Category Archives: Waste and pollution

September 13, 2016

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

Events

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

Pregnancy and birth

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

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

Human urinary tract microbiome

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

Human gut microbiome

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

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

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

Animal experiments

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

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

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

Animal microbiome

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

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

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

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

Plant, root, and soil microbiome

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

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

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

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

Water microbiome

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

Microbiome of death

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

Wastewater and pollution microbiology

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

Probiotics

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

Food microbiology

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

Microbial ecology

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

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

Bioinformatics and metagenomics

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

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

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

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

Microbes in the news

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

August 29b, 2016

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Male grey cockatiel, Wikipedia

Factors that shape early life microbiome, pet birds, robust ambient temperature storage of stool samples, antibacterial activity of wasabi.

Pregnancy and birth

Joint effects of pregnancy, sociocultural, and environmental factors on early life gut microbiome structure and diversity – Albert M. Levin – Scientific Reports

Human gut microbiome

Theoretical Review: The shift work and health research agenda: Considering changes in gut microbiota as a pathway linking shift work, sleep loss and circadian misalignment, and metabolic disease – Amy C. Reynolds – Sleep Medicine Reviews

Review: Mechanisms of inflammation-driven bacterial dysbiosis in the gut – M Y Zeng – Mucosal Immunology

Animal experiments

Review: Experimental Models to Study the Role of Microbes in Host-Parasite Interactions – Megan A. Hahn – Frontiers in Microbiology

Animal microbiome

Comprehensive Molecular Characterization of Bacterial Communities in Feces of Pet Birds Using 16S Marker Sequencing – Jose F. Garcia-Mazcorro – Microbial Ecology

Effects of environment, dietary regime and ageing on the dengue vector microbiota: evidence of a core microbiota throughout Aedes aegypti lifespan – Mariana Rocha David – Memórias do Instituto Oswaldo Cruz

Plants, roots, and soil microbiome

Visual Comparative Omics of Fungi for Plant Biomass Deconstruction – Shingo Miyauchi – Frontiers in Microbiology

Bacterial Abilities and Adaptation Toward the Rhizosphere Colonization – Lucas D. Lopes – Frontiers in Microbiology

Review: Advances in research on Epichloë endophytes in Chinese native grasses – Hui Song – Frontiers in Microbiology

Water microbiome

Phytoplankton-associated bacterial community composition and succession during toxic diatom bloom and non-bloom events – Marilou P. Sison-Mangus – Frontiers in Microbiology

Distinct distribution patterns of prokaryotes between sediment and water in the Yellow River estuary – Guangshan Wei – Applied Microbiology and Biotechnology

Waste and pollution microbiome

Evaluating robustness of a diesel-degrading bacterial consortium isolated from contaminated soil – Mateusz Sydow – New Biotechnology

Metagenomic analysis of an ecological wastewater treatment plant’s microbial communities and their potential to metabolize pharmaceuticals – Ian N. Balcom – F1000 Research Preprint

Food microbiology

Review: Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing – J. Ronholm – Clinical Microbiology Reviews

Techniques

A robust ambient temperature collection and stabilization strategy: Enabling worldwide functional studies of the human microbiome – Ericka L. Anderson – Scientific Reports

Press: DNA Genotek’s OMNIgene®Ÿ GUT Kit is Proposed as Standardized Test for Worldwide Studies of the Human Microbiome – Globe NewsWire

More microbiology

Antibacterial activities of wasabi against Escherichia coli O157:H7 and Staphylococcus aureus – Zhongjing Lu – Frontiers in Microbiology

Resource Availability Modulates the Cooperative and Competitive Nature of a Microbial Cross-Feeding Mutualism – Tim A. Hoek – PLOS Biology

Microbes in the news

The women who discovered India’s first HIV cases – Geeta Pandey – BBC News

Captivity Makes Monkey Microbiomes More Human-Like – Ed Yong – The Atlantic

Interview with author of The Germ Files – Jason Tetro – Ben Libberton – Nature Microbiology Community

UGent researchers create bacteria that turns organic waste into plastic – Toon Lambrechts – Flanders Today

First DNA Sequencing in Space a Game Changer – NASA

UCSD alumna first to sequence DNA in space – Gary Robbins – San Diego Union Tribune

 

August 26, 2016

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MRI scans of colonic contents in setting of diet or defaecation, fecal transplants, the microbiome of ambulances, and a core taxa tool.

Pregnancy and birth

Longitudinal study on clinical and microbial analysis of periodontal status in pregnancy – Fernanda Campos Machado – Brazilian Oral Research

Review: Role of microbiota function during early life and children neurodevelopment – Tomás Cerdó – Trends in Food Science & Technology

Human oral microbiome (also see above)

Evaluation of oral microbiota in undernourished and eutrophic children using checkerboard DNA-DNA hybridization – M. Testa – Anaerobe

Review: Human neutrophils and oral microbiota: a constant tug-of-war between a harmonious and a discordant coexistence – Silvia M. Uriarte – Immunological Reviews

Human skin microbiome

Temporal stability in chronic wound microbiota is associated with poor healing – Michael Loesche – Journal of Investigative Dermatology

Human gut microbiome

Colonic content: effect of diet, meals, and defecation – R. A. Bendezú – Neurogastroenterology & Motility

Gut microbiota associated with HIV infection is significantly enriched in bacteria tolerant to oxygen – Grégory Dubourg – BMJ Open Gastroenterology

Prevalence and genetic diversity of Blastocystis in family units living in the United States – Pauline D. Scanlan – Infection, Genetics and Evolution

Nitrogen fixation and nifH diversity in human gut microbiota – Katsura Igai – Scientific Reports

Letter: Intestinal Microbiota and Health of Adults Who Were Born by Cesarean Delivery – James J. Goedert – JAMA Pediatrics

Opinion: The microbiome, microbial generated pro-inflammatory neurotoxins, and Alzheimer’s disease – Walter J. Lukiw – Journal of Sport and Health Science

Review: Estrogen and Microbiota Crosstalk: Should We Pay Attention? – Karen L. Chen – Trends in Endocrinology & Metabolism

Review: Gender, aging and longevity in humans: an update of an intriguing/neglected scenario paving the way to a gender-specific medicine – Rita Ostan – Clinical Science

Fecal transplants

Estimating the risks of faecal transplants – K. Patel – The Journal of Hospital Infection

Effect of Fecal Microbiota Transplantation on Recurrence in Multiply Recurrent Clostridium difficile Infection: A Randomized Trial – Colleen R. Kelly – Annals of Internal Medicine

Plant, root, and soil microbiome

Arbuscular mycorrhizal fungi communities from tropical Africa reveal strong ecological structure – Susana Rodríguez-Echeverría – New Phytologist

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

Water microbiome

Structure and function of methanogenic microbial communities in sediments of Amazonian lakes with different water types – Yang Ji – Environmental Microbiology

Built environment microbiome

Detection and characterization of surface microbial contamination in emergency ambulances – Aketza Varona-Barquin – American Journal of Infection Control

Fitness and recovery of bacterial communities and antibiotic resistance genes in urban wastewaters exposed to classical disinfection treatments – Andrea Di Cesare – Environmental Science & Technology

Bioinformatics and metagenomics

PhyloCore: A phylogenetic approach to identifying core taxa in microbial communities – Tiantian Ren – Gene

Microbes in the news

Gut reaction: the surprising power of microbes – Ed Yong – The Guardian

Want to feel better? Be kind to your bugs. Ed Yong’s new book will give you a positive outlook on your body’s trillions of bacteria – Kate Womersley – The Spectator

The world’s largest bacterial study of baby poo – MedicalXpress

What’s in Your Poo? The nonmicrobial components of feces may have important consequences as we try to grapple with microbiome research – Kevin Bonham – Scientific American

Solving a 48-year-old mystery: scientists succeed at growing noroviruses in human intestinal cell cultures in the lab – Graciela Gutierrez – Baylor College of Medicine

MSU researchers spread the buzz about bee viruses – Marshall Swearingen – Montana State University

Science, publishing, and career

Family ties ‘help scientists to get ahead’ in some countries. Levels of nepotism in scientific publishing have been revealed by report – Jack Grove  – Times Higher Education

Supervisors can do a lot more to support PhD students. Many doctoral candidates feel poorly looked after. More awareness and empathy from academics can help fight that – Geoffrey Cantor – Times Higher Education

New leader of NIH’s research watchdog faces staff revolt – Jocelyn Kaiser – Science

August 25, 2016

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Microbiome of the Graduate Student Gut, allergic cats, tree phyllosphere, milk tanker trucks, and microbes of soda lakes.

Pregnancy and birth

Review: Role of microbiota function during early life and children neurodevelopment – Tomás Cerdó – Trends in Food Science & Technology

General microbiome

Now published after preprint earlier this year and article in Cell: Revised Estimates for the Number of Human and Bacteria Cells in the Body – Ron Sender – PLOS Biology

Enemies and brothers in arms: Candida albicans and gram-positive bacteria – Toni M. Förster – Cellular Microbiology

Human respiratory microbiome

General antibiotic exposure is associated with increased risk of developing chronic rhinosinusitis – Alice Z. Maxfield – The Laryngoscope

Evidence and Role for Bacterial Mucin Degradation in Cystic Fibrosis Airway Disease – Jeffrey M. Flynn – PLOS Pathogens

Human gut microbiome

Master Thesis: Characterizing Microbiome Changes in the Graduate Student Gut – Justin Roy Lund – University of Oklahoma

Altered Fecal Microbiota Correlates with Liver Biochemistry in Nonobese Patients with Non-alcoholic Fatty Liver Disease – Baohong Wang – Scientific Reports

Prosteatotic and Protective Components in a Unique Model of Fatty Liver: Gut Microbiota and Suppressed Complement System – Long Liu – Scientific Reports

Is there a role for stool metabolomics in cystic fibrosis? – Nadeem O Kaakoush – Pediatrics International

Animal microbiome

Allergic to humans? Characterization of the cutaneous mycobiota in healthy and allergic cats using next generation sequencing – Courtney Meason-Smith – Veterinary Dermatology

Fish: The influence of weight and gender on intestinal bacterial community of wild largemouth bronze gudgeon (Coreius guichenoti, 1874) – Xuemei Li – BMC Microbiology

Plant, root, and soil microbiome

Tree phyllosphere bacterial communities: exploring the magnitude of intra- and inter-individual variation among host species – Isabelle Laforest-Lapointe – PeerJ

Long-Term Recovery of Microbial Communities in the Boreal Bryosphere Following Fire Disturbance – Nick A. Cutler – Microbial Ecology

Autochthonous Microbiota in Arsenic-Bearing Technosols from Zemianske Kostoľany (Slovakia) and Its Potential for Bioleaching and Biovolatilization of Arsenic – Alexandra Šimonovičová – Water, Air, & Soil Pollution

Built environment microbiology

Fungi and Bacteria in Indoor Cultural Heritage Environments: Microbial-related Risks for Artworks and Human Health – Enza Di Carlo – Environment and Ecology Research

Fitness and recovery of bacterial communities and antibiotic resistance genes in urban wastewaters exposed to classical disinfection treatments – Andrea Di Cesare – Environmental Science & Technology

Bacterial diversity and antibiotic resistances of abundant aerobic culturable bacteria in input and output samples of fifteen German biogas plants – Thorsten Schauss – Journal of Applied Microbiology

Food microbiology

The Core and Seasonal Microbiota of Raw Bovine Milk in Tanker Trucks and the Impact of Transfer to a Milk Processing Facility – Mary E. Kable – mBio

Water and extremophile microbiome

Microbial community diversity and composition varies with habitat characteristics and biofilm function in macrophyte-rich streams – Peter S. Levi – Oikos

Evaluation of Alternative High-Throughput Sequencing Methodologies for the Monitoring of Marine Picoplanktonic Biodiversity Based on rRNA Gene Amplicons – Isabel Ferrera- Frontiers in Marine Science

Book Chapter: Bacteria, Archaea and Viruses of Soda Lakes – William D. Grant – Soda Lakes of East Africa

Bioinformatics and metagenomics

ResistoMap – online visualization of human gut microbiota antibiotic resistome – Konstantin Yarygin – bioRxiv

Techniques

Protocols.io: Virtual Communities for Protocol Development and Discussion – Leonid Teytelman – PLOS Biology

More microbiology

The Ecology and Evolution of Microbial Competition – Melanie Ghoul – Trends in Microbiology

Microbes in the news

How Designers and Scientists Are Using Bees to Map NYC’s Microbes – Liz Stinson – Wired

Graphic novel about World War I depicts gross realities of dysentery – Carolyn Webb – The Age Victoria

The newest food trend: fermentation – Ted Weesner – Boston Globe

 

 

August 20, 2016

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Microbial eukaryotes along a pollution gradient, bacteria binding to ice, and testing the neutral theory.

Jobs and events

Assistant Professor in Genomics and Ecology of Microbial Pathogens in Food Systems Department of Food Science & Technology, University of California, Davis (via Jonathan Eisen – MicroBE.net)

Human gut microbiome

Gastrointestinal microbial populations can distinguish pediatric and adolescent Acute Lymphoblastic Leukemia (ALL) at the time of disease diagnosis – Seesandra V. Rajagopala – BMC Genomics

Review: Diet and Gut Microbial Function in Metabolic and Cardiovascular Disease Risk – Katie A. Meyer – Current Diabetes Reports

Review: Other Helicobacters and gastric microbiota – Chloë De Witte – Helicobacter

Plant, root, and soil microbiome

Spatial Distribution of Eukaryotic Communities Using High-Throughput Sequencing Along a Pollution Gradient in the Arsenic-Rich Creek Sediments of Carnoulès Mine, France – A. Volant – Microbial Ecology

Water and extremophile microbiome

Putting life on ice: bacteria that bind to frozen water – Maya Bar Dolev – Journal of the Royal Society Interface

Genetic signatures of ecological diversity along an urbanization gradient – Ryan P. Kelly – PeerJ Preprint

Surveys, simulation and single-cell assays relate function and phylogeny in a lake ecosystem – Sarah P. Preheim – Nature Microbiology

Book: Microbes from Hell: archaea and hyperthermophiles – Patrick Forterre

Drinking water and water treatment microbiology

Elucidation of Taste- and Odor-Producing Bacteria and Toxigenic Cyanobacteria in a Midwestern Drinking Water Supply Reservoir by Shotgun Metagenomic Analysis – Timothy G. Otten – Applied and Environmental Microbiology

Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics – Johan Bengtsson-Palme – Science of the Total Environment

Microbial Ecology

Testing the Neutral Theory of Biodiversity with Human Microbiome Datasets – Lianwei Li – Scientific Reports

Review: The Ecology and Evolution of Microbial Competition – Melanie Ghoul – Trends in Microbiology

Microbes in the news

We need to stop sanitizing everything and let bacteria back in our lives – Joselin Linder – New York Post

Bacteria may be key to environmentally friendly extraction of minerals – Angela Kean – S&P Capital IQ

Science, publishing, and career

What lurks in ageing academics’ unvisited personal archives? – Ron Iphofen – Times Higher Education
Army report says science director creating ‘environment of fear’ at USAMRIID – Sylvia Carignan – Frederick News Post

July 24, 2016

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Songbird, soil nitrogen-cycling around the world, and parasites on an ancient butt-wipe stick.

Pregnancy and birth

Dysfunctional gut microbiota and relative co-abundance network in infantile eczema – Heping Wang – Gut Pathogens

Human oral microbiome

Review: From focal sepsis to periodontal medicine: A century of exploring the role of the oral microbiome in systemic disease – Purnima S Kumar – The Journal of Physiology

Human gut microbiome

Review: The Role of the Gut Microbiome on Chronic Kidney Disease – B. Sampaio-Maia – Advances in Applied Microbiology

Review: The Microbiota, Immunoregulation, and Mental Health: Implications for Public Health – Christopher A. Lowry – Current Environmental Health Reports

Animal and other experiments

Insulin resistance, microbiota and fat distribution changes by a new model of vertical sleeve gastrectomy in obese rats – Nicola Basso – Diabetes

Establishment of microbiota in larval culture of Pacific oyster, Crassostrea gigas – Katia Asmani – Aquaculture

Changes in the structure of the microbial community associated with Nannochloropsis salina following treatments with antibiotics and bioactive compounds – Haifeng Geng – Frontiers in Microbiology

Animal microbiome
Social environment has a primary influence on the microbial and odor profiles of a chemically signaling songbird – Danielle J. Whittaker – Frontiers in Ecology and Evolution

16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife – Maxime Galan – mSystems

Plant, root, and soil microbiome

Global biogeography of microbial nitrogen-cycling traits in soil – Michaeline B. Nelson – PNAS

Mammalian engineers drive soil microbial communities and ecosystem functions across a disturbance gradient – David J Eldridge – Journal of Animal Ecology

Biogeochemical drivers of microbial community convergence across actively retreating glaciers – Sarah C. Castle – Soil Biology and Biochemistry

The structure of bacterial communities along two vertical profiles of a deep colluvial soil – Marketa Sagova-Mareckova – Soil Biology and Biochemistry

Silver nanoparticles, ions and shape governing soil microbial functional diversity: nano shapes micro – Yujia Zhai – Frontiers in Microbiology

Water microbiome

Metagenomic signatures of a tropical mining-impacted stream reveal complex microbial and metabolic networks – Mariana P. Reis – Chemosphere

Effects of Copper, Nickel, and Sulphate from the Smelters at Sudbury, Ontario (Canada) on Microbial Communities in Lakes – Togwell A. Jackson – Geomicrobiology Journal

Archeological microbes

Early evidence for travel with infectious diseases along the Silk Road: Intestinal parasites from 2000 year-old personal hygiene sticks in a latrine at Xuanquanzhi Relay Station in China – Hui-Yuan Yeh – Journal of Archaeological Science: Reports

Press: Ancient Faeces Provide Earliest Evidence of Infectious Disease Being Carried on Silk Road – SciCasts
Ancient bottom wipers yield evidence of diseases carried along the Silk Road – Maev Kennedy – The Guardian

Built environment microbiome

Microorganisms associated with corrosion of structural steel in diverse atmospheres – Laura L. Machuca – International Biodeterioration & Biodegradation

More microbes

Individuals hospitalized with acute mania have increased exposure to antimicrobial medications – Robert Yolken – Bipolar Disorders

Metagenomics and bioinformatics

Multiplexed Metagenomic Deep Sequencing To Analyze the Composition of High-Priority Pathogen Reagents – Michael R. Wilson – mSystems

Microbes in the news

Everyday chemicals may be messing up our microbiomes—but we don’t know – Beth Mole – Ars Technica
The jury is still out on whether antibacterial chemical impacts microbiome or causes resistance – Bob Yirka – Medical Xpress

Some Microbes Have Been With Us Since Before We Existed. Certain gut bacteria have evolved in parallel with apes, so that their family tree perfectly mirrors our own. – Ed Yong – The Atlantic

Plants have a microbiome just like humans — and it could transform how our food is produced – Ariel Schwartz – Tech Insider

New book: The Human Superorganism: How the Microbiome Is Revolutionizing the Pursuit of a Healthy Life – Rodney Dietert
Your Microbes, Yourself. In his new book, Rodney Dietert argues that it’s time to re-configure our relationship with germs: – Louise Fabiani – Pacific Standard

Science, publishing, and career

The Women and the Science
Rachel Ignotofsky tells the stories of 50 women in science in her fantastic new science art book – Scientific American
Women in Science: An Illustrated Who’s Who – Julie Leibach – Science Friday

Women in Science: An Illustrated Who’s Who

July 22, 2016

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Fungi in human GI tract, antibiotics reduce Alzheimer’s lesions in mouse model, cospeciation of primates and gut microbes, dangerous bacteria after sewer spill.

Jobs

Research scientists to engineer microbiome engineering therapies – Eligo Bioscience

General microbiome

Perspective: Is triclosan harming your microbiome? – Alyson L. Yee – Science

Understanding How Microbiomes Influence the Systems they Inhabit: Insight from Ecosystem Ecology – Ed Hall – bioRxiv

Pregnancy and birth microbiome

Midtrimester Cervicovaginal Microbiota: Identification of Microbial Variations Associated with Puerperal Infection at Term – Akila Subramaniam – American Journal of Perinatology

Human mouth microbiome

Salivary and fecal microbiota and metabolome of celiac children under gluten-free diet – Maria De Angelis – International Journal of Food Microbiology

Human respiratory microbiome

Lung Microbiome in HIV Infection – Homer L. Twigg III – Translational Research

Human vaginal microbiome

Proceedings of the 2015 NIH/NIAID Bacterial Vaginosis Expert Consultation – The Journal of Infectious Diseases

Human gut microbiome

Age and gender affect the composition of fungal population of the human gastrointestinal tract – Francesco Strati – Frontiers in Microbiology

A reduction in the butyrate producing species Roseburia spp. and Faecalibacterium prausnitzii is associated with chronic kidney disease progression – Shuanghong Jiang – Antonie van Leeuwenhoek

Review: An update discussion on the current assessment of the safety of veterinary antimicrobial drug residues in food with regard to their impact on the human intestinal microbiome – Carl E. Cerniglia – Drug Testing and Analysis

Animal experiments

Antibiotic-induced perturbations in gut microbial diversity influences neuro-inflammation and amyloidosis in a murine model of Alzheimer’s disease – Myles R. Minter – Scientific Reports

Press: Antibiotics weaken Alzheimer’s disease progression through changes in the gut microbiome – EurekAlert
Could antibiotics reduce levels of Alzheimer’s-causing plaques? – Hannah Nichols – MedicalNewsToday

Pathogenic shifts in endogenous microbiota impede tissue regeneration via distinct activation of TAK1/MKK/p38 – Christopher P Arnold – eLIFE

Bacterial community characterization of water and intestine of the shrimp Litopenaeus stylirostris in a biofloc system – Emilie Cardona – BMC Microbiology

Impact of Helminth Infections and Nutritional Constraints on the Small Intestine Microbiota – Isabella M. Cattadori – PLOS ONE

Nutrient Deprivation Affects Salmonella Invasion and Its Interaction with the Gastrointestinal Microbiota – Sophie Yurist-Doutsch – PLOS ONE

Celecoxib alters the intestinal microbiota and metabolome in association with reducing polyp burden – David C. Montrose – Cancer Prevention Research

Review: Interactions between host genetics and gut microbiome in diabetes and metabolic syndrome – Siegfried Ussar – Molecular metabolism

Animal microbiome

Cospeciation of gut microbiota with hominids – Andrew H. Moeller – Science

Press: Primates, Gut Microbes Evolved Together. Symbiotic gut bacteria evolved and diverged along with ape and human lineages, researchers find – Anna Azvolinsky – The Scientist
Microbes in our guts have been with us for millions of years – Ann Gibbons – Science
Your gut bacteria predates appearance of humans, genetic study finds – Naomi Stewart – The Guardian

A snapshot of the microbiome of Amblyomma tuberculatum ticks infesting the gopher tortoise, an endangered species – Khemraj Budachetri – Ticks and Tick-borne Diseases

Do Vertebrate Gut Metagenomes Confer Rapid Ecological Adaptation? –
Antton Alberdi – Trends in Ecology & Evolution

Vaginal microbial communities from synchronized-heifers and cows with reproductive disorders – Candelaria Gonzalez Moreno – Journal of Applied Microbiology

Review: The woodrat gut microbiota as an experimental system for understanding microbial metabolism of dietary toxins – Kevin D. Kohl – Frontiers in Microbiology

Plant, root, and soil microbiome

Plant Identity Exerts Stronger Effect than Fertilization on Soil Arbuscular Mycorrhizal Fungi in a Sown Pasture – Yong Zheng – Microbial Ecology

Beneficial cyanobacteria and eubacteria synergistically enhance bioavailability of soil nutrients and yield of okra – Mallappa Manjunath – Heliyon

Naming Potentially Endangered Parasites: Foliicolous Mycobiota of Dimorphandra wilsonii, a Highly Threatened Brazilian Tree Species– Meiriele da Silva – PLOS ONE

Contribution of the seed microbiome to weed management – D Müller-Stöver – Weed Research

Mycorrhizal associations of trees have different indirect effects on organic matter decomposition – Melanie K. Taylor – Journal of Ecology

Water and extremophile microbiome

Vancomycin resistant enterococci and bacterial community structure following a sewage spill into an aquatic environment – Suzanne Young – Applied and Environmental Microbiology

Press: USF researchers find dangerous bacteria after sewer spills – EurekAlert
USF researchers say they found dangerous bacteria after sewage spill – Anne Lindberg – Saint Peters Blog

Hospital Effluents Are One of Several Sources of Metal, Antibiotic Resistance Genes, and Bacterial Markers Disseminated in Sub-Saharan Urban Rivers – Amandine Laffite – Frontiers in Microbiology

Microbial communities in sediments of Lagos Lagoon, Nigeria: Elucidation of community structure and potential impacts of contamination by municipal and industrial wastes – Chioma C. Obi – Frontiers in Microbiology

Cryoconite pans on Snowball Earth: supraglacial oases for Cryogenian eukaryotes? – P. F. Hoffman – Geobiology

Effects of multiple dimensions of bacterial diversity on functioning, stability and multifunctionality – Fabian Roger – Ecology

Heterotrophic bacteria in Antarctic lacustrine and glacial environments – Johanna Laybourn-Parry – Polar Biology

Microbial diversity and activity in seafloor brine lake sediments (Alaminos Canyon block 601, Gulf of Mexico) – M. Crespo-Medina – Geobiology

Bioinformatics and metagenomics

MetaG: a graph-based metagenomic gene analysis for big DNA data – Linkon Chowdhury – Network Modeling Analysis in Health Informatics and Bioinformatics

DFAST and DAGA: web-based integrated genome annotation tools and resources – Yasuhiro Tanizawa – Bioscience of Microbiota, Food and Health

Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion – Inka Vanwonterghem – Environmental Microbiology

Microbes in the news

Breast-feeding the Microbiome (Excerpt from his book) – Ed Yong – New Yorker

Janet Jansson Among Nine Authors of Nature Review Article – PNNL

Northern Arizona University professor Bruce Hungate named a fellow of the American Academy of Microbiology – Arizona Business Daily

UF scientists identify seal as source of new strain of bacteria that caused disease in hunter – Sarah Carey – University of Florida

Gut Bacteria May Drive Inflammation in Sepsis, ARDS – Salynn Boyles – MedPageToday

With Rob Knight as keynote speaker: Fermenting Knowledge at Fermentation Festivals (with Kombucha Recipe) – John D. Ivanko – Mother Earth News

Your death microbiome could catch your killer – Anna Williams – New Scientist

Microbes and money

Osel, Inc. Comments on New Study Showing Role of Vaginal Microbiome in Women’s Health – PharmiWeb

Q&A: Indigo’s CEO Reveals the Strategy Behind Its Plant Microbiome Technology – Olivia Vanni – BostInno

Eminent Harvard Geneticist Professor George Church Joins uBiome Advisory Board – Benzinga

Immuron to Cooperate with Leading Australian Universities on Autism Research – Nasdaq

July 12, 2016

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Two papers on plant/root/soil microbiomes of interest, analysis of transcriptional regulatory networks, and too much non-prescription antibiotic use  in the US.

Human vaginal microbiome

Review: Bacterial vaginosis: a critical analysis of current knowledge – D Nasioudis – BJOG

Human gut microbiome

Gut microbiome analysis in neuromyelitis optica reveals over-abundance of Clostridium perfringens – Bruce A.C. Cree – Annals of Neurology

Review: Gut Microbiota and Intestinal Decolonization of Pathogenic Microorganisms – De-Chang Chen – Chinese Medical Journal

Animal experiments

Human Gut-Derived Prevotella histicola Suppresses Inflammatory Arthritis in Humanized Mice – Eric V. Marietta – Arthritis & Rheumatology

Press: Gut bacteria can cause, predict and prevent rheumatoid arthritis – Science Daily

Gastric Bypass Surgery Reverses Diabetic Phenotypes in Bdnf-Deficient Mice – Shujun Jiang – American Journal of Pathology

Press: New study suggests potential role for gut microbiota in diabetes remission after bypass surgery – News Medical

Plant, root, and soil microbiome

Host genotype and age shape the leaf and root microbiomes of a wild perennial plant – Maggie R. Wagner – Nature Communications

Press: Breeding plants with more beneficial bacteria to feed the world won’t be simple, study says – Robin A. Smith – Phys.org

Soil inoculation steers restoration of terrestrial ecosystems – E. R. Jasper Wubs – Nature Plants

Soil microbes transplants could help restore damaged ecosystems – The dirt makes all the difference – Meaghan Lee Callaghan – PopSci

Combined Flux Chamber and Genomics Approach Links Nitrous Acid Emissions to Ammonia Oxidizing Bacteria and Archaea in Urban and Agricultural Soil – Nicole K. Scharko – Environmental Science & Technology

Opinion: Plant microbiota affects seed transmission of phytopathogenic microorganisms – Matthieu Barret – Molecular Plant Pathology

Metagenomics and bioinformatics

A Bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data – Elizabeth T. Hobbs – Algorithms for Molecular Biology

Metagenome and Metatranscriptome Analyses Using Protein Family Profiles – Cuncong Zhong – PLOS Computational Biology

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights – Edoardo Pasolli – PLOS Computational Biology

Review: Metagenome-wide association studies: fine-mining the microbiome – Jun Wang – Nature Reviews Microbiology

Proteomics

An alignment-free ‘metapeptide’ strategy for metaproteomic characterization of microbiome samples using shotgun metagenomic sequencing – Damon H. May – Journal of Proteome Research

Bioreactor microbiology

A light-induced shortcut in the planktonic microbial loop – Robert Ptacnik – Scientific Reports

More microbiology

Non-prescription antimicrobial use in a primary care population in the United States: evidence for action – Roger Zoorob – Antimicrobial Agents and Chemotherapy

Press: Self-prescribing antibiotics is a big problem – American Society for Microbiology – EurekAlert

Transfer of DNA from Bacteria to Eukaryotes – Benoît Lacroix – mBio

Origins of pandemic clones from environmental gene pools – B. Jesse Shapiro – bioRxiv

UTSA professor’s study describes new strategies for investigating microbial outbreaks – EurekAlert

Microbes in the news

Railroad spanning Great Salt Lake helps MSU scientists understand origins of reef-like structures – Skip Anderson – Montana State University

The colon is defended from bacteria by a self-sacrificing sentinel cell – EurekAlert

July 9, 2016

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Bacteroidales from homeothermic animals, 136 microbial genomes from the Red Sea, corrosion of concrete sewers, and the microbiology lab in 2050 (still sexist!).

Pregnancy and birth

Integrated network-diversity analyses suggest suppressive effect of Hodgkin’s lymphoma and slightly relieving effect of chemotherapy on human milk microbiome – Zhanshan (Sam) Ma – Scientific Reports

Review: The Microbiome, Antibiotics, and Health of the Pediatric Population – Ravi S Misra- EC Microbiology

Human oral microbiome

Metagenomic Analysis of Sputum Microbiome as a Tool Towards Culture-independent Pathogen Detection of Patients with Ventilator-associated Pneumonia – Qiulong Yan – American Journal of Respiratory and Critical Care Medicine

Human respiratory microbiome

Smoking Cessation and the Microbiome in Induced Sputum Samples from Cigarette Smoking Asthma Patients – Christian Munck – PLOS ONE

Association of sputum microbiota profiles with severity of community-acquired pneumonia in children – Melinda M. Pettigrew – BMC Infectious Diseases

Human gut microbiome

Review: Polysaccharide degradation by the intestinal microbiota and its influence on human health and disease – Darrell W. Cockburn – Journal of Molecular Biology

Review: Microbiota at the crossroads of autoimmunity – Oded Shamriz – Autoimmunity Reviews

Editorial: A Role for Chemists in Microbiome Research – Courtney C. Aldrich – ACD Infectious Diseases

Animal experiments

Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection – Alison Morris – Microbiome

Animal microbiome

Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals – Kate L. Ormerod – Microbiome

Biodiversity and Activity of the Gut Microbiota across the Life History of the Insect Herbivore Spodoptera littoralis – Bosheng Chen – Scientific Reports

Long-term effect of heavy-metal pollution on diversity of gastrointestinal microbial community of Bufo raddei – Wenya Zhang – Toxicology Letters

Plants, roots, and soil microbiome

Multiscale assemblage of an ectomycorrhizal fungal community: The influence of host functional traits and soil properties in a 10-ha miombo forest – David Bauman – FEMS Microbiology Ecology

Impact of Soil Salinity on the Structure of the Bacterial Endophytic Community Identified from the Roots of Caliph Medic (Medicago truncatula) – Mahmoud W. Yaish – PLOS ONE

Diversity of fungal endophytes in recent and ancient wheat ancestors Triticum dicoccoides and Aegilops sharonensis – Maya Ofek-Lalzar – FEMS Microbiology Ecology

The effect of bullet removal and vegetation on mobility of Pb in shooting range soils – Abioye O. Fayiga – Chemosphere

Water and extremophile microbiome

A catalogue of 136 microbial draft genomes from Red Sea metagenomes – Mohamed F. Haroon – Scientific Data

A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples – Miguel I. Uyaguari-Diaz – Microbiome

Hydrocarbon biodegradation by Arctic sea-ice and sub-ice microbial communities during microcosm experiments, Northwest Passage (Nunavut, Canada) – Marie-Ève Garneau – FEMS Microbiology Ecology

Built environment microbiome

Wastewater Enhanced Microbial Corrosion of Concrete Sewers – Guangming Jiang – Environmental Science & Technology

Bioreactors

The bioleaching potential of a bacterial consortium – Mauricio Latorre – Bioresource Technology

Biofilms

DGGE: Representative sampling of natural biofilms: influence of substratum type on the bacterial and fungal communities structure – Jennifer Hellal – SpringerPlus

Bioinformatics and metagenomics

GUTSS: An Alignment-Free Sequence Comparison Method for Use in Human Intestinal Microbiome and Fecal Microbiota Transplantation Analysis – Mitchell J. Brittnacher – PLOS ONE

Icarus: visualizer for de novo assembly evaluation – Alla Mikheenko – Bioinformatics

deBGA: read alignment with de Bruijn Graph-based seed and extension – Bo Liu – Bioinformatics

ConsPred – a rule-based (re-)annotation framework for prokaryotic genomes – Thomas Weinmaier – Bioinformatics

Proteomics

Review: Metaproteomic data analysis at a glance: advances in computational microbial community proteomics – Expert Review of Proteomics

Bik’s Picks

A typical day working in a laboratory in 2050: Are microbiologists becoming chemists and serene workers? – Daniele Sohier – Current Opinion in Food Science

Napa native on space mission showed early signs of promise – Jonathan Bloom – ABC News

 

 

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