Category Archives: Human reproductive or urinary

July 6, 2016

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Two microbiology jobs, a Nature special on intestinal gut microbiota, coral dark spot syndrome, extremophiles from Yellowstone springs, and sugar-coating the envelope.

Jobs

Assembly Biosciences in San Francisco is looking for a Bioinformatics Scientist for supporting their microbiome programs. Contact Jared Kaleck at Klein Hersh for more info.

Nature Microbiology is looking for an Associate Editor, based in New York or London.

Events

4th Annual International Raising Clostridium difficile Awareness Conference and Health EXPO – September 20, 2016 – Atlanta

Human skin microbiome

Normal Skin Microbiota is Altered in Pre-clinical Hidradenitis Suppurativa – Hans Christian Ring – Acta Dermato-venereologica

The cutaneous microbiome and aspects of skin antimicrobial defense system resist acute treatment with topical skin cleansers – Aimee M. Two – Journal of Investigative Dermatology

Review: Bacterial and Viral Infections in Atopic Dermatitis: a Comprehensive Review – Peck Y. Ong – Clinical Reviews in Allergy & Immunology

Human urinary tract microbiome

Review: The urinary microbiota: a paradigm shift for bladder disorders? – Linda Brubaker – Current Opinion in Obstetrics & Gynecology

Human vaginal microbiome

Analysis of the Vaginal Microbiome by Next-Generation Sequencing and Evaluation of its Performance as a Clinical Diagnostic Tool in Vaginitis – Ki Ho Hong – Annals of Laboratory Medicine

Human gut microbiome

Fecal microbiota transplantation for recurrent Clostridium difficile infection in hematopoietic stem cell transplant recipients – B.J. Webb – Transplant Infectious Disease

The Esophageal Microbiome in Eosinophilic Esophagitis – Evan S. Dellon – Gastroenterology

Trimethylamine-N-oxide (TMAO) response to animal source foods varies among healthy young men and is influenced by their gut microbiota composition: a randomized controlled trial – Clara E. Cho – Molecular Nutrition & Food Research

Review: The Role of Gut Microflora and the Cholinergic Anti-inflammatory Neuroendocrine System in Diabetes Mellitus – Parth J. Parekh – Frontiers in Endocrinology

Review: Bifidobacteria and Their Role as Members of the Human Gut Microbiota – Amy O’Callaghan – Frontiers in Microbiology

Review: Navigating the Microbial Basis of Inflammatory Bowel Diseases: Seeing the Light at the End of the Tunnel – Laura E. Raffals – Gut and Liver

Animal and in vitro experiments

Composition of Gut Microbiota Influences Resistance of Newly Hatched Chickens to Salmonella Enteritidis Infection – Karolina Varmuzova – Frontiers in Microbiology

Pterostilbene-induced changes in gut microbiota composition in relation to obesity – Usune Etxeberria – Molecular Nutrition & Food Research

An Integrated Multi-Omics Approach Reveals the Effects of Supplementing Grass or Grass Hay with Vitamin E on the Rumen Microbiome and Its Function – Alejandro Belanche – Frontiers in Microbiology

Enterocyte-Associated Microbiome of the Hadza Hunter-Gatherers – Silvia Turroni – Frontiers in Microbiology

Animal microbiome

Composition and Functional Characterization of Microbiome Associated with Mucus of the Coral Fungia echinata Collected from Andaman Sea – Jhasketan Badhai – Frontiers in Microbiology

Epimicrobiota Associated with the Decay and Recovery of Orbicella Corals Exhibiting Dark Spot Syndrome – Julie L. Meyer – Frontiers in Microbiology

Plant, root, and soil microbiome

Temperature mediates continental-scale diversity of microbes in forest soils – Jizhong Zhou – Nature Communications

Molecular biosignatures reveal common benthic microbial sources of organic matter in ooids and grapestones from Pigeon Cay, The Bahamas – S. S. O’Reilly – Geobiology

Availability and function of arbuscular mycorrhizal and ectomycorrhizal fungi during revegetation of dewatered reservoirs left after dam removal – Andrew M. Cortese – Restoration Ecology

A metagenomic-based survey of microbial (de)halogenation potential in a German forest soil – Pascal Weigold – Scientific Reports

Limited recovery of soil microbial activity after transient exposure to gasoline vapors – Jakub J. Modrzyński – Environmental Pollution

Petroleum hydrocarbon contamination, plant identity and arbuscular mycorrhizal fungal community determine assemblages of the AMF spore-associated microbes – Bachir Iffis – Environmental Microbiology

Water and extremophile microbiome

Linking internal and external bacterial community control gives mechanistic framework for pelagic virus-to-bacteria ratios – Selina Våge – Environmental Microbiology

The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. I. Microbial Diversity Based on 16S rRNA Gene Amplicons and Metagenomic Sequencing – Vera Thiel – Frontiers in Microbiology

Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment – Louie Wurch – Nature Communications

Press: Scientists isolate, culture elusive Yellowstone microbe – Science Daily

Fungal and Prokaryotic Activities in the Marine Subsurface Biosphere at Peru Margin and Canterbury Basin Inferred from RNA-Based Analyses and Microscopy – Maria G. Pachiadaki – Frontiers in Microbiology

Unexpected biodiversity of ciliates in marine samples from below the photic zone – Jean-David Grattepanche – Molecular Ecology

Spatial and temporal variability of aerobic anoxygenic photoheterotrophic bacteria along the east coast of Australia – Jaime Bibiloni-Isaksson – Environmental Microbiology

Bioreactor microbiology

Perspectives for microbial community composition in anaerobic digestion: From abundance and activity to connectivity – Jo De Vrieze – Environmental Microbiology

Other microbiology

Opinion: Sugar Coating the Envelope: Glycoconjugates for Microbe–Host Crosstalk – Hanne L.P. Tytgat – Trends in Microbiology

A Combinatorial Algorithm for Microbial Consortia Synthetic Design – Alice Julien-Laferrière – Scientific Reports

Bioinformatics and metagenomics – viruses and phages

Freshwater Metaviromics and Bacteriophages: A Current Assessment of the State of the Art in Relation to Bioinformatic Challenges – Katherine Bruder – Evolutionary Bioinformatics

Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer – Guillaume Bernard – Scientific Reports

Microbes in the news

Dear Science: How many germs are actually on a toilet seat — and should I care? – Rachel Feltman and Sarah Kaplan – Washington Post

‘Super bacteria’ discovered in Rio’s waters as Olympics near – Flora Charner – CNN
‘Super Bacteria’ Detected at Rio de Janeiro’s Beaches – Rosalie Chen – Time

Scientists Discover A Sponge Extract In Antarctica, Can Kill ‘SuperBug’ MRSA Bacterium – Science World Report

Training in microbiology, molecular biology concludes – The Tribune

Science, publishing, and career

The past, present and future of the PhD thesis – Nature

Let’s make peer review scientific – Drummond Rennie – Nature

Bik’s Picks

Warning: contains autoplay video with sound and light-flashes that might not be suitable for epileptics. Sneak peek: The ‘Game of Genomes’ is coming – sequencing Carl Zimmer’s genome – STAT News

June 22, 2016

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Nipple aspirate, CNS infections, fiber and food allergies, horses and honeybee bacteria, and a report from the subway citizen science project.

General human microbiome

Commentary: Lessons Learned from Probing for Impacts of Triclosan and Triclocarban on Human Microbiomes – Rolf U. Halden – mSphere

Human nipple microbiome

Characterization of the microbiome of nipple aspirate fluid of breast cancer survivors – Alfred A. Chan – Scientific Reports

Human vaginal microbiome

Impact of Probiotic SYNBIO® Administered by Vaginal Suppositories in Promoting Vaginal Health of Apparently Healthy Women – Maria Cristina Verdenelli – Current Microbiology

Human gut microbiome

Alterations of Intestinal Microbiome by Antibiotic Therapy in Hospitalized Children – Miriam R. Fernandes – Microbial Drug Resistance

Could gut microbiota serve as prognostic biomarker associated with colorectal cancer patients’ survival? A pilot study on relevant mechanism – Zhiliang Wei – Oncotarget

ASM Microbe 2016 abstract: Increased Akkermansia muciniphila and Bacteroides fragilis Group Abundance After Islamic Fasting – C. Erdogdu – ASM Microbe 2016

Press: Happy Ramadan From Your Microbiome! – Gastroenterology & Endoscopy News

Review: Inflammation and the microbiome: implications for depressive disorders – Shawn Hayley – Current Opinion in Pharmacology

Review: Role of the microbiome, probiotics, and ‘dysbiosis therapy’ in critical illness.– Wischmeyer, Paul E. – Current Opinion in Critical Care

Infection and microbiology

Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system – Steven L. Salzberg – Neurology Neuroimmunology & Neuroinflammation

Press: Diagnosing brain infections using metagenomics – Julian Harris – PHG Foundation

Animal experiments

Dietary Fiber and Bacterial SCFA Enhance Oral Tolerance and Protect against Food Allergy through Diverse Cellular Pathways – Jian Tan – Cell Reports

Press: Diet high in fiber and vitamin A key to preventing allergies to peanuts and other triggers – EurekAlert

Gut microbiota translocation to the pancreatic lymph nodes triggers NOD2 activation and contributes to T1D onset – Frederico R.C. Costa – Journal of Experimental Medicine

Cutting Edge: Commensal Microbiota Has Disparate Effects on Manifestations of Polyglandular Autoimmune Inflammation – Camilla H. F. Hansen – The Journal of Immunology

Fighting Off Wound Pathogens in Horses with Honeybee Lactic Acid Bacteria – Tobias C. Olofsson – Current Microbiology

Plant, root, and soil microbiome

Local diversity of heathland Cercozoa explored by in-depth sequencing – Christoffer Bugge Harder – the ISME Journal

Press: Immense species richness of bacterial-eating microorganisms discovered in soil – Phys.org

Characterization of cadmium-resistant bacteria and their potential for reducing accumulation of cadmium in rice grains – Xiaoyan Lin – Science of The Total Environment
Editorial special issue: Soil, plants and endophytes – Stéphane Compant – Plant and Soil

Water and extremophile microbiome

Diverse Sulfur Metabolisms from Two Subterranean Sulfidic Spring Systems – Karen Rossmassler – FEMS Microbiology Letters

Metabolic potential of microbial mats and microbialites: autotrophic capabilities described by an in silico stoichiometric approach from shared genomic resources – Daniel Cerqueda-García – Journal of Bioinformatics and Computational Biology

Waste and pollution microbiology

Microbial contamination along the main open wastewater and storm water channel of Hanoi, Vietnam, and potential health risks for urban farmers – Samuel Fuhrimann – Science of The Total Environment

Isolation of Bdellovibrio bacteriovorus from a tropical wastewater treatment plant and predation of mixed species biofilms assembled by the native community members – Shugeng Feng – Environmental Microbiology

Microbial forensics

Microbial forensics: next‐generation sequencing as catalyst – Irene Kuiper – EMBO Reports

Bioinformatics and metagenomics

MEGAN Community Edition – Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data – Daniel H. Huson – PLOS Computational Biology

Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses – François Enault – The ISME Journal

More microbiology

Rates and mechanisms of bacterial mutagenesis from maximum-depth sequencing – Justin Jee – Nature

Press: Sequencing method precise enough to reveal mechanisms by which bacteria resist antibiotics – Phys.org

Darwinolide, a New Diterpene Scaffold That Inhibits Methicillin-Resistant Staphylococcus aureus Biofilm from the Antarctic Sponge Dendrilla membranosa – Jacqueline L. von Salm – Organic Letters

Press: Antibiotics from a Sponge. Could a new compound from Antarctic sea sponges be the key to breaching MRSA’s impregnable barricades? – Michael Lucibella – Antarctic Sun

Microbes in the news

MetaSUB Citizen Science Project:
With video of researchers swabbing away: Biologists Study What Kind Of Bacteria Is On New York City Subways – CBS Local
Qiagen, CosmosID Join International Urban Microbiome Project – Genome Web

New Life Found That Lives Off Electricity. Scientists have figured out how microbes can suck energy from rocks. Such life-forms might be more widespread than anyone anticipated – Emily Singer – Quanta Magazine

High-tech program on microbiome-based research launched in Qingdao – Hu Qing – China Daily

Explained: flesh eating bacteria in the Gulf of Mexico – Dylan Baddour – Houston Chronicle

Science, publishing, and career

Your Science Conference Should Have a Code of Conduct – Brett Favaro – Frontiers in Marine Science

Science in China – A special issue looks at the country’s astonishing scientific trajectory as it seeks to secure its spot among the leaders in innovation – Nature
China by the numbers. Research capacity has grown rapidly, and now quality is on the rise – Richard Van Noorden – Nature

Global Research Council: Commit to equity for women researchers – France A. Córdova – Nature

June 21, 2016

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An invertebrate gets its amino acids from microbial symbionts, microbiota and allograft rejection, high-altitude Andes lakes, and determining absolute microbiota abundances by spiking-in bacteria.

Jobs and events

Postdoctoral Researcher Microbial Ecology & Bioinformatics – NIOO-KNAW, WUR, Wageningen, The Netherlands

Report from the Microbiome R&D and Business Collaboration Forum, April 11–12, 2016, London, UK – Duc H. Le – EBioMedicine

General microbiome

Review: Diversity at low abundance: The phenomenon of the rare bacterial biosphere – M. Yu. Skopina – Microbiology

Workshop report: Culture-Independent Diagnostics for Health Security – Doggett Norman A.- Health Security

Viewpoint: Addressing Infectious Disease Challenges by Investigating Microbiomes – Emily P. Balskus – ACS Infectious Diseases

Human oral microbiome

Molecular analysis of fungal populations in patients with oral candidiasis using next-generation sequencing – Yumi Imabayashi – Scientific Reports

Human reproductive tract microbiome

Review: Chlamydia trachomatis Genital Tract Infections: When Host Immune Response and the Microbiome Collide – Noa Ziklo – Trends in Microbiology

Human gut microbiome

Review: Microbes, Immunity and Behaviour: Psychoneuroimmunology Meets the Microbiome – Timothy G Dinan – Neuropsychopharmacology

Review: Emerging roles for antigen presentation in establishing host–microbiome symbiosis – Nicholas J. Bessman – Immunological Reviews

Book Chapter: The Effect of H. pylori Infection on the Gastric Microbiota – Hyun Jin Jo – Helicobacter Pylori (Springer book)

Animal and in vitro experiments

The composition of the microbiota modulates allograft rejection – Yuk Man Lei – The Journal of Clinical Investigation

Press: Microbiota affect the rate of transplant acceptance and rejection – MedicalXpress

Maternal Metabolic Syndrome Programs Mitochondrial Dysfunction via Germline Changes across Three Generations – Jessica L. Saben – Cell Reports

Press, extrapolated conclusion: Obese Pregnant Women With Poor Diets May Worsen The Childhood Obesity Epidemic: Study – Samantha Olson – Medical Daily

Diet-dependent, microbiota-independent regulation of IL-10-producing lamina propria macrophages in the small intestine – Takanori Ochi – Scientific Reports

Characterization of Cimex lectularius (bedbug) defensin peptide and its antimicrobial activity against human skin microflora – Akanksha Kaushal – Biochemical and Biophysical Research Communications

Variability of arsenic bioaccessibility and metabolism in soils by human gut microbiota using different in vitro methods combined with SHIME – Naiyi Yin – Science of The Total Environment

Transient activation of mucosal effector immune responses by resident intestinal bacteria in normal hosts is regulated by interleukin-10 signalling – Cong Wu – Immunology

Mining of hemicellulose and lignin degrading genes from differentially enriched methane producing microbial community – Prabhakar D. Pandit – Bioresource Technology

Review: Strategies to modulate the intestinal microbiota of Tilapia (Oreochromis sp.) in aquaculture: a review – Alyssa M. Haygood – Reviews in Aquaculture

Animal microbiome

Seasonality and Locality Affect the Diversity of Anopheles gambiae and Anopheles coluzzii Midgut Microbiota from Ghana – Jewelna Akorli – PLOS ONE

A Nightmare for Males? A Maternally Transmitted Male-Killing Bacterium and Strong Female Bias in a Green Lacewing Population – Masayuki Hayashi – PLOS ONE
http://journals.plos.org/plosone/article?

Testosterone levels are positively correlated with cloacal bacterial diversity and the relative abundance of Chlamydiae in breeding male rufous-collared sparrows
– Camilo Escallón – Functional Ecology

The dominant detritus-feeding invertebrate in arctic peat soils derives its essential amino acids from gut symbionts – Thomas Larsen – Journal of Animal Ecology

Genomic characterization of symbiotic mycoplasmas from the stomach of deep-sea isopod Bathynomus sp – Yong Wang – Environmental Microbiology

Review: Is gastrointestinal microbiota relevant for endogenous mercury methylation in terrestrial animals? – R.C. Rodríguez Martín-Doimeadios – Environmental Research

Plant, root, and soil microbiome

Multi-targeted metagenetic analysis of the influence of climate and environmental parameters on soil microbial communities along an elevational gradient – Anders Lanzén – Scientific Reports

Integrated analysis of root microbiomes of soybean and wheat from agricultural fields – Nicolás Rascovan – Scientific Reports

Dark stains on rock surfaces in Driny Cave (Little Carpathian Mountains, Slovakia)
Rafał Ogórek – Extremophiles

Water and extremophile microbiome

Diversity of extremophilic bacteria in the sediment of high-altitude lakes located in the mountain desert of Ojos del Salado volcano, Dry-Andes – Júlia Margit Aszalós – Extremophiles

Microbial interactions lead to rapid micro-scale successions on model marine particles –
Manoshi S. Datta – Nature Communications

Bacteriophages in Arctic and Antarctic low-temperature systems – S. N. Filippova – Microbiology

Diversity of methanogenic archaea from the 2012 terrestrial hot spring (Valley of Geysers, Kamchatka) – A. Y. Merkel – Microbiology

Comparative analysis of prokaryotic diversity in solar salterns in eastern Anatolia (Turkey) – Seval Çınar – Extremophiles

Techniques

Adjusting microbiome profiles for differences in microbial load by spike-in bacteria – 
Frank Stämmler – Microbiome

Metagenomics and bioinformatics

Data Labours: How the Sequence Databases GenBank and EMBL-Bank Make Data – Tahani Nadima – Science as Culture

Principle, analysis, application and challenges of next-generation sequencing: a review – Khalid Raza – arXIv

Microbes in the news

Does a pipette work in space? with NASA Astronaut Dr Kate Rubins – Microbe Talk – Microbe Post

An Antarctic sponge offers new hope against deadly MRSA infection – Matt Windsor – UAB

Dental Microbes Not All in the Family. Kids often acquire cavity-causing bacteria from non-family members, researchers report at the American Society for Microbiology annual meeting – Tanya Lewis – The Scientist

Never-Before Human-Detected, Potentially Pathogenic Bacterium Found in Children With Acute Leukemia Human Microbiology Institute investigates potential role of previously unknown bacteria – PR Newswire

Geisinger’s Donna Wolk recognized for work in microbiology – Daily Item

Microbial mass extinctions were kicked off by human evolution – Andy Coghlan – New Scientist

Global Microbiome Initiative Explores Subways for Drug-Resistance Markers:
MetaSUB Consortium will collect DNA and RNA samples from high-traffic areas in subway systems, buses, and parks in 54 cities worldwide – GenEngNews

June 10, 2016

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Volunteers taking ETEC, 3 new E. coli phages, oral microbiomes of cats and dogs, skin microbes in Japanese amphibians, fungi and bacteria in floor dust.

Human oral microbiome

The oral microbiome of patients with axial spondyloarthritis compared to healthy individuals – Jordan E. Bisanz – PeerJ

Human vaginal microbiome

Association of Sexual Debut in Adolescents With Microbiota and Inflammatory Markers – Jespers, Vicky – Obstetrics & Gynecology

Human blood ‘microbiome’

Rapid identification of fungi in culture-negative clinical blood and respiratory samples by DNA sequence analyses – Farida Sidiq – BMC Research Notes

Human gut microbiome

Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment – Mihai Pop – BMC Genomics

Mucosa-Associated Ileal Microbiota in New-Onset Pediatric Crohn’s Disease – Assa, Amit – Inflammatory Bowel Diseases

Three New Escherichia coli Phages from the Human Gut Show Promising Potential for Phage Therapy – Marion Dalmasso – PLOS ONE

“Free living females” sounded… weird. Soluble Corn Fiber Increases Calcium Absorption Associated with Shifts in the Gut Microbiome: A Randomized Dose-Response Trial in Free-Living Pubertal Females – Corrie M Whisner – Journal of Nutrition

Similar Fecal Microbiota Signatures in Patients With Diarrhea-predominant Irritable Bowel Syndrome and Patients With Depression – Yixuan Liu – Clinical Gastroenterology and Hepatology

DGGE: Differences in the Biodiversity of the Fecal Microbiota of Infants With Rotaviral Diarrhea and Healthy Infants – Peng Fei – Jundishapur Journal of Microbiology

Opinion: How Our Other Genome Controls Our Epi-Genome – Antonella Celluzzi – Trends in Microbiology

Review: The role of the gut microbiota in NAFLD – Christopher Leung – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

Diet may influence the oral microbiome composition in cats – Christina J. Adler – Microbiome

Characterising the Canine Oral Microbiome by Direct Sequencing of Reverse-Transcribed rRNA Molecules – James E. McDonald – PLOS ONE

Bacterial microbiomes from vertically-transmitted fungal inocula of the leaf-cutting ant Atta texana – Lucas A. Meirelles – Environmental Microbiology Reports

Defensive insect symbiont leads to cascading extinctions and community collapse – Dirk Sanders – Ecology Letters

Plant, root, and soil microbiome

Subalpine conifers in two different geographic locations host highly similar foliar bacterial endophyte communities – Alyssa A. Carrell – FEMS Microbiology Ecology

Effect of plant growth-promoting bacteria on the growth and fructan production of Agave americana L. – Neyser De La Torre-Ruiz – Brazilian Journal of Microbiology

Composition of the Cutaneous Bacterial Community in Japanese Amphibians: Effects of Captivity, Host Species, and Body Region – Joana Sabino-Pinto – Microbial Ecology

Water and extremophile microbiome

Benthic protists: the under-charted majority – Dominik Forster – FEMS Microbiology Ecology

Methane release from sediment seeps to the atmosphere is counteracted by highly active Methylococcaceae in the water column of deep oligotrophic Lake Constance – Maren Bornemann – FEMS Microbiology Ecology

Review: How mutualisms arise in phytoplankton communities: building eco-evolutionary principles for aquatic microbes – Elena Kazamia – Ecology Letters

Review: All ecosystems potentially host electrogenic bacteria – Nicolas Chabert – Bioelectrochemistry

Pollution and waste and bioreactor microbiology

Arsenic metabolism and toxicity influenced by ferric iron in simulated gastrointestinal tract and the roles of gut microbiota – Haiyan Yu – Environmental Science & Technology

Pyrosequencing analysis of bacterial diversity in soils contaminated long-term with PAHs and heavy metals: Implications to bioremediation – Saranya Kuppusamy – Journal of Hazardous Materials

A strange combination of samples: Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies – Simon Güllert – Biotechnology for Biofuels

Monitoring the impact of bioaugmentation with a PAH-degrading strain on different soil microbiomes using pyrosequencing – S. Festa – FEMS Microbiology Ecology

Built environment microbiome

Fungal and bacterial growth in floor dust at elevated relative humidity levels – Karen C. Dannemiller – Indoor Air

Bioinformatics and statistics

An Introduction to Programming for Bioscientists: A Python-Based Primer – Berk Ekmekci – PLOS Computational Biology

Ten Simple Rules for Effective Statistical Practice – Robert E. Kass – PLOS Computational Biology

Bipartite Graphs for Visualization Analysis of Microbiome Data – Karel Sedlar – Evolutionary Bioinformatics

Techniques

The source of SYBR green master mix determines outcome of nucleic acid amplification reactions – Jianxin Yang – BMC Research Notes

More microbiology

Ancestral Tryptophan Synthase Reveals Functional Sophistication of Primordial Enzyme Complexes – Florian Busch – Cell Chemical Biology

Press: Ancient enzyme resurrected from the ancestor of all bacteria – Conor Gearin – New Scientist
Bacteria perfected protein complexes more than 3.5 billion years ago – Science Daily

Microbes in the news

Tufts microbiologist Cecilia A. Silva-Valenzuela, Ph.D., named Pew Latin American Fellow
Silva-Valenzuela, in Andrew Camilli’s lab, will investigate novel approaches to prevent cholera outbreaks – EurekAlert

Bio-statistician Albert Parker with MSU’s Center for Biofilm Engineering earns top EPA award – Amanda Eggert – Montana State University

Video series with James Hamblin – The Atlantic
Should You Map Your Microbiome? A visit to uBiome
Your Probiotics Aren’t Doing Anything (Yet)
You Probably Don’t Need to Shower – James Hamblin – The Atlantic

Banking on stool despite an uncertain future – Tina Amirtha – Science

Science, publishing, and career

In effort to understand continuing racial disparities, NIH to test for bias in study sections – Jeffrey Mervis – Science

Triplicated paper with multiplicated cells and images – Leonid Schneider – For Better Science
Author denies accusations of blatant duplication – Shannon Palus – Retraction Watch

Bik’s Picks (it’s not microbiology, but pretty cool)

RhizoTubes as a new tool for high throughput imaging of plant root development and architecture: test, comparison with pot grown plants and validation – Christian Jeudy – Plant Methods

June 3, 2016

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Microbes around a methane seep that look like ancient ruins, microbial metabolites protecting intestinal stem cells, and human-derived microbes in a Mars-like simulator.

Jobs and events

For everyone anxious to see the videos of the Stanford Bioinformatics for the Microbiome Symposium (including me!), please be patient. The AV team is working hard to generate videos for each individual talk, but that will take some time. Check in at this blog under the “Jobs and Events” header where I will post them once they are ready.

Assistant Professor in the Department of Biology – Macalester College, St. Paul, MN

Human vaginal microbiome

Predictive value of the composition of the vaginal microbiota in bacterial vaginosis, a dynamic study to identify recurrence-related flora – Bingbing Xiao – Scientific Reports

Human gut microbiome

Review: Reframing the Teenage Wasteland: Adolescent Microbiota-Gut-Brain Axis – Karen-Anne McVey Neufeld – The Canadian Journal of Psychiatry
Editorial to their own paper (?): Stress and the Microbiota-Gut-Brain Axis. An Evolving Concept in Psychiatry – John F. Cryan – The Canadian Journal of Psychiatry

Review: Emerging evidence of the role of gut microbiota in the development of allergic diseases – Kotryna Simonyte Sjödin – Current Opinion Allergy Clinical Immunology

Review: Microbiota and pathogen ‘pas de deux’: setting up and breaking down barriers to intestinal infection – Elizabeth S. McKenney – Pathogens and Disease

Review: Linking Gut Microbiota and Inflammation to Obesity and Insulin Resistance – M. J. A. Saad – Physiology

Research Highlight: Sensing gene–microbiota signals in IBD – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Editorial: Probiotics and microbiota composition – Mary Ellen Sanders – BMC Medicine

Animal / tissue culture experiments

The Colonic Crypt Protects Stem Cells from Microbiota-Derived Metabolites – Gerard E. Kaiko – Cell

Press: Gut microbes’ metabolite dampens proliferation of intestinal stem cells – Science Daily

Animal microbiome

Unfortunately no reference to our recent paper,  which included dolphin blowhole samples: Isolation of culturable aerobic bacteria and evidence of Kerstersia gyiorum from the blowhole of captive Yangtze finless porpoises – Xiaoling Wan – Antonie van Leeuwenhoek

Plants, roots, and soil microbiome

Seeing is believing: cell biology at the plant–microbe interface: report from the 36th New Phytologist Symposium – Mike Deeks – New Phytologist

Bacteria with Phosphate Solubilizing Capacity Alter Mycorrhizal Fungal Growth Both Inside and Outside the Root and in the Presence of Native Microbial Communities – Yuli Marcela Ordoñez – PLOS ONE

Water and extremophile microbiome

Exhumed hydrocarbon-seep authigenic carbonates from Zakynthos island (Greece): Concretions not archaeological remains – Julian E Andrews – Marine and Petroleum Geology

Press:
Ancient Civilization of Microbes, Not Greeks, Built ‘Lost City’ – Henry Fountain – The New York Times
The lost (microbe) colony: bacteria make underwater ‘ruins’ off Greek island – Alan Yuhas – The Guardian
This “Lost Underwater City” Was Actually Made by Microbes. Though these formations may not be evidence of a lost city, they show off some intriguing chemistry – Danny Lewis – Smithsonian
Microfungal oasis in an oligotrophic desert: diversity patterns and community structure in three freshwater systems of Cuatro Ciénegas, Mexico – Patricia Velez – PeerJ

Built environment microbiome

Microbial succession in an inflated lunar/Mars analog habitat during a 30-day human occupation – Teresa Mayer – Microbiome

In Situ Microbial Community Succession on Mild Steel in Estuarine and Marine Environments: Exploring the Role of Iron-Oxidizing Bacteria – Joyce M. McBeth – Frontiers in Microbiology

Ecology and bioinformatics

Applications of species accumulation curves in large-scale biological data analysis – Chao Deng – Quantitative Biology

Microbes in the news

See beautiful gif below: Educate Your Immune System. Our bodies are confused by this 21st-century world – Moises Velasquez-Manoff – NY Times

Will Microbes Save Agriculture? Experts Aim To Find Out – Geoffrey Mohan – Sci Tech Today

Alzheimer’s May Defend Against Microbes – Paul Rodgers – Forbes

Methane-producing microbes in California rocks – Science Daily

Science, publishing, and career

Science launches the 2016 ‘Dance Your Ph.D.’ contest – John Bohannon – Science Magazine

Let’s talk about preprint servers – Emilie Marcus – Crosstalk Cell

Bik’s Picks

A New Origin Story for Dogs. The first domesticated animals may have been tamed twice – Ed Yong – The Atlantic

The meteoritic origin of Tutankhamun’s iron dagger blade – Daniela Comelli – Meteoritics & Planetary Science

05valasquez-manoff-superJumbo.gif

Gif by Santtu Mustonen, New York Times

 

June 2, 2016

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Neck radiation and oral pathogen increase, menopause and the vaginal microbiome, nectar microbes, raw camel milk, and a review on short-chain fatty acids.

Human skin microbiome

Review: Microbial Ecology of the Human Skin – Anthony M. Cundell – Microbial Ecology

Human oral microbiome

Head and neck intensity modulated radiation therapy leads to an increase of opportunistic oral pathogens – Jennifer M. Schuurhuis – Oral Oncology

Human respiratory microbiome

Airway Microbiota Determines Innate Cell Inflammatory or Tissue Remodeling Profiles in Lung Transplantation – Eric Bernasconi – American Journal of Respiratory and Critical Care Medicine

Human vaginal microbiome

Review: Menopause and the Vaginal Microbiome – Alicia L. Muhleisen – Maturitas

Human gut microbiome

Not sure why this got published in Neurocomputing, also very poor English:
Gut microbiota community adaption during young children fecal microbiota transplantation by 16s rDNA sequencing – Jian-Lei Gu – Neurocomputing

Commentary: Transkingdom interactions: Liver flukes and the microbiota in cancer – Lisa Osborne – EBioMedicine

Review: Complex Relationships Between Food, Diet, and the Microbiome – Laura A. Pace – Gastroenterology Clinics of North America

Animal microbiome

Caribbean corals house shared and host-specific microbial symbionts over time and space – Nathaniel D. Chu – Environmental Microbiology Reports

Genome evolution and nitrogen-fixation in bacterial ectosymbionts of a protist inhabiting wood-feeding cockroaches – Vera Tai – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Nectar microbes can reduce secondary metabolites in nectar and alter effects on nectar consumption by pollinators – Rachel L. Vannette – Ecology

The Root-Associated Microbial Community of the World’s Highest Growing Vascular Plants – Roey Angel – Microbial Ecology

Plant community and soil chemistry responses to long-term nitrogen inputs drive changes in alpine bacterial communities – Xia Yuan – Ecology

Forest composition modifies litter dynamics and decomposition in regenerating tropical dry forest – Erik M. Schilling – Oecologia

Metal contamination status of the soil-plant system and effects on the soil microbial community near a rare metal recycling smelter – Zhu Li – Environmental Science and Pollution Research

Tree species, spatial heterogeneity, and seasonality drive soil fungal abundance, richness, and composition in Neotropical rainforests – Stephanie N. Kivlin – Environmental Microbiology

Review: Emerging Insights on Brazilian Pepper Tree (Schinus terebinthifolius) Invasion: The Potential Role of Soil Microorganisms – Karim Dawkins – Frontiers in Plant Science

Food microbiology

Bacteriological quality of raw camel milk along the market value chain in Fafen zone, Ethiopian Somali regional state – Tsegalem Abera – BMC Research Notes

Bioreactor microbiology

Comparison of microbial communities of activated sludge and membrane biofilm in 10 full-scale membrane bioreactors – Sung Jun Jo – Water Research

Phages and viruses

Phagonaute: A web-based interface for phage synteny browsing and protein function prediction – Hadrien Delattre – Virology

Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes – Branko Rihtman – PeerJ

Metagenomics and bioinformatics

Identification and analysis of integrons and cassette arrays in bacterial genomes – Jean Cury – Nucleic Acids Research

Uncovering oral Neisseria tropism and persistence using metagenomic sequencing – Claudio Donati – Nature Microbiology

Improved metagenome screening efficiency by random insertion of T7 promoters – Yu Jung Kim – Journal of Biotechnology

Experiences in integrated data and research object publishing using GigaDB – Scott C Edmunds – International Journal on Digital Libraries

Techniques

An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples – Satyabrata Bag – Scientific Reports

Proteomics, metabolomics

In vitro metabolic labeling of intestinal microbiota for quantitative metaproteomics – Xu Zhang – Analytical Chemistry

Syntrophic metabolism of vitamins and amino acids in gut microbial community as revealed by in silico genomic analyses – Matvei Sergeevich Khoroshkin – The FASEB Journal

Review: From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites – Ara Koh – Cell

More microbiology

Survey of laboratory-acquired infections around the world in biosafety level 3 and 4 laboratories – N. Wurtz – European Journal of Clinical Microbiology & Infectious Diseases

Effects of temperature variability on community structure in a natural microbial food web – Axel Zander – Global Change Biology

Perspective: Cooperative Microbial Tolerance Behaviors in Host-Microbiota Mutualism – Janelle S. Ayres – Cell

Review: Multifaceted Interfaces of Bacterial Competition – Reed M. Stubbendieck – Journal of Bacteriology

Microbes in the news

Featuring our former lab member Kate Rubins: Napa native heading to International Space Station on 1st space mission – ABC7news

American Gut Project Expands to Asia – Crowdsourced microbiome sequencing effort seeks participant diversity – Heather Buschman – UC San Diego Health

Making sense of microbiomes – UCI biochemist studies the effect of unique virus, bacteria and fungi on kids’ health – Tom Vasich – UCI News

11 deaths at Huntington Hospital among patients infected by dirty scopes, city report says – LA Times
Deadly dirty medical scopes still threaten trusting patients – My News LA

Walnuts may improve your colon health: Eating walnuts changes the gut microbiome and reduces cancer growth – EurekAlert

Gluten-Free Diet Induces Changes In Gut Microbiome – Interview with Ettje Tigchelaar – Medical Research

Fecal Transplants Effective for Healing Ulcerative Colitis – HCP Live

Gut Microbiome Tied to Metabolic Hormones in Early Pregnancy – Doctors Lounge

Human Gut Microbiome May Help Identify New Ways of Preventing and Treating Diabetes – Endocrinology Advisor

Researchers poo poo antibiotics – Vet Practice Magazine

Video: Susannah Tringe talks about metagenomics analysis tools and the challenges of gaining a systems-level understanding of a microbial community – Vizbi

Cold shock: E.coli bacteria found in 92 per cent ice samples in Mumbai – MidDay

Science, publishing, and career

The scientist’s guide to summer reading – Science

What does scientific reproducibility mean, anyway? – Ivan Oransky and Adam Marcus – STAT News

May 25, 2016

Posted on by

The sinonasal microbiome in chronic rhinosinusitis, walnut consumption in a mouse model, and treatment of cows with antibiotics has effects on dung beetle microbiomes.

Jobs and Grants

Assistant professor of food science, microbial ecology – Penn State

American Gastroenterological Association Invites Applications for Gut Microbiome Award – Philanthropy news digest

Three Post-Doctoral Fellowships for Tropical Microbial Ecologists in Panama – Smithsonian Tropical Research Institute

Events

1st International Conference on the Marine Microbiome – Discovery & Innovation for science and industry, 27 June 2016 — 30 June 2016, Berlin, Germany

Pregnancy and birth

Connections between the gut microbiome and metabolic hormones in early pregnancy in overweight and obese women – Luisa F Gomez-Arango – Diabetes

Human oral microbiome

Minireview: A practical guide to the oral microbiome and its relation to health and disease – K Krishnan – Oral Diseases

Human respiratory microbiome

Review: A systematic review of the sinonasal microbiome in chronic rhinosinusitis – Martin Anderson – American Journal of Rhinology & Allergy

Human gut microbiome

Letter: Faecal microbiota profiles as diagnostic biomarkers in primary sclerosing cholangitis – Malte Christoph Rühlemann – Gut

Review: Cesarean delivery is associated with celiac disease but not inflammatory bowel disease in children – Evalotte Decker – Gut Microbes

Human vaginal microbiome

Progresses in vaginal microflora physiology and implications for bacterial vaginosis and candidiasis – Gary Ventolini – Women’s Health

Animal experiments

Pulmonary Th17 Antifungal Immunity Is Regulated by the Gut Microbiome – Jeremy P. McAleer – The Journal of Immunology

Microbial modulation of behavior and stress responses in zebrafish larvae – Daniel J. Davis – Behavioural Brain Research

Effects of walnut consumption on colon carcinogenesis and microbial community structure – Masako Nakanishi – Cancer Prevention Research

Animal microbiome

Mucus Sugar Content Shapes the Bacterial Community Structure in Thermally Stressed Acropora muricata – Sonny T. M. Lee – Frontiers in Microbiology

Free-Living Species of Carnivorous Mammals in Poland: Red Fox, Beech Marten, and Raccoon as a Potential Reservoir of Salmonella, Yersinia, Listeria spp. and Coagulase-Positive Staphylococcus – Aneta Nowakiewicz – PLOS ONE

Treating cattle with antibiotics affects greenhouse gas emissions, and microbiota in dung and dung beetles – Tobin J. Hammer – Proceedings of the Royal Society B

Immune response and gut microbial community structure in bumblebees after microbiota transplants – Kathrin Näpflin – Proceedings of the Royal Society B

Plant, root, and soil microbiome

Effects of consecutive monoculture of Pseudostellaria heterophylla on soil fungal community as determined by pyrosequencing – Linkun Wu – Scientific Reports

Effects of heavy metals and chelants on phytoremediation capacity and on rhizobacterial communities of maize – Giovanni Vigliotta – Journal of Environmental Management

Comparative assessment of fungal augmentation treatments of a fine-textured and historically oil-contaminated soil – Stefano Covino – Science of the Total Environment

Water microbiome

Metagenomic covariation along densely sampled environmental gradients in the Red Sea – Luke R Thompson – bioRxiv

Variations in Bacterial Community in a Temperate Lake Associated with an Agricultural Watershed – Liyan Song – Microbial Ecology

Built environment microbiome

Review: The roles of the outdoors and occupants in contributing to a potential pan-microbiome of the built environment: a review – Marcus H. Y. Leung – Microbiome

Review: Use of Homogeneously-Sized Carbon Steel Ball Bearings to Study Microbially-Influenced Corrosion in Oil Field Samples – Gerrit Voordouw – Frontiers in Microbiology

Food microbiology

Indigenous Georgian Wine-Associated Yeasts and Grape Cultivars to Edit the Wine Quality in a Precision Oenology Perspective – Ileana Vigentini – Frontiers in Microbiology

Review: Diversity of Microorganisms in Global Fermented Foods and Beverages – Jyoti P. Tamang – Frontiers in Microbiology

Bioinformatics

mockrobiota: a public resource for microbiome bioinformatics benchmarking – Nicholas A Bokulich – PeerJ Preprints

SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals – Yevgeny Nikolaichik

Techniques

Flow cytometry combined with viSNE for the analysis of microbial biofilms and detection of microplastics – Linn Sgie – Nature Communications

Optimized Illumina PCR-free library preparation for bacterial whole genome sequencing and analysis of factors influencing de novo assembly – Christopher Huptas – BMC Research Notes

Microbes in the news

Inner Workings: Ancient teeth reveal clues about microbiome evolution – Jyoti Madhusoodanan – PNAS

Study shows cows on antibiotics produce dung with higher levels of greenhouse gases – DW

May 3, 2016

Posted on by

Counting the microbial species on Earth, goat rumen microbiome development, red kangaroos who died a tragic death, fungi in burgundy vineyards, Archaea in  Yellowstone, and image irregularities at a Pfizer lab in La Jolla.

Jobs and Events

Postdoctoral Fellowship Opportunity: Microbiology of the Built Environment – Sloan Foundation

Bioinformatics for the Microbiome, May 27 – Stanford Center for Genomics and Personalized Medicine, $49

General microbiology

Scaling laws predict global microbial diversity: Earth is home to as many as 1 trillion (10exp12) microbial species – Kenneth J. Locey – PNAS

Pregnancy and birth

Impact of Prematurity and Perinatal Antibiotics on the Developing Intestinal Microbiota: A Functional Inference Study – Silvia Arboleya – MDPI International Journal of Molecular Sciences

Review: Young microbes for adult obesity – M. Serino – Pediatric Obesity

Review: Microbial therapeutic interventions – Nicole G. Grady – Seminars in Fetal and Neonatal Medicine

Human oral microbiome

Microbiome of Deep Dentinal Caries Lesions in Teeth with Symptomatic Irreversible Pulpitis – Isabela N. Rôças – PLOS ONE

Human respiratory tract microbiome

Nasopharyngeal Microbiota, Host Transcriptome and Disease Severity in Children with Respiratory Syncytial Virus Infection – Wouter A.A. de Steenhuijsen Piters – Am J Respir Crit Care Med.

Human reproductive tract microbiome

Detection of DNA viruses in prostate cancer – Vitaly Smelov – Scientific Reports

Human gut microbiome

Effect of probiotic yoghurt on animal-based diet-induced change in gut microbiota: an open, randomised, parallel-group study – T. Odamaki – Beneficial Microbes

Fecal microbiota transplant for Clostridium difficile infection in older adults – William M. Tauxe – Therapeutic Advances in Gastroenterology

Review: Fine-tuning of the mucosal barrier and metabolic systems using the diet-microbial metabolite axis – Motoyoshi Nagai – International Immunopharmacology

Review: Gut Microbiome in CKD: challenges and opportunities – Anitha Nallu – Translational Research

Editorial: Transplanting a Microbial Organ: the Good, the Bad, and the Unknown – Dionysios A. Antonopoulos – mBio

Animal models
A polyphenol-rich fraction obtained from table grapes decreases adiposity, insulin resistance and markers of inflammation and impacts gut microbiota in high-fat-fed mice – Brian Collins – The Journal of Nutritional Biochemistry

Diet-induced obesity, energy metabolism and gut microbiota in C57BL/6J mice fed Western diets based on lean seafood or lean meat mixtures – Jacob Bak Holm – The Journal of Nutritional Biochemistry

Colonic Inflammation Accompanies An Increase of β-Catenin Signaling and Lachnospiraceae/Streptococcaceae in the Hind Gut of High-Fat Diet-Fed Mice – Huawei Zeng – The FASEB Journal

Gut commensal Bacteroides acidifaciens prevents obesity and improves insulin sensitivity in mice – J-Y Yang – Mucosal Immunology

Composition and Predicted Metabolic Capacity of Upper and Lower Airway Microbiota of Healthy Dogs in Relation to the Fecal Microbiota – Aaron C. Ericsson – PLOS ONE

Cultivation and qPCR Detection of Pathogenic and Antibiotic-Resistant Bacterial Establishment in Naive Broiler Houses – J. P. Brooks – Journal of Environmental Quality

Exploring the Goat Rumen Microbiome from Seven Days to Two Years – Lizhi Wang – PLOS ONE

Bacteriocin from epidemic Listeria strains alters the host intestinal microbiota to favor infection – Juan J. Quereda – PNAS

Animal microbiome

Spatial dynamics of the bacterial community structure in the gastrointestinal tract of red kangaroo (Macropus rufus) – Meirong Li – World Journal of Microbiology and Biotechnology

Assessment of Bacterial Communities in Thirteen Species of Laboratory-Cultured Domestic Mites (Acari: Acaridida) – Jan Hubert – Journal of Economic Entomology

Bacterial community in Haemaphysalis ticks of domesticated animals from the Orang Asli communities in Malaysia – Jing-Jing Khoo – Ticks and Tick-borne Diseases

Metabolomics of reef benthic interactions reveals a bioactive lipid involved in coral defence – Robert A. Quinn – Proceedings of the Royal Society B

Taxonomic and functional diversity of the culturable microbiomes of epigeic earthworms and their prospects in agriculture – Arjun Singh – Journal of Basic Microbiology

Methanogen Diversity in Indigenous and Introduced Ruminant Species on the Tibetan Plateau – Xiao Dan Huang – Archaea

Horse Species Symposium abstracts: Journal of Animal Science
Recent advances in the microbiome and physiology of the hindgut of the horse and dog – F. Camargo
Canine intestinal microbiology and metagenomics: From phylogeny to function – B. C. Guard – Journal of Animal Science
The microbiome of the horse hindgut: History and current knowledge – V. Julliand

Plant, root, and soil microbiome

Bacterial diversity and composition in major fresh produce growing soils affected by physiochemical properties and geographic locations – Jincai Ma – Science of the Total Environment

Microbial diversity limits soil heterotrophic respiration and mitigates the respiration response to moisture increase – Fen-Guo Zhang – Soil Biology and Biochemistry

Total and active microbial communities and phoD as affected by phosphate depletion and pH in soil – Sabine A. Ragot – Plant and Soil

Genetically modified WYMV-resistant wheat exerts little influence on rhizosphere microbial communities – Zhenhua Zhang – Applied Soil Ecology

Loss of testate amoeba functional diversity with increasing frost intensity across a continental gradient reduces microbial activity in peatlands – Vincent E.J. Jassey – European Journal of Protistology

Regional-scale analysis of arbuscular mycorrhizal fungi: the case of burgundy vineyards – Marie-Lara Bouffaud – Oeno One

Review: Role of Plant Growth Promoting Rhizobacteria in Agricultural Sustainability—A Review – Pravin Vejan – MDPI Molecules

Chapter: Mycorrhizas in Agroecosystems – Marcela C. Pagano – Recent Advances on Mycorrhizal Fungi

Water and extremophile microbiome

Next-Generation Sequencing Assessment of Eukaryotic Diversity in Oil Sands Tailings Ponds Sediments and Surface Water – Maria Aguilar – The Journal of Eukaryotic Microbiology

Drift in ocean currents impacts intergenerational microbial exposure to temperature – Martina A. Doblin – PNAS

Low Genome Content Diversity of Marine Planktonic Thaumarchaeota – Haiwei Luo – Environmental Microbiology Reports

The distribution, diversity and function of predominant Thermoproteales in high-temperature environments of Yellowstone National Park – Zackary J. Jay – Environmental Microbiology

Multidrug resistance phenotypes are widespread over different bacterial taxonomic groups thriving in surface water – Carlos Narciso-da-Rocha – Science of the Total Environment

A 150-year record of phytoplankton 1 community succession controlled by hydroclimatic variability in a tropical lake – Kweku Afrifa Yamoah – Biogeosciences

Review: Hydrothermal Vents and Methane Seeps: Rethinking the Sphere of Influence – Lisa A. Levin – Frontiers in Marine Science

Review: Microbial associations with macrobiota in coastal ecosystems: patterns and implications for nitrogen cycling – Orissa M Moulton – Frontiers in Ecology and the Environment

Book: Biotechnology of Extremophile – Springer

Waste and pollution microbiology

Revealing colonisation and biofilm formation of an adherent coal seam associated microbial community on a coal surface – Silas H.W. Vick – International Journal of Coal Geology

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

Built environment microbiology

Urban Microbiomes and Urban Agriculture: What Are the Connections and Why Should We Care? – Gary M. King – Sowing Seeds in the City

Bioinformatics, transcriptomics, metagenomics

rnaQUAST: a quality assessment tool for de novo transcriptome assemblies – Elena Bushmanova – Bioinformatics

Feature: Microbiology: the road to strain-level identification – Vivien Marx – Nature Methods

Protocol Book: Data Mining Techniques for the Life Sciences – Springer
Bacterial Genomic Data Analysis in the Next-Generation Sequencing Era – Massimiliano Orsini
Update on Genomic Databases and Resources at the National Center for Biotechnology Information – Tatiana Tatusova
Big Data, Evolution, and Metagenomes: Predicting Disease from Gut Microbiota Codon Usage Profiles – Maja Fabijanić

More microbiology

Riches of phenotype computationally extracted from microbial colonies – Tzu-Yu Liu – PNAS

Microbes in the news

UB’s microbiome hunters. These are exciting times at UB as its work on the human genome and microbiome matures. – Research Foundation for The State University of New York

Video: How Your City Has Its Own Unique Microbiome – Discovery News – YouTube

Wrapping up multiple sclerosis at UCSF – Claire Conway – UC San Francisco

Stalking Cave Bacteria to Make Secret Weapons Against Superbugs: Dr. Naowarat Cheeptham – Sam Grobart – Bloomberg

Seres Therapeutics Announces Achievement of Target Enrollment of SER-109 Phase 2 Study for the Prevention of Recurrent Clostridium difficile Infection – Business Wire

Bacteria use traffic-cop-like mechanism to infect gut. WSU scientists discover mechanism critical to pathogens’ success – EurekAlert

Tesla’s Bioweapon Defense Mode can protect you from bacteria, and reduce pollution
Cars. Tesla’s AC unit is available on the Model X and the new Model S – Alphr

Bacteria Hysteria

This odor-fighting, bacteria-killing underwear is made with pure silver – Christian de Looper – Yahoo Digital Trends
Millions of people are drinking mold and bacteria with their coffee. This is how to avoid it! – David Wolfe

Science, publishing and career

Image integrity concerns in papers from a Pfizer lab – Leonid Schneider – For Better Science

April 28, 2016

Posted on by

A special issue of Science with 2 papers on lifestyle factors that determine composition of the stool microbiome in large human cohorts, variation in microbiome LPS immunogenicity contributes to autoimmunity, SEM analysis of cave speleothem microbial communities, and saliva bacteria in Chicha (Ecuadorian beer).

Jobs and Events

Early Career Microbiome Meal, during European Respiratory Society Meeting 2016 London, September 2016

Caporaso Lab is hiring a software engineer to work on QIIME and scikit-bio – Greg Caporaso – MicroBEnet

General microbiome

A special Science Issue called The Microbiota At Work: Screen Shot 2016-04-28 at 12.42PM, Apr 28 1.jpg

Introduction: Manipulating the Microbiota – Caroline Ash, Kristen Mueller  – Science

Review: Cross-species comparisons of host genetic associations with the microbiome – Julia K. Goodrich – Science

Review: How colonization by microbiota in early life shapes the immune system – Thomas Gensollen – Science

Review: Antibiotic use and its consequences for the normal microbiome – Martin J. Blaser – Science

Review: The healthy human microbiome – Jason Lloyd-Price – Genome Medicine

Pregnancy and birth

Infant formula with galacto-oligosaccharides (OM55N) stimulates the growth of indigenous bifidobacteria in healthy term infants – T. Matsuki – Beneficial Microbes

Human oral microbiome

Comparison of Boiling and Robotics Automation Method in DNA Extraction for Metagenomic Sequencing of Human Oral Microbes – Junya Yamagishi – PLOS ONE

Human respiratory microbiome

[PDF] The impact of different methods of DNA extraction on microbial community measures of BALF samples based on metagenomic data – Yan Wen – Am J Transl Res

Human reproductive tract microbiome

[PDF] Barcoded sequencing reveals diverse intrauterine microbiomes in patients suffering with endometrial polyps – Rui-Li Fang – Am J Transl Res

Opinion: Cervicovaginal Microbiomes–Threats and Possibilities – Gregor Reid – Trends in Endocrinology & Metabolism

Review: Foodomics as part of the host-microbiota-exposome interplay – Lorenza Putignani – Journal of Proteomics

Human gut microbiome

Population-level analysis of gut microbiome variation – Gwen Falony – Science

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity – Alexandra Zhernakova – Science

Durable coexistence of donor and recipient strains after fecal microbiota transplantation – Simone S. Li – Science

Review: Resurrecting the intestinal microbiota to combat antibiotic-resistant pathogens – Eric G. Pamer – Science

Associations between dietary flavonoid intake and gut microbiota in a group of adults with cystic fibrosis (CF) – L. Li – Journal of Nutrition & Intermediary Metabolism

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans – Tommi Vatanen – Cell

Gut Bacteria Metabolism Impacts Immune Recovery in HIV-infected Individuals – Sergio Serrano-Villar – EBioMedicine

Serologic microbial associated markers can predict Crohn’s disease behaviour years before disease diagnosis – R. S. Choung – Alimentary Pharmacology & Therapeutics

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: Human gut microbiota and healthy aging: Recent developments and future prospective – Manish Kumar – Nutrition an Healthy Aging

Animal and other models

Soluble and Insoluble Fiber Differentially Impact Canine Fecal Microbiome and Circulating Metabolome – Matthew Irick Jackson – The FASEB Journal

Germ-free and antibiotic-treated mice are highly susceptible to epithelial injury in DSS colitis – Cristina Hernández-Chirlaque – Journal of Crohn’s and Colitis

High intensity exercise training increases the diversity and metabolic capacity of the mouse distal gut microbiota during diet-induced obesity – Emmanuel Denou – American Journal of Physiology

Induction of Subacute Ruminal Acidosis Affects the Ruminal Microbiome and Epithelium – Joshua C. Mccann – Frontiers in Microbiology

Review: Oral microbial biofilm models and their application to the testing of anticariogenic agents – Christina P.C. Sim – Journal of Dentistry

Animal microbiome

Patterns of bacteria-host associations suggest different ecological strategies between two reef building cold-water coral species – Anne-Leila Meistertzheim – Deep Sea Research Part I: Oceanographic Research Papers

Plant, root, and soil microbiome

Characterizing and handling different kinds of AM fungal spores in the rhizosphere – Xueguang Sun – World Journal of Microbiology and Biotechnology

Illumina-based analysis of the rhizosphere microbial communities associated with healthy and wilted Lanzhou lily (Lilium davidii var. unicolor) plants grown in the field – Qianhan Shang – World Journal of Microbiology and Biotechnology

Microbial community structures and metabolic profiles response differently to physiochemical properties between three landfill cover soils – Xi-En Long – Environmental Science and Pollution Research

The effects of host age and spatial location on bacterial community composition in the English Oak tree (Quercus robur) – S. Meaden – Environmental Microbiology Reports

Universal indicators for oil and gas prospecting based on bacterial communities shaped by light-hydrocarbon microseepage in China – Chunping Deng – Journal of Microbiology and Biotechnology

Performance of 16s rRNA primer pairs in the study of rhizosphere and endosphere bacterial microbiomes in metabarcoding studies – Bram Beckers – Frontiers in Microbiology

Water and extremophiles

The unexpected extremophile: Tolerance to fluctuating salinity in the green alga Picochlorum – Fatima Foflonker – Algal Research

Microbial communities in a range of carbon dioxide fluxes from a natural volcanic vent in Campo de Calatrava, Spain – Irena Fernández-Montiel – International Journal of Greenhouse Gas Control

On the use of high-throughput sequencing for the study of cyanobacterial diversity in Antarctic aquatic mats – Igor Stelmach Pessi – Journal of Phycology

Quorum sensing plays a complex role in regulating the enzyme hydrolysis activity of microbes associated with sinking particles in the ocean – Andreas Krupke – Frontier in Marine Science

Succession of bacterial community structure during the early stage of biofilm development in the Antarctic marine environment – Yung Mi Lee – Korean Journal of MIcrobiology

Using scanning electron microscopy to study microbial communities in speleothem samples collected from Iron Curtain Cave – Cohord Mason – The Journal of Experimental Microbiology & Immunology

Large differences in potential denitrification and sediment microbial communities across the Laurentian great lakes – Gaston E. Small – Biogeochemistry

Built environment microbiome

Ecological succession of the microbial communities of an air conditioning cooling coil in the tropics – Enzo Acerbi – Indoor Air

Web Alert: Microbiology in archaeology: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology – Lawrence P. Wackett – Environmental Microbiology

Food microbiology

Bacteria associated with human saliva are major microbial components of Ecuadorian indigenous beers (chicha) – Ana L. Freire – PeerJ

A method to isolate bacterial communities and characterize ecosystems from food products: Validation and utilization in as a reproducible chicken meat model – Amélie Rouger – International Journal of Food Microbiology

Bioinformatics and metagenomics

BaitFisher: A Software Package for Multispecies Target DNA Enrichment Probe Design – Christoph Mayer – Molecular Biology and Evolution

Microbial ecology

The Evolution of Quorum Sensing as a Mechanism to Infer Kinship – Jonas Schluter – PLOS Computational Biology

Co-existence facilitates interspecific biofilm formation in complex microbial communities – Jonas S Madsen – Environmental Microbiology

Viruses and phages

Molecular evolution of epizootic hemorrhagic disease viruses in North America based on historical isolates using motif fingerprints – W. C. Wilson – Virus Genes

Techniques

[Video Protocol] Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization – Melis N. Anahtar – Journal of Visualized Experiments

Comparison of Boiling and Robotics Automation Method in DNA Extraction for Metagenomic Sequencing of Human Oral Microbes – Junya Yamagishi – PLOS ONE

The impact of different methods of DNA extraction on microbial community measures of BALF samples based on metagenomic data – Yan Wen – Am J Transl Res

Microbes in the news

Your gut bacteria are more than what you eat – Elizabeth Pennisi – Science

With quotes from me! New research confirms thriving gut bacteria is linked to a healthier body – Russell Brandom – The Verge

Want more good bugs in your gut? Try yogurt. And coffee – Patrick Skerrett – STAT News

This Bacteria Strain Offers a Curious Mix of Hope and Danger. The Elizabethkingia strain could cure malaria, but it’s also sickened dozens in Wisconsin – Lisa Margonelli – Slate

Bacteria beneficial to plants have spread across California – UC Riverside study shows spread of Bradyrhizobium has important implications for biofertilizers – EurekAlert

The Benefits of Slathering Your Newborn Baby with Vaginal Bacteria – Rebecca Schiller – Vice Broadly

A Timely Gut Check. At the American Museum of Natural History, meet your microbiome – Ralph Gardner – The Wall Street Journal

A Comprehensive Survey of Pre-Clinical Microbiology Curricula Among United States Medical Schools – Dora Melber – Clinical Infectious Diseases

Mayo Clinic Ventures Firm Explores Commercialization Of Gut Microbe Treatment – Don Jacobson – Twin City Business

Microbes and art

Quilting with soil: soil microorganisms had “painted” their efforts on the cloth in an unexpected variety of colors. – Martha Pings – Soils

Science, publishing, and career

Is most published research really false? – Jeffrey T Leek, Leah R Jager – bioRxiv

Who’s downloading pirated papers? Everyone. In rich and poor countries, researchers turn to the Sci-Hub website – John Bohannon – Science

The frustrated science student behind Sci-Hub – John Bohannon – Science

Plagiarism: A worm poking holes into the quality of our academic work – Christine Osae – The New Times

Bik’s Picks
Doctor ready to perform first human head transplant – Ross Kenneth Urken – News Week

April 27, 2016

Posted on by

Cervical microbiome during cancer, distinct gut microbiome in kidney stone formers? (unclear due to vaguely formulated control group), culturing marine microbes in artificial seawater, codon usage to predict pathogenicity.

Events

Science Diplomats to present ‘Trust Your Gut: How Helpful Bacteria Impact Health’ – Free talk given 3 times at Yale in May

Pregnancy and birth

News & Views: Immunology: Mum’s microbes boost baby’s immunity – Mihir Pendse & Lora V. Hooper – Nature

Human respiratory microbiome

Culture based: Microbiology of peritonsillar abscess in the South Estonian population – Risto Vaikjärv – Microbial Ecology in Health and Disease

Human reproductive tract microbiome

Cervical Microbiome and Cytokine Profile at Various Stages of Cervical Cancer: A Pilot Study – Astride Audirac-Chalifour – PLOS ONE

Human gut microbiome

Note that the control group is poorly described: Evidence for a distinct gut microbiome in kidney stone formers compared to non-stone formers – Joshua M. Stern – Urolithiasis

Review: Macrobiota — helminths as active participants and partners of the microbiota in host intestinal homeostasis – William C Gause – Current Opinion in Microbiology

Review: The possible mechanisms of the human microbiome in allergic diseases – Kagan Ipci – European Archives of Oto-Rhino-Laryngology

Review: Towards a functional hypothesis relating anti-islet cell autoimmunity to the dietary impact on microbial communities and butyrate production – David Endesfelder – Microbiome

Animal and bioreactor models

Biochar, Bentonite and Zeolite Supplemented Feeding of Layer Chickens Alters Intestinal Microbiota and Reduces Campylobacter Load – Tanka P. Prasai – PLOS ONE

Applying theories of microbial metabolism for induction of targeted enzyme activity in a methanogenic microbial community at a metabolic steady state – Jutta Speda – Applied Microbiology and Biotechnology

A humanized microbiota mouse model of ovalbumin-induced lung inflammation – Marie-Claire Arrieta – Gut Microbes

Plant, root, and soil microbiome

Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria – Edward W. Davis II – PeerJ Preprint

Water and extremophile microbiome

Artificial Seawater Media Facilitate Cultivating Members of the Microbial Majority from the Gulf of Mexico – Michael W. Henson – mSphere

Salinity shapes microbial diversity and community structure in surface sediments of the Qinghai-Tibetan Lakes – Jian Yang – Scientific Reports

Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations – Alexander J. Probst – Environmental Microbiology

Metabolome-mediated biocryomorphic evolution promotes carbon fixation in Greenlandic cryoconite holes – J.M. Cook – Environmental Microbiology

Pollution and waste microbiology

Microbial density and diversity in constructed wetland systems and the relation to pollutant removal efficiency – Yang Zhang – Water Science & Technology

A mesophilic anaerobic digester for treating food waste: process stability and microbial community analysis using pyrosequencing – Lei Li – Microbial Cell Factories

Microbial ecology

Inhibitory interactions promote frequent bistability among competing bacteria –
Erik S. Wright – Nature Communications

Bioinformatics and metagenomics

Protocol: Big Data, Evolution, and Metagenomes: Predicting Disease from Gut Microbiota Codon Usage Profiles – Maja Fabijani – Data Mining Techniques for the Life Sciences

Review: High definition for systems biology of microbial communities: metagenomics gets genome-centric and strain-resolved – Dmitrij Turaev – Current Opinion in Biotechnology

Microbes in the news

Elizabethkingia: The bacteria strain that could kill you. Or cure malaria. Small Science: Genomic data is showing us how little we know – Lisa Margonelli – Houston Chronicle

New Anti-Biofilm Nano Coating Prevents Bacterial Growth on Metal Surfaces – Azo Nano

Quick mapping of our microbiomes and metabolomes – Science Daily

Viral Skin Infections – Tomislav Meštrović – News Medical

Bacteria pill is ‘better than statins’ in the war on cholesterol, say researchers – Joe Smith – Mirror UK

Bacterial virulence is stimulated by burns – EurekAlert

Science, publishing, and career

Meet The New CEO Of The $22 Billion Genomics Company You’ve Never Heard Of: Francis deSouza to lead Illumina – Christina Farr – Fast Company

What Happened When I Pushed Myself to Interview More Women: Increasing the breadth of sources in journalism – John R. Platt – Motherboard

The quiet revolutionary: How the co-discovery of CRISPR explosively changed Emmanuelle Charpentier’s life. The microbiologist spent years moving labs and relishing solitude. Then her work on gene-editing thrust her into the scientific spotlight – Alison Abbott – Nature

Speak up about subtle sexism in science: Female scientists face everyday, often-unintentional microaggression in the workplace, and it won’t stop unless we talk about it – Tricia Serio – Nature

Bik’s Picks

Effects of a Closed Space Environment on Gene Expression in Hair Follicles of Astronauts in the International Space Station – Masahiro Terada – PLOS ONE