrestrial Deep Subsurface Microbiomes – M. Itävaara – Advances in Applied Microbiology

Waste and pollution microbiology

Bacterial ecology of abattoir wastewater treated by an anaerobic digestor – Linda Jabari – Brazilian Journal of Microbiology

High-Resolution Phylogenetic Analysis of Residual Bacterial Species of Fouled Membranes after NaOCl Cleaning – Ronald R. Navarro – Water Research

Microbial diversity and hydrocarbon degrading gene capacity of a crude oil field soil as determined by metagenomics analysis – Firouz Abbasian – Biotechnology Progress

Bioinformatics

Now peer reviewed: cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies – John H. Chase – mSystems

Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation – Cecilia Noecker – mSystems

Assessing the performance of DNA barcoding using posterior predictive simulations – Anthony J. Barley – Molecular Ecology

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform – Po-E Li – BioRxiv

GenSeed-HMM: A tool for progressive assembly using profile HMMs as seeds and its application in Alpavirinae viral discovery from metagenomic data – João Marcelo P. Alves – Frontiers in Microbiology

Metabolomics

Human microbial metabolites as a source of new drugs – Somdutta Saha – Drug Discovery Today

More microbiology

Microbiota–mitochondria inter-talk: consequence for microbiota-host interaction – Yann Saint-Georges-Chaumet – Pathogens and Disease

Exploitation by cheaters facilitates the preservation of essential public goods in microbial communities – Clara Moreno-Fenoll – bioRxiv

Accurate and semi-automated analysis of bacterial association with mammalian cells – C.M. Murphy – Journal of Microbiological Methods

Microbes in the news

Fungal DNA, mycotoxins, cat allergens and fatigue in classrooms – Holly Ganz – MicroBEnet

Gum Disease Bacteria Linked to Esophageal Cancer Risk – Newsmax

Video: Virginia Tech scientists turn poo into power – Virginia Tech

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February 24, 2016

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Women in space, cacti, celiac disease, and traveling dust.

Event

Not endorsing – full of quackery and folks trying to sell their books and food supplements, little science: Microbiome Medicine Summit

Human oral microbiome

Review: Porphyromonas gingivalis: An Overview of Periodontopathic Pathogen below the Gum Line – Kah Yan How – Frontiers in Microbiology

Human reproductive tract microbiome

The potential influence of the microbiota and probiotics on women during long spaceflights – Camilla Urbaniak – Future Medicine

Human gut microbiome

Study of duodenal bacterial communities by 16S rRNA gene analysis in adults with active celiac disease versus non celiac disease controls – Esther Nistal – Journal of Applied Microbiology

High Molecular Weight Barley β-Glucan Alters Gut Microbiota Toward Reduced Cardiovascular Disease Risk – Yanan Wang – Frontiers in Microbiology

Review: A glance at … dietary emulsifiers, the human intestinal mucus and microbiome, and dietary fiber – Michael J. Glade – Nutrition

Review: Chemical conversations in the gut microbiota – Jessica A. Thompson – Gut Microbes

Review: Atopic dermatitis and the intestinal microbiota in humans and dogs – J. Mark Craig – Veterinary Medicine and Science

Animal models

Composition of fecal microbiota of laboratory mice derived from Japanese commercial breeders using 16S rRNA gene clone libraries – Ryoko Nozu – Journal of Veterinary Medical Science

Animal microbiome

News in livestock research — use of Omics-technologies to study the microbiota in the gastrointestinal tract of farm animals – Simon Deusch – Computational and Structural Biotechnology Journal

Plant, root, and soil microbiome

The Cacti Microbiome: Interplay between Habitat-Filtering and Host-Specificity – Citlali Fonseca-García – Frontiers in Microbiology

Comparison of Fungal Community in Black Pepper-Vanilla and Vanilla Monoculture Systems Associated with Vanilla Fusarium Wilt Disease –
Wu Xiong – Frontiers in Microbiology

Bacterial-Plant-Interactions: Approaches to Unravel the Biological Function of Bacterial Volatiles in the Rhizosphere – Marco Kai – Frontiers in Microbiology

Short-Term Rhizosphere Effect on Available Carbon Sources, Phenanthrene Degradation, and Active Microbiome in an Aged-Contaminated Industrial Soil – François Thomas – Frontiers in Microbiology

Changes in rhizosphere bacterial gene expression following glyphosate treatment – Molli M. Newman – Science of the Total Environment

Pepino (Solanum muricatum) planting increased diversity and abundance of bacterial communities in karst area – Jinxiang Hu – Scientific Reports

Friend or foe? Biological and ecological traits of the European ash dieback pathogen Hymenoscyphus fraxineus in its native environment – Michelle Cleary – Scientific Report

An interdomain network: the endobacterium of a mycorrhizal fungus promotes antioxidative responses in both fungal and plant hosts – Candida Vannini – New Phytologist

Water and extremophile microbiome

The effect of temperature change on the microbial diversity and community structure along the chronosequence of the sub-arctic glacier forefield of Styggedalsbreen (Norway) – Alejandro Mateos-Rivera – FEMS Microbiology Ecology

Water level changes affect carbon turnover and microbial community composition in lake sediments – Lukas Weise – FEMS Microbiology Ecology

Evaluation of the treatment performance and microbial communities of a combined constructed wetland used to treat industrial park wastewater – Ming Xu – Environmental Science and Pollution Research

Bacterial Composition and Survival on Sahara Dust Particles Transported to the European Alps – Marco Meola – Frontiers in Microbiology

Review: Bridging the divide: a model-data approach to Polar and Alpine microbiology – James A. Bradley – FEMS Microbiology Ecology

Bioinformatics and metagenomics

ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses – Jennifer Fouquier – Microbiome

More microbiology

Peracetic Acid Treatment Generates Potent Inactivated Oral Vaccines from a Broad Range of Culturable Bacterial Species – Kathrin Moor – Frontiers in Immunology

Microbes in the news

Bacteria From the Sahara Desert Found on Swiss Glaciers – Nellie Van Driska – GlacierHub

Wolbachia Bacteria Could Be Answer To Malaria, Dengue: Bill Gates – NDTV

Student Research Focus: Drew Gukeisen discovers and visualizes new virus – Indiana University SouthEast

Bacteria swabbing trend for newborns medically in doubt – Carina Storrs – CNN

Microbes and art

Navel gazing: portraits of the bacteria in our belly buttons – in pictures by Joana Ricou – The Guardian

Science, publishing, and career

Activism: Frustrated postdocs rise up – Paul Smaglik – Nature

Don’t trust an image in a scientific paper? Manipulation detective’s company wants to help – Retraction Watch
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February 23, 2016

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An introduction to 16S rRNA gene sequencing, gut microbiome disruptions in long-term care, microbial responses to oil contamination, colors and k-mers, and how to build your own Winogradsky column.

Jobs and events

PhD position on metagenomics-driven natural product discovery from plant microbiomes – Wageningen University, The Netherlands

Festival of Genomics: Has microbiome session, 27-29 June 2016, Boston

Human skin microbiome

Good introduction for other sample types too! Research Techniques Made Simple: Bacterial 16S Ribosomal RNA Gene Sequencing in Cutaneous Research – Jay-Hyun Jo – Journal of Investigative Dermatology

Human gut microbiome

Intestinal microbiome disruption in patients in a long-term acute care hospital: A case for development of microbiome disruption indices to improve infection prevention – Alison Laufer Halpin – American Journal of Infection Control

Association of dietary type with fecal microbiota and short chain fatty acids in vegans and omnivores – Alina Reiss – Journal of International Society of Microbiota

Microbiome models

Aging and serum MCP-1 are associated with gut microbiome composition in a murine model – Melissa N. Conley – PeerJ Preprint

Isolation and Characterization of a Novel Gammaherpesvirus from a Microbat Cell Line – Reed S. Shabman – mSphere

Animal microbiome

Review: Molecular trophic markers in marine food webs and their potential use for coral ecology – Miguel Costa Leal – Marine Genomics

Plant, root, and soil microbiome

Microbial diversity in European alpine permafrost and active layers – Beat Frey – FEMS Microbiology Ecology

Responses of microbial community from tropical pristine coastal soil to crude oil contamination – Daniel Morais – PeerJ

Zinc treatment increases the titer of ‘Candidatus Liberibacter asiaticus’ in HLB-affected citrus plants while affecting the bacterial microbiomes – Muqing Zhang – Journal of Applied Microbiology

Draft Genome Sequences of Two Vibrio splendidus Strains, Isolated from Seagrass Sediment – Ruth D. Lee – Genome Announcements

Draft Genome Sequences of Two Pseudoalteromonas Strains Isolated from Roots and Leaf Blades of the Seagrass Zostera marina – Alexandra Alexiev – Genome Announcements

Deep RNA-Seq profile reveals biodiversity, plant–microbe interactions and a large family of NBS-LRR resistance genes in walnut (Juglans regia) tissues – Sandeep Chakraborty – AMB Express

Water microbiome

Environmental heterogeneity among lakes promotes hyper β-diversity across phytoplankton communities – Selma Maloufi – Freshwater Biology

Bacterial community structure and variation in a full-scale seawater desalination plant for drinking water production – A. Belila – Water Research

Bimodal occupancy-frequency distributions uncover the importance of regional dynamics in shaping marine microbial biogeography – Markus V. Lindh – BioRxiv

Microbial Ecology

Eco-evolutionary dynamics in a coevolving host–virus system – Jens Frickel – Ecology Letters

Bioinformatics and metagenomics

Succinct Colored de Bruijn Graphs – Keith Belk – BioRxiv preprint

Metapalette: A k-mer painting approach for metagenomic taxonomic profiling and quantification of novel strain variation – David Koslicki – ArXiv

Microbes in the news

Grow a bacterial zoo in a bottle: How to build your own Winogradsky column – Steph Yin – Popular Science

Exploring the Humane and Canine Microbiome: Q&A with Dr. Robynne Chutkan – Claudia Kawczynska – The Bark

Ancient bacteria in Utah waters blamed for deaths of pets, people – Todd Tanner – Fox13

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