April 17, 2016

Guggenheim Securities Microbiome Day, April 21, New York. I cannot find a website for the conference, but got several links to press releases from companies that will participate, such as Enterome and Evelo Biosciences

General microbiome

Intricacies of assessing the human microbiome in epidemiological studies – Courtney K. Robinson – Annals of Epidemiology

Pregnancy and birth

Secretory IgA in the Coordination of Establishment and Maintenance of the Microbiota – Oliver Pabst – Trends in Immunology

Human skin microbiome

The microbiological signature of human cutaneous leishmaniasis lesions exhibits restricted bacterial diversity compared to healthy skin – Vanessa R Salgado – Memórias do Instituto Oswaldo Cruz

Human respiratory microbiome

Conference abstract: Analysis of the Sputum Microbiome in the Severe Asthma – Rihuang Qiu – Chest Journal

Human gut microbiome

(also contains animal experiments): Helminth infection promotes colonization resistance via type 2 immunity – Deepshika Ramanan – Science

Assessing the Colonic Microbiota in Children: Effects of Sample Site and Bowel Preparation – Shaw, Alexander G. – Journal of Pediatric Gastroenterology & Nutrition

Editorial: further evidence that proton pump inhibitors may impact on the gut microbiota – A. W. Walker – Alimentary Pharmacology & Therapeutics

Couple of papers from the Didier Raoult lab in New Microbes and New Infections (half of the next issue of that journal is by people from his group)
Isolation of a new species Peptoniphilus phoceensis from the human gut – Gaël Mourembou
Romboutsia timonensis, a new Species isolated from human Gut – Davide Ricaboni
« Bariatricus massiliensis », as a new bacterial species from the human gut microbiota – Simon Bessis

Review: Adaptation of Candida albicans to commensalism in the gut – Daniel Prieto – Future Microbiology

Review: Potential Role of the Microbiome in Barrett’s Esophagus and Esophageal Adenocarcinoma – Erik J. Snider – Digestive Diseases and Sciences

Review: Gut barrier structure, mucosal immunity and intestinal microbiota in the pathogenesis and treatment of HIV infection – Camilla Tincati – AIDS Research and Therapy

Review: Gut microbiota, inflammation and colorectal cancer – Jun Sun – Genes & Diseases

Review: Age-mediated changes in the gastrointestinal tract – Hamid A. Merchant – International Journal of Pharmaceutics

Review: Current Understanding of Dysbiosis in Disease in Human and Animal Models – DeGruttola, Arianna K. – Inflammatory Bowel Diseases

Animal models

Resilience of the intestinal microbiota following pathogenic bacterial infection is independent of innate immunity mediated by NOD1 or NOD2 – Susan J. Robertson – Microbes and Infection

Changes of Mouse Gut Microbiota Diversity and Composition by Modulating Dietary Protein and Carbohydrate Contents: A Pilot Study – Eunjung Kim – Preventive Nutrition and Food Science

Chemopreventive Metabolites Are Correlated with a Change in Intestinal Microbiota Measured in A-T Mice and Decreased Carcinogenesis – Amrita K. Cheema – PLOS ONE

Animal microbiome

Analysis of the rumen bacteria and methanogenic archaea of yak (Bos grunniens) steers grazing on the Qinghai-Tibetan Plateau – Dan Xue – Livestock Science

Evolution of the nasopharyngeal microbiota of beef cattle from weaning to 40 days after arrival at a feedlot – Edouard Timsit – Veterinary Microbiology

The gut microbiome and degradation enzyme activity of wild freshwater fishes influenced by their trophic levels – Han Liu – Scientific Reports

Plant, root, and soil microbiome

Multiple effects of a commercial Roundup® formulation on the soil filamentous fungus Aspergillus nidulans at low doses: evidence of an unexpected impact on energetic metabolism – Valérie Nicolas – Environmental Science and Pollution Research

Environmental Filtering Process Has More Important Roles than Dispersal Limitation in Shaping Large-Scale Prokaryotic Beta Diversity Patterns of Grassland Soils – Peng Cao – Microbial Ecology

Rhizosphere of Avicennia marina (Forsk.) Vierh. as a landmark for polythene degrading bacteria – Mohd. Shahnawaz – Environmental Science and Pollution Research

Wastewater microbiology

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

Characterization of microbial communities in wetland mesocosms receiving caffeine-enriched wastewater – Dongqing Zhang – Environmental Science and Pollution Research

Food microbiology

Bacterial community analysis of Tatsoi cultivated by hydroponics – Ok K. Koo – Journal of Environmental Science and Health, Part B

Heterofermentative lactic acid bacteria dominate in Korean commercial kimchi – Hee-Young Kim – Food Science and Biotechnology

Spatial Distribution of the Metabolically Active Microbiota within Italian PDO Ewes’ Milk Cheeses – Ilaria De Pasquale – PLOS ONE

Effect of postharvest practices on the culturable filamentous fungi and yeast microbiota associated with the pear carpoplane – Quinton Volschenk – Postharvest Biology and Technology

Review: Control of ochratoxin A-producing fungi in grape berry by microbial antagonists: A review – Hongyin Zhang – Trends in Food Science & Technology

More microbiology

Implementing an Antibiotic Stewardship Program: Guidelines by the Infectious Diseases Society of America and the Society for Healthcare Epidemiology of America – Tamar F. Barlam – Clinical Infectious Diseases

Zero-inflated negative binomial mixed model: an application to two microbial organisms important in oesophagitis – R. Fang – Epidemiology and Infection
http://journals.cambridge.org/action/displayAbstract?

Density-Dependent Differentiation of Bacteria in Spatially Structured Open Systems – Jan Ribbe – Biophysical Journal

Opinion: Harnessing the Power of Defensive Microbes: Evolutionary Implications in Nature and Disease Control – Suzanne A. Ford – PLOS Pathogens

Review: Directed evolution and synthetic biology applications to microbial systems – Marcelo C Bassalo – Current Opinion in Biotechnology

Microbes in the news

Gut bacteria could help prevent cancer – Science Daily

AmpliPhi Bio’s bacteriophage cocktail shows encouraging infection-fighting prowess in cystic fibrosis isolates; shares up 13% – Seeking Alpha

What do you want to know about your microbiome? uBiome opens poll on which of 6 top projects should win $100K in research help – Beth Mole – Ars Technica

Worm Infection Counters Inflammatory Bowel Disease by Drastically Changing Gut Microbiome – PR Newswire

The Microbiome: What Is It and How Does It Affect You? – Marsha Nunley – PR web

Science, publishing, and career

Why our peer review system is a toothless watchdog – Ivan Oransky and Adam Marcus – STAT News

Don’t dismiss science fairs. Make them better – Patrick Skerrett – STAT News

Dutch push for a quantum leap in open access – Martin Enserink – Science

April 13, 2016

Posted on April 13, 2016 by eliesbik

Thematic issue on effect of antibiotics on microbiomes, limited effect of probiotics on stool proteomics, culex mosquito development, ocean acidification, and new technique to determine microbial growth.

General microbiome

Thematic Issue: the effects of anthropogenic use of antibiotics on the microbiomes in various ecosystems and the implications for human health. Guest edited by Prof. Kornelia Smalla, the articles included in this issue are freely available to read til 11th May 2016. Environmental Dimension of Antibiotic Resistance – FEMS Microbiology Ecology
Review: Network-based metabolic analysis and microbial community modeling – Cesar Cardona – Current Opinion in Microbiology

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

Editorial: Microbiome: Eating for trillions – Derrick M. Chu – Nature

Pregnancy and birth

Preview: Another Reason to Thank Mom: Gestational Effects of Microbiota Metabolites – Seth Rakoff-Nahoum – Cell Host & Microbe

Review: The interplay of host immunity and environment on risk for bacterial vaginosis and associated reproductive health outcomes – Kerry Murphy – The Journal of Infectious Diseases

Human respiratory microbiome

Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype – Leopoldo N. Segal – Nature Microbiology

Human gut microbiome

Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults – Carolin A. Kolmeder – PLOS ONE

Review: The gut microbiota and metabolic disease: current understanding and future perspectives – T. Arora – Journal of Internal Medicine

Animal models

A Host-Produced Autoinducer-2 Mimic Activates Bacterial Quorum Sensing – Anisa S. Ismail – Cell Host & Microbe

Depletion of Butyrate-Producing Clostridia from the Gut Microbiota Drives an Aerobic Luminal Expansion of Salmonella – Fabian Rivera-Chávez – Cell Host & Microbe

Lipocalin 2 Protects from Inflammation and Tumorigenesis Associated with Gut Microbiota Alterations – Alexander R. Moschen – Cell Host & Microbe

Animal microbiome

Culex pipiens Development Is Greatly Influenced by Native Bacteria and Exogenous Yeast – Leonardo M. Díaz-Nieto – PLOS ONE

Plant, root, and soil microbiome

Convergence of soil microbial properties after plant colonization of an experimental plant diversity gradient – Katja Steinauer – BMC Ecology

Bacterial community associated to the pine wilt disease insect vectors Monochamus galloprovincialis and Monochamus alternatus – Marta Alves – Scientific Reports

Relationship between presence of the desert shrub Haloxylon ammodendron and microbial communities in two soils with contrasting textures – Yanfeng Cao – Applied Soil Ecology

Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil – Samiran Banerjee – Soil Biology and Biochemistry

Belowground response to drought in a tropical forest soil. I. Changes in microbial functional potential and metabolism – Nick Bouskill – Frontiers in Microbiology

Water and extremophile microbiome

Spatiotemporal Dynamics of Vibrio spp. within the Sydney Harbour Estuary – Nachshon Siboni – Frontiers in Microbiology

Assimilation of microbial and plant carbon by active prokaryotic and fungal populations in glacial forefields – Thomas Rime – Soil Biology and Biochemistry

Implications of Ocean Acidification for Marine Microorganisms from the Free-Living to the Host-Associated – Paul A. O’Brien – Frontiers in Marine Science

Waste and pollution microbiology

Shifts in microbial community structure and diversity in a MBR combined with worm reactors treating synthetic wastewater – Jia Liu – Journal of Environmental Sciences

Biomineralization of atrazine and analysis of 16S rRNA and catabolic genes of atrazine degraders in a former pesticide mixing site and a machinery washing area – James F. Douglass – Journal of Soils and Sediments

The effect of seasonality upon the development of lotic biofilms and microbial biostabilisation – Holger Schmidt – Freshwater Biology

Review: The importance of sewer biofilms – Henriette Jensen – Water

Food microbiology and functional foods

Lactobacillus plantarum TWK10 Supplementation Improves Exercise Performance and Increases Muscle Mass in Mice – Yi-Ming Chen – MDPI Nutrients

Investigation of the activity of the microorganisms in a Reblochon-style cheese by metatranscriptomic analysis – Christophe Monnet – Frontiers in Microbiology

Review: Prebiotics as a modulator of gut microbiota in paediatric obesity – A. C. Nicolucci – Pediatric Obesity

Techniques

Stable isotope probing with 18O-water to investigate microbial growth and death in environmental samples – Egbert Schwartz – Current Opinion in Biotechnology

Review: A priori Considerations When Conducting High-Throughput Amplicon-Based Sequence Analysis – Aditi Sengupta – Agricultural & Environmental Letters

Microbial ecology

Lack of functional redundancy in the relationship between microbial diversity and ecosystem functioning – Manuel Delgado-Baquerizo

Influence of dormancy on microbial competition under intermittent substrate supply: Insights from model simulations – Konstantin Stolpovsky – FEMS Microbiology Ecology

More microbiology

Metabolic Requirements of Escherichia coli in Intracellular Bacterial Communities during Urinary Tract Infection Pathogenesis – Matt S. Conover – mBio

Biostatistics

Reinventing Biostatistics Education for Basic Scientists – Tracey L. Weissgerber – PLOS Biology

Microbes in the news

MSU professor Gemma Reguera making tiny innovations with a big impact – Erin F. Wasinger – Lansing State Journal

SCSU prof Elizabeth Lewis Roberts discovers fungus, bacteria help grass (really) – Anna Bisaro – New Haven Register

Probiotics for Livestock – Reducing Antibiotic Reliance – Alex Alexiev – MicroBEnet

Taking Cues From Human Nutrition To Reduce Antibiotic Use In Livestock – Amy Mayer – NPR

Why bacteria can’t get any bigger—or smaller – Elizabeth Pennisi – Science

Digestion of lignin in the gut – Science Daily

“Truly exciting”: Probiotic may increase muscle mass, energy & performance – Stephen Daniells – Nutraingredients

Breakthrough at Binghamton furthers development of bacteria-powered energy – The Engineer

Vibrio: Aggressive infectious bacteria species found in Sydney Harbour – Daisy Dumas – Sydney Morning Herald

Science, publishing, and career

Do interventions to reduce misconduct actually work? Maybe not, says new report – Alison McCook – Retraction Watch

$250 million, 300 scientists and 40 labs: Sean Parker’s revolutionary project to ‘solve’ cancer – Ariana Eunjung Cha – Washington Post

Science fairs are as flawed as my solar-powered hot dog cooker – Carl Zimmer – STATnews

The dark side of Guardian comments: part of a series on the rising global phenomenon of online harassment – the Guardian

How one lab challenged a grant rejection and won €5 million – Ewen Callaway – Nature

Problems with paper on Bread and Mental Diseases

Posted on April 12, 2016 by eliesbik

A Storify Story of my tweets today about this paper:

Screen Shot 2016-04-13 at 12.13.44 AM.png

Bread and Other Edible Agents of Mental Disease – Paola Bressan* and Peter Kramer – Department of General Psychology, University of Padua, Padova, Italy – Frontiers in Human Neuroscience.

Abstract: Perhaps because gastroenterology, immunology, toxicology, and the nutrition and agricultural sciences are outside of their competence and responsibility, psychologists and psychiatrists typically fail to appreciate the impact that food can have on their patients’ condition. Here we attempt to help correct this situation by reviewing, in non-technical, plain English, how cereal grains—the world’s most abundant food source—can affect human behavior and mental health. We present the implications for the psychological sciences of the findings that, in all of us, bread (1) makes the gut more permeable and can thus encourage the migration of food particles to sites where they are not expected, prompting the immune system to attack both these particles and brain-relevant substances that resemble them, and (2) releases opioid-like compounds, capable of causing mental derangement if they make it to the brain. A grain-free diet, although difficult to maintain (especially for those that need it the most), could improve the mental health of many and be a complete cure for others.

I tried to embed the Storify Story here, but this Embedding is Trickier Than I Thought (or maybe I ate too much bread?). Ah well, I apologize. You will just have to click on the link:

[View the story “Problems with “Bread and Mental Disease” paper in Frontiers” on Storify]

April 12, 2016, the late one

Posted on April 12, 2016 by eliesbik

Events

Standards for Microbiome Measurements Workshop – August 9-10, NIST, Gaithersburg, Md

General microbiome

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

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

Moving microbiota research towards establishing causal associations that represent viable targets for effective public health interventions – Volker Mai – Annals of Epidemiology

Evolution of Koch’s postulates: towards a twenty-first century understanding of microbial infection – Guido Antonelli – Clinical Microbiology and Infection

Thematic Issue: Environmental Dimension of Antibiotic Resistance – FEMS Microbiology Ecology

Human oral microbiome

http://www.sciencedirect.com/science/article/pii/S104727971630076XThe Effects of Family, Dentition and Dental Caries on the Salivary Microbiome – Betsy Foxman – Annals of Epidemiology

Red fluorescent biofilm: the thick, the old, and the cariogenic – Catherine M.C. Volgenant – Journal of Oral Microbiology

Human gut microbiome

DNA from fecal immunochemical test can replace stool for microbiota-based colorectal cancer screening – Nielson T Baxter – BioRxiv Preprint

Changes in Korean Adult Females’ Intestinal Microbiota Resulting from Kimchi Intake – Kim JY – Omics Journal of Nutrition & Food Sciences

Review: The Fiber Gap and the Disappearing Gut Microbiome: Implications for Human Nutrition – Edward C. Deehan – Trends in Endocrinology & Metabolism

Animal model microbiome

Gut microbiome remodeling induces depressive-like behaviors through a pathway mediated by the host’s metabolism – P Zheng – Molecular Psychiatry

Temperate phages enhance pathogen fitness in chronic lung infection – Emily V Davies – The ISME Journal

Bacteraemia before during and after tooth extraction in horses in the absence of antimicrobial administration – I. Kern – Equine Veterinary Journal

Animal microbiome

Population and individual level dynamics of intestinal microbiota of a small primate – Tuomas Aivelo – Applied and Environmental Microbiology

The nasopharyngeal microbiota in feedlot cattle and its role in respiratory health – Edouard Timsit – Animal Frontiers

Review: Gut microbiome and omics: a new definition to ruminant production and health – Nilusha Malmuthuge – Animal Frontiers

Plant, root, and soil microbiome

Structural and functional differentiation of the root-associated bacterial microbiomes of perennial ryegrass – Lin Chen – Soil Biology and Biochemistry

Assessing microbial activities in metal contaminated agricultural volcanic soils – An integrative approach – C. Parelho – Ecotoxicology and Environmental Safety

Review: The role of locally adapted mycorrhizas and rhizobacteria in plant-soil feedback systems – Daniel Revillini – Functional Ecology

Water microbiome

Metagenomic analysis of nitrogen and methane cycling in the Arabian Sea oxygen minimum zone – Claudia Lüke – PeerJ

Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms – Hanno Teeling

Transporting Ocean Viromes: Invasion of the Aquatic Biosphere – Yiseul Kim – PLOS ONE

Seasonal changes in microbial community composition in river water studied using 454-pyrosequencing – Marija Kaevska – SpringerPlus

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

Substantial Variability of Multiple Microbial Communities Collected at Similar Acidic Mine Water Outlets – Lukáš Falteisek – Microbial Ecology

Bioinformatics and metagenomics

Chapter: Improving Bloom Filter Performance on Sequence Data Using kk-mer Bloom Filters – David Pellow – Research in Computational Molecular Biology

Microbial ecology

A Game Theoretical Approach to Microbial Coexistence – Monica Abrudan – Advances in Dynamic and Evolutionary Games

The ecologist’s field guide to sequence-based identification of biodiversity –
Simon Creer – Methods in Ecology and Evolution

Microbes in the news

MSU professor Gemma Reguera making tiny innovations with a big impact – Erin F. Wasinger – Lansing State Journal

Mind the fibre gap: The case of the vanishing gut microbiome – Will Chu – NutraIngredients

uBiome Opens Voting to all Citizen Scientists to Select $100k Microbiome Research Grant Winner – uBiome

Here’s the mounting evidence against using antibacterial soaps; Few pros, but cons include upped risk of infection, microbiome changes, drug resistance – Beth Mole – Ars Technica

Six-step hand-washing technique most effective for reducing bacteria in hospitals – Glasgow Chamber of Commerce

Hacking Gut Bacteria Could Be The Future Of Medicine. MIT biologists are reprogramming gut bacteria as “live therapeutics.” – Carolyn Gregoire – Huffington Post

Feeding Bacteria to Livestock Could Cut Antibiotic Use – Amy Mayer – Iowa Public Radio

Drug-resistant bacteria found scattered in soil – V. Nilesh – Deccan Chronicle

Sweet Siren call of surface lures bacteria to their death – Anthony King – Chemistry World

New Tree of Life Beautifully Illustrates the Enormous World of Bacteria – Kate Horowitz – Mental Floss

April 12, 2016, part 1

Posted on April 12, 2016 by eliesbik

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 8, 2016

Posted on April 8, 2016 by eliesbik

Bacterial mucin degradation in CF, gastric mucosa vs gastric juice, cockroaches, penguins, estimating post-mortem interval, and effects of sound on growth of E. coli.

Pregnancy and birth

Perinatal microbial exposure may influence aortic intima-media thickness in early infancy – Kate McCloskey – International Journal of Epidemiology

Human skin microbiome

A method for culturing Gram-negative skin microbiota – Ian A. Myles – BMC Microbiology

Human respiratory microbiome

Haemophilus parainfluenzae as a marker of the upper respiratory tract microbiota changes under the influence of preoperative prophylaxis with or without postoperative treatment in patients with lung cancer
Urszula Kosikowska – BMC Microbiology

Evidence and role for bacterial mucin degradation in cystic fibrosis airway disease – Jeffrey M Flynn – BioRxiv

Human oral microbiome

Identification of microorganisms in biofluids of individuals with periodontitis and chronic kidney disease using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry – Levy Anderson César Alves – Rapid Communications in Mass Spectrometry

Review: Host-Microbiome Cross-talk in Oral Mucositis – RM Vasconcelos – Journal of Dental Research

Human stomach microbiome

Comparison of Gastric Microbiota Between Gastric Juice and Mucosa by Next Generation Sequencing Method – Jihee Sung – Journal of Cancer Prevention

Human gut microbiome

Long-Term Green Tea Supplementation Does Not Change the Human Gut Microbiota – Pilou L. H. R. Janssens – PLOS ONE

Fecal bacterial microbiome diversity in chronic HIV-infected patients in China – Yang Sun – Emerging Microbes & Infections

Review: Gut microbiome and lipid metabolism: from associations to mechanisms – Wang, Zheng – Current Opinion in Lipidology

Review: Mood by microbe: towards clinical translation – Timothy G. Dinan – Genome Medicine

Animal models

Microbial-Derived Metabolites Reflect an Altered Intestinal Microbiota during Catch-Up Growth in Undernourished Neonatal Mice – Geoffrey A Preidis – Journal of Nutrition

Reduced Epithelial Na+/H+ Exchange Drives Gut Microbial Dysbiosis and Promotes Inflammatory Response in T Cell-Mediated Murine Colitis – Daniel Laubitz – PLOS ONE

Animal microbiome

Gut Bacterial Community of the Xylophagous Cockroaches Cryptocercus punctulatus and Parasphaeria boleiriana – Mercedes Berlanga – PLOS ONE

Plant, root, and soil microbiome

Functional breadth and home-field advantage generate functional differences among soil microbial decomposers – Nicolas Fanin – Ecology

Greater carbon allocation to mycorrhizal fungi reduces tree nitrogen uptake in a boreal forest – Niles J. Hasselquist – Ecology

Shifts in plant foliar and floral metabolomes in response to the suppression of the associated microbiota – Albert Gargallo-Garriga – BMC Plant Biology

Does arsenic play an important role in the soil microbial community around a typical arsenic mining area? – Fan Wu – Environmental Pollution

Groundwater–surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover – James C. Stegen – Nature Communications

Waste and pollution microbiology

Altitude-scale variation in nitrogen-removal bacterial communities from municipal wastewater treatment plants distributed along a 3600-m altitudinal gradient in China – Lihua Niu – Science of The Total Environment

Performance Assessment of Full-Scale Wastewater Treatment Plants Based on Seasonal Variability of Microbial Communities via High-Throughput Sequencing – Tang Liu – PLOS ONE

Review: Microbial Ecology and Evolution in the Acid Mine Drainage Model System – Li-Nan Huang – Trends in Microbiology

Forensic microbiology

Potential use of bacterial community succession for estimating post-mortem interval as revealed by high-throughput sequencing – Juanjuan Guo – Scientific Reports

Musical microbes

Effects of sound exposure on the growth and intracellular macromolecular synthesis of E. coli k-12 – Shaobin Gu – PeerJ

Functional foods

Special issue on Pre- and Probiotics in Gastroenterology Practice – Clinical Gastroenterology

Microbes in the news

Saving the Tasmanian devil with microbiome research – Yuanyuan Cheng, Carolyn Hogg & Kathy Belov – BioMedCentral Blog

Bacteria used to extract precious metals from e-waste in NUS study – Straits Times

Fighting Indoor Air Pollution with Plant Root Bacteria – Launch UMD

Latest #spacemicrobes Paper is Out… Built Environment Strains Grown on the ISS – David Coil – MicroBEnet

UChicago and Evelo Biosciences sign licensing deal for microbiome-based cancer immunotherapy – PR Newswire

Journal Club: Crowdfunding Science: all that we learned during our first crowdfunding campaigns – Katherine Dahlhausen – MicroBEnet

Maldonado-Contreras recognized by American Gastroenterological Association for gut microbiome research – Megan Bard – University of Massachusetts

Satire: Pope Francis To Award Sainthood To All Microbiome Researchers – The Allium HT: Tomer Altman

Microbes and art

Celling point: scientist makes Darwin’s Origin of Species with bacteria. Molecular biologist Dr Simon Park has made a very unusual edition of the classic text, using bacteria to create the cover – The Guardian

The Microverse: Children books about microbes. Cool titles, such as Escher Surfs the Sewer, and Vibri Finds Her Glow.

April 7, 2016

Posted on April 7, 2016 by eliesbik

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

Some followers will need to sign up again

Posted on April 6, 2016 by eliesbik

Last week I migrated the blog from an independent server to a WordPress server, and it seems that a subset of my followers were not transferred during the migration. In other words, if you had signed up to get an email whenever I posted something new, you might not have received anything in the last week. I am so sorry about that! I actually lost a large number of followers (the list had ~700 followers, and now only has 150).

I tried to figure out how to fix this but could not find an easy solution. For now, it’s probably the best to sign up again. Since I am now on a different server, the “Follow” box is now at the bottom right.

It looks like this: Screen Shot 2016-04-06 at 05.42PM, Apr 06

Click on it and enter your email, and you should get a confirmation email.

If you don’t see it, that means you are already logged in. Sometimes, signing in in Incognito mode might help to sign up again.

Again, my apologies! Let me know if you still are having troubles.

Elies

April 6, 2016

Posted on April 6, 2016 by eliesbik

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:

Turning Participatory Microbiome Research into Usable Data: Lessons from the American Gut Project – Justine W. Debelius
Crowdsourced Data Indicate Widespread Multidrug Resistance in Skin Flora of Healthy Young Adults – Scott Freeman
Symbiosis in the Soil: Citizen Microbiology in Middle and High School Classrooms – Erin McKenney
Using Scavenger Hunts to Familiarize Students with Scientific Journal Articles – Rebeccah S. Lijek
More of an Art than a Science: Using Microbial DNA Sequences to Compose Music – Peter E. Larsen

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

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Microbiome Digest – Bik's Picks

A daily digest of scientific microbiome papers, by the MD team. Founded by Elisabeth Bik, microbiome and science integrity consultant. Twitter: @microbiomdigest

April 17, 2016

April 14, 2016

April 13, 2016

Problems with paper on Bread and Mental Diseases

April 12, 2016, the late one

April 12, 2016, part 1

April 8, 2016

April 7, 2016

Some followers will need to sign up again

April 6, 2016