Category Archives: Microbial Ecology

September 5, 2015

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Events

The Individual Microbe: Single-cell Analysis and Agent-based Modeling – ASM conference – March 18-20, 2016, Washington DC, USA

R workshop for microbial ecology – Pat Schloss – Nov 2-4, 2015, Detroit – No link but can email Pat at: pschloss@umich.edu

General microbiome

Privacy-Preserving Microbiome Analysis Using Secure Computation – Justin Wagner – BioRxiv

Pregnancy and birth microbiome

Phylogenetic and Metabolic Tracking of Gut Microbiota during Perinatal Development – Federica Del Chierico – PLOS ONE

Human oral microbiome

The Effect of Fixed Orthodontic Appliances and Fluoride Mouthwash on the Oral Microbiome of Adolescents – A Randomized Controlled Clinical Trial – Jessica E. Koopman – PLOS ONE

Review: Oral Paleomicrobiology: study of the ancient oral microbiome – Namrata Dagli

Human gut microbiome

The effect of dietary resistant starch type 2 on the microbiota and markers of gut inflammation in rural Malawi children – M. Isabel Ordiz – Microbiome

Gastrointestinal Microbiome Modulator Improves Glucose Tolerance in Overweight and Obese Subjects: A Randomized Controlled Pilot Trial – Candida J. Rebello – Journal of Diabetes and its Complications

Faecal proteomics: A tool to investigate dysbiosis and inflammation in patients with cystic fibrosis – Griet Debyser – Journal of Cystic Fibrosis

Review: Pathways and functions of gut microbiota metabolism impacting host physiology – Smitha Krishnan – Current Opinion in Biotechnology

Review: Microbiome in Inflammatory Arthritis and Human Rheumatic Diseases – Jose U. Scher – Arthritis & Rheumatology

Review: The human microbiome: opportunities and challenges for clinical care – G. B. Rogers – Internal Medicine Journal

Human respiratory microbiome (see also gut microbiome above)

MRSA Colonization and the Nasal Microbiome in Adults at High Risk for Colonization and Infection – Mary T. Bessesen – Journal of Infection

Review: Cystic fibrosis lung microbiome: Opportunities to reconsider management of airway infection – Lindsay J. Caverly – Pediatric Pulmonology

Human other sites

In silico analyses of metagenomes from human atherosclerotic plaque samples – Suparna Mitra – Microbiome

Microbiome models

Distinct Shifts in Microbiota Composition during Drosophila Aging Impair Intestinal Function and Drive Mortality – Rebecca I. Clark – Cell Reports

Perspective: Metabolic labeling puts the microbiome under the microscope – Graham J Britton & Jeremiah J Faith – Nature Medicine

Animal microbiome

The composition of the zebrafish intestinal microbial community varies across development – W Zac Stephens – ISME Journal

Shifts in the Midgut/Pyloric Microbiota Composition within a Honey Bee Apiary throughout a Season – Jane Ludvigsen – Microbes and Environments

The genome of Aiptasia, a sea anemone model for coral symbiosis – Sebastian Baumgarten – PNAS

Special Issue: The Mammalian Microbiome and Its Importance in Laboratory Animal Research – André Bleich and James G. Fox – ILAR Journal

Plant, root, and soil microbiome

Predicting Ecological Roles in the Rhizosphere Using Metabolome and Transportome Modeling – Peter E. Larsen – PLOS ONE

Microbiome change by symbiotic invasion in lichens – Wedin Mats – Environmental Microbiology

Plant-associated microbiomes in arid lands: diversity, ecology and biotechnological potential – Asma Soussi – Plant and Soil

Geological connectivity drives microbial community structure and connectivity in polar, terrestrial ecosystems – Belinda C. Ferrari – Environmental Microbiology

Water microbiome

Anthropogenic activities drive the microbial community and its function in urban river sediment – Xu Zhang – Journal of Soils and Sediments

Built environment microbiome

Bacterial Communities and Midgut Microbiota Associated with Mosquito Populations from Waste Tires in East-Central Illinois – Chang-Hyun Kim – Journal of Medical Entomology

Hospital’s Hidden Environmental Hazards: Probing the Microbiome – BioScience

Pyrosequencing analysis of bacterial communities in biofilms from different pipe materials in a city drinking water distribution system of East China – Hongxing Ren – Applied Microbiology and Biotechnology

Food microbiology

The genomics of microbial domestication in the fermented food environment –
John G Gibbons – Current Opinion in Genetics & Development

Bioinformatics

Functional Basis of Microorganism Classification – Chengsheng Zhu – PLOS Computational Biology

ReproPhylo: An Environment for Reproducible Phylogenomics – Amir Szitenberg – PLOS Computational Biology

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities – Dongwan D. Kang – PeerJ

More Microbiology

Evolution of coexistence in a crowded microplate well – J. Arjan G. M. de Visser – PNAS

The rpb2 gene represents a viable alternative molecular marker for the analysis of environmental fungal communities – Tomáš Větrovský – Molecular Ecology Resources

Microbes in the news

Microbial diversity insights are often strongly biased – Suffield Times
Small advances: understanding the microbiome – Amanda Smith – ABC Australia

Science, publishing and career

When science fails a scientist – Kim Hunter-Schaedle – Science

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August 12, 2015

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Drug metabolism by gut microbiota, nature vs. nurture in inbred strains of mice, gnotobiotic Drosophila, bat virome, and influence of protist predation on marine microbiomes.

General microbiome

Short-chain fatty acids in control of body weight and insulin sensitivity – Emanuel E. Canfora – Nature Reviews Endocrinology

Pregnancy and birth microbiome

Streptococcal Diversity of Human Milk and Comparison of Different Methods for the Taxonomic Identification of Streptococci – Virginia Martín – Journal of Human Lactation

Human gut microbiome

Editorial: Drug Metabolism by the Host and Gut Microbiota: A Partnership or Rivalry?
Hollie I Swanson – Drug Metabolism and Disposition
Review: Mechanisms of How the Intestinal Microbiota Alters the Effects of Drugs and Bile Acids – Curtis D. Klaassen – Drug Metabolism and Disposition

Comparison of the gut microbiota composition between obese and non-obese individuals in a Japanese population, as analyzed by terminal restriction fragment length polymorphism and next-generation sequencing – Chika Kasai – BMC Gastroenterology

Animal and other models

Microbiota in 110 diverse inbred strains of mice: Genetic and environmental control of host-gut microbiota interactions – Elin Org – Genome Research

Co-culturing Escherichia coli O157:H7 with a non-pathogenic E. coli strain increases toxin production and virulence in a germ-free mouse model – Kakolie Goswami – Infection and Immunity

Ovariectomy results in differential shifts in gut microbiota in low versus high aerobic capacity rats – Kimberly A. Cox-York – Physiological Reports

Studying host-microbiota mutualism in Drosophila: Harnessing the power of gnotobiotic flies – Dali Ma – Biomedical Journal

MyD88 Signaling Regulates Steady-State Migration of Intestinal CD103+ Dendritic Cells Independently of TNF-α and the Gut Microbiota – Karin Hägerbrand – The Journal of Immunology

Animal microbiome

Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases – Zhiqiang Wu – ISME Journal

Plant, root, and soil microbiome

Host promiscuity in symbiont associations can influence exotic legume establishment and colonization of novel ranges – Metha M. Klock – Diversity and Distributions

Temporal and spatial influences incur reconfiguration of Arctic heathland soil bacterial community structure – Richard Hill – Environmental Microbiology

Water microbiome

Marine bacterial community structure resilience to changes in protist predation under phytoplankton bloom conditions – Federico Baltar – ISME Journal

Waste and water treatment microbiology

The activated sludge ecosystem contains a core community of abundant organisms – Aaron M Saunders – ISME Journal

Core-satellite populations and seasonality of water meter biofilms in a metropolitan drinking water distribution system – Fangqiong Ling – ISME Journal

More microbes

Levels and limits in artificial selection of communities – Manuel Blouin – Ecology Letters

Editorial: Origin of the Yeast Whole-Genome Duplication – Kenneth H. Wolfe – PLOS Biology
Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker’s Yeast Lineage – Marina Marcet-Houben – PLOS Biology

Microbes in the news

Global Human Microbiome Market: Asia is expected to show high growth rates by 2020 – MedGadget

Things I Tell My Mom: Five ways for you to participate in science – Cathy Seiler – Ahwatukee Foothills News

Why making and taking fermented drinks is becoming popular again – John McKenna – The Irish Times

Protein Goes Green: Can Algae Become The Next Soy? – Jessie Rack – NPR

Cultured Coffee offers the flavor of poop-brewed coffee without the crap – TJ Dietsch – Geek

Making kefir at home is easy, healthy – Kit Waskom Pollard – Baltimore Sun

‘Genomic Archaeology’ Reveals That Lager Yeast Was Born More Than Once – Andrea Alfano -Tech Times

Researchers resurrect extinct virus to use for gene therapy: Evolutionary ancestors remade based on current viruses – Ars Technica

Science, publishing, and career

Make Peer Review Public: How to make science faster and more robust – Adam Marcus and Ivan Oransky – Slate

Despite concerted effort, barriers to women in science remain – Jennifer Ann Thomson – The Conversation

Outreach: Primary School outreach – inspiring young minds with science – Mariya Lobanovska – SGM

Physics: She did it all: Val Gibson enjoys the autobiography of Mary K. Gaillard, the first female physics professor at Berkeley – Val Gibson – Nature

Bik’s Picks

Octopus Genome Offers Insights Into One Of Ocean’s Cleverest Oddballs – Nell Greenfieldboyce – NPR

Meteor time! How to watch the big Perseid shower – Paul Rogers – San Jose Mercury News

MIT tackling more serious science: they program beer-delivering robots – ZME Science

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August 5, 2015

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Microbiome in patients with Irritable Bowel Syndrome, gastric bypass operations induces long-term microbiome changes, environmental enteropathy in a mouse model, respiratory viruses in large families, and microbiology of restaurant grease waste.

Events

Microbiome R&D and Business Collaboration Forum – September 10-11, 2015, San Diego, USA

European Microbiome Congress 2015 – 18 and 19 November 2015, London, UK

Microbiome of pregnancy and birth

Review: Antibiotics and the developing infant gut microbiota and resistome – Molly K Gibson – Current Opinion in Microbiology

Review: Early Life Experience and Gut Microbiome: The Brain-Gut-Microbiota Signaling System – Cong, Xiaomei – Advances in Neonatal Care

Review: The Prescient Placenta – Christopher Coe – The Scientist

Human respiratory microbiome

Community Surveillance of Respiratory Viruses Among Families in the Utah Better Identification of Germs-Longitudinal Viral Epidemiology (BIG-LoVE) Study –  L. Byington – Clinical Infectious Diseases

Human gut microbiome

Reduction of butyrate- and methane-producing microorganisms in patients with Irritable Bowel Syndrome – Marta Pozuelo – Scientific Reports

Roux-en-Y Gastric Bypass and Vertical Banded Gastroplasty Induce Long-Term Changes on the Human Gut Microbiome Contributing to Fat Mass Regulation – Valentina Tremaroli – Cell Metabolism

Gut-Microbiota-Metabolite Axis in Early Renal Function Decline – Clara Barrios – PLOS ONE

Editorial: Microbiome reflects status of RA and response to therapy – Robert Phillips – Nature Reviews Rheumatology

Microbiome models

Bacterial sensing underlies artificial sweetener-induced growth of gut Lactobacillus – Kristian Daly – Environmental Microbiology

Diet and specific microbial exposure trigger features of environmental enteropathy in a novel murine model – Eric M. Brown – Nature Communications

Animal microbiome

Dominant ectosymbiotic bacteria of cellulolytic protists in the termite gut also have the potential to digest lignocellulose – Masahiro Yuki – Environmental Microbiology

Two gut community enterotypes recur in diverse bumblebee species – Jilian Li- Current Biology

Unique metabolites protect earthworms against plant polyphenols – Manuel Liebeke – Nature Communications

Streptococcus panodentis sp. nov., from the oral cavities of chimpanzees – Masaaki Okamoto – Microbiology and Immunology

Plant, root, and soil microbiome

Fungal root endophytes of Quercus robur subjected to flooding – H. Kwaśna – Forest Pathology

Land Use and Precipitation Affect Organic and Microbial Carbon Stocks and the Specific Metabolic Quotient in Soils of Eleven Ecosystems of Mt. Kilimanjaro, Tanzania – Holger Pabst – Land Degradation & Development

The Phytophthora species assemblage and diversity in riparian alder ecosystems of western Oregon, USA – Laura Lee Sims – Mycologia

Bacterial community structures as a diagnostic tool for watershed quality assessment – Luigimaria Borruso – Research in Microbiology

Water microbiome

Planktonic and sedimentary bacterial diversity of Lake Sayram in summer – Lei Fang – Microbiology Open

Waste and bioreactor microbiome

Reactor performance and microbial community dynamics during anaerobic co-digestion of municipal wastewater sludge with restaurant grease waste at steady state and overloading stages – Vahid Razaviarani – Bioresource Technology

Arsenic toxicity effects on microbial communities and nutrient cycling in indoor experimental channels mimicking a fluvial system – Baigal-Amar Tuulaikhuu – Aquatic Toxicology

Metagenomics and bioinformatics

Xander: employing a novel method for efficient gene-targeted metagenomic assembly – Qiong Wang – Microbiome

Metabolomics

Symposium report: Olfaction in the Kidney: ‘Smelling’ gut microbial metabolites – Niranjana Natarajan and Jennifer L. Pluznick – Experimental Physiology

Microbial Ecology

Clustering in community structure across replicate ecosystems following a long-term bacterial evolution experiment – Hasan Celiker & Jeff Gore – Nature Communications

Microbes in the news

Interview with Peter DiLaura, CEO of Second Genome: Data Mining The Microbiome Toward A Cure For Inflammatory Disease – Peter High – Forbes

Weight loss surgery benefits for gut microbiome last at least a decade – MedicalXpress

Extreme weight loss surgery works, but is it thanks to the knife—or the microbes? – Mitch Leslie – Science

A Belated Look at New York’s Cooling Towers, Prime Suspect in Legionnaires’ Outbreak – Winnie Hu and Noah Remnick – NY Times

Amid Legionnaires’ Fears, City Proposes New Cooling Tower Rules – Mara Gay and Corinne Ramey – Wall Street Journal
Randomised clinical study: Aspergillus niger-derived enzyme digests gluten in the stomach of healthy volunteers – B. N. Salden – Alimentary Pharmacology & Therapeutics

Study: Citrus Greening Bacterium Gives Vector Unexpected Boost – Paul Rusnak – Growing Produce

Team identifies mutations that allow bacteria to resist antibiotics – Phys.org

Africa is within reach of being declared a polio free region – The Conversation

Viruses Thrive In Big Families, In Sickness and In Health – University of Utah

Science, career, and publishing

Where Next for Genetics and Genomics? – Chris Tyler-Smith – PLOS Biology

Tech Women Triumph: $30k Funding In A Day, Success Under Pressure, True Leaders Inspire – Leo King – Forbes

#ilooklikeanengineer wants to challenge your ideas about who can be a scientist – Susan Svrluga – Washington Post

#FieldWorkFail: Gluing Yourself to a Live Crocodile and Other Mistakes: Scientists share the gross, scary, and often hilarious reality of doing experiments in the wild – Robinson Meyer – The Atlantic

9 Scientists Told Us What Scares Them The Most – Kelly Oakes – BuzzFeed

Bik’s Picks

Jack the Ripper’s final victim set to be exhumed following new theory on the killer’s identity – Doug Bolton – Independent

Scientists unearth earthworm’s ability to digest plant toxins – LiveMint

Are monarch butterflies really being massacred? A new study says it’s a lot more complicated than it seems – Sarah Kaplan – Washington Post

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August 4, 2015

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Diet-induced metabolic changes, rhythmicity of mouse gut microbiome, the microbiome of Lake Michigan, and chicken skin virome.

General microbiome

Antibiotics, microbiota and health: are there dangers hiding in plain sight? – A. Clinton White Jr – Current Opinion in Infectious Diseases

Short Course in the Microbiome: Meeting Dispatch – Kimberly Falana – Journal of Circulating Biomarkers

Pregnancy and birth microbiome

Influence of Intrapartum Antibiotic Prophylaxis for Group B Streptococcus on Gut Microbiota in the First Month of Life – Corvaglia, Luigi – Journal of Pediatric Gastroenterology and Nutrition

Human gut microbiome

Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome – Saeed Shoaie – Cell Metabolism

Effect of daily intake of pomegranate juice on fecal microbiota and feces metabolites from healthy volunteers – Juana I. Mosele – Molecular Nutrition & Food Research

Gut microbiota richness promotes its stability upon increased dietary fiber intake in healthy adults – Julien Tap – Environmental Microbiology

Review: The intestinal microbiome and health – Susan Tuddenham – Current Opinion in Infectious Diseases

Review: Trimethylamine N-Oxide From Gut Microbiota in Chronic Kidney Disease Patients: Focus on Diet – Cristiane Moraes – Journal of Renal Nutrition

Review: Gut permeability, its interaction with gut microflora and effects on metabolic health are mediated by the lymphatics system, liver and bile acid – Cuong D Tran – Future Medicine

Microbiome models

Rhythmicity of the intestinal microbiota is regulated by gender and the host circadian clock – Xue Liang – PNAS

Viability of gut microbes as a complementary earthworm biomarker of metal exposure – Shin Woong Kim – Ecological Indicators

Adaptation of the human aryl hydrocarbon receptor to sense microbiota-derived indoles – Troy D. Hubbard – Scientific Reports

Which games are growing bacterial populations playing? – Xiang-Yi Li – Interface

Animal microbiome

Chicken skin virome analyzed by high-throughput sequencing shows a composition highly different from human skin – Caroline Denesvre – Virus Genes

Variations in microbiota of culex (melanoconion) ocossa and culex (culex) declarator across periurban and rural environments – M Nelson Starkey – Honors Thesis – Andrews University

Plasmids from the gut microbiome of cabbage root fly larvae encode SaxA that catalyzes the conversion of the plant toxin 2-phenylethyl isothiocyanate – Cornelia U. Welte – Environmental Microbiology

Plant, root, and soil microbiome

Successional Trajectories of Rhizosphere Bacterial Communities over Consecutive Seasons
Shengjing Shi – mBio

Compositional differences in simulated root exudates elicit a limited functional and compositional response in soil microbial communities – Michael S. Strickland – Frontiers in Microbiology

Changes in soil microbial community functionality and structure in a metal-polluted site: The effect of digestate and fly ash applications – M. Garcia-Sánchez – Journal of Environmental Management

Metatranscriptome analysis reveals host-microbiome interactions in traps of carnivorous Genlisea species – Hieu X. Cao – Frontiers in Microbiology

Microbial composition alters the response of litter decomposition to environmental change – Kristin L. Matulich – Ecology

Plant community richness and microbial interactions structure bacterial communities in soil – Daniel C. Schlatter – Ecology

Plant diversity effects on soil microbial functions and enzymes are stronger than warming in a grassland experiment – Katja Steinauer – Ecology

Persistence of the dominant soil phylum Acidobacteria by trace gas scavenging – Chris Greening – PNAS

Review: Current overview on the study of bacteria in the rhizosphere by modern molecular techniques: a mini‒review – L. Lagos – Journal of soil science and plant nutrition

Review: Harnessing phytomicrobiome signaling for rhizosphere microbiome engineering – Liliana Quiza – Frontiers in Plant Science

Water microbiome

The quality of organic matter shapes the functional biogeography of bacterioplankton across boreal freshwater ecosystems – Clara Ruiz-González – Global Ecology and Biogeography

Dissimilatory Arsenate Reduction and In Situ Microbial Activities and Diversity in Arsenic-rich Groundwater of Chianan Plain, Southwestern Taiwan – Suvendu Das – Microbial Ecology

Freshwater ice as habitat: Partitioning of phytoplankton- and bacteria between ice and water in central European reservoirs – R.M.L. McKay – Environmental Microbiology Reports

Urban microbial ecology of a freshwater estuary of Lake Michigan – Jenny C. Fisher – Elementa

Review: Bacterial microcompartments: widespread prokaryotic organelles for isolation and optimization of metabolic pathways – Thomas A. Bobik – Molecular Microbiology

Metagenomics and bioinformatics

SuRankCo: supervised ranking of contigs in de novo assemblies – Mathias Kuhring – BMC Bioinformatics

More microbe research

Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri – Thomas R Conno – eLIFE

The Cipher Code of Simple Sequence Repeats in “Vampire Pathogens” – Geng Zou – Scientific Reports

Analysis of IS6110 insertion sites provide a glimpse into genome evolution of Mycobacterium tuberculosis – Tanmoy Roychowdhury – Scientific Reports

Protein synthesis by ribosomes with tethered subunits – Cédric Orelle – Nature

Long-term social dynamics drive loss of function in pathogenic bacteria – Sandra Breum Andersen – PNAS

New approaches to understanding the immune response to vaccination and infection –
David Furman – Vaccine

Microbes in the news

Would You Wear a Face Mask Made From Bacteria? – Jenna Rosenstein – Allure

Times-Picayune asks – Did a moldy building kill 4 New Orleans Professors – Jonathan Eisen – MicroBEnet

How the bugs in your gut keep you healthy – Keri Wiginton – Chicago Tribune

Scientists successfully breed symbiotic bacteria in mosquitoes to control dengue fever – ZeeNews India

Weight-Loss Surgery Changes Gut Bacteria – Rachael Rettner – Live Science

Volcanic bacteria take minimalist approach to survival – Otago University

Science, publishing, and career

Achieving Speaker Gender Equity at the American Society for Microbiology General Meeting – Arturo Casadevall – mBio

Bik’s Picks

This one was striking: Lightning strike as a possible cause of mortality of Australian sea lions, Neophoca cinerea – Peter D. Shaughnessy – Marine Mammal Science

Chilly at Work? Office Formula Was Devised for Men – Pam Belluck – New York Times
Belongs to: Energy consumption in buildings and female thermal demand – Boris Kingma & Wouter van Marken Lichtenbelt – Nature Climate Change

This Map Shows How New Yorkers View The Rest Of The United States. Finally, proof! – Carly Ledbetter – Huffington Post

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August 3, 2015

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Comparing bifidobacterial strains from mom and baby using metagenomics, finding good markers for human fecal matter, the microbiome of a meat processing facility, and a review on community assembly.

Pregnancy and birth microbiome

Metagenomics: Exploring vertical transmission of bifidobacteria from mother to child – Christian Milani – Applied and Environmental Microbiology

Animal microbiome

Comparison of sewage and animal fecal microbiomes using oligotyping reveals potential human fecal indicators in multiple taxonomic groups – Jenny C. Fisher – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Nitrogen Cycling Potential of a Grassland Litter Microbial Community – Michaeline B. Nelson – Applied and Environmental Microbiology

Water microbiome

Impact of silver nanoparticles on benthic prokaryotes in heavy metal-contaminated estuarine sediments in a tropical environment – B. Antizar-Ladislao – Marine Pollution Bulletin

Built environment and food microbiology

Meat processing plant microbiome and contamination patterns of cold-tolerant bacteria causing food safety and spoilage risks in the manufacture of vacuum-packaged, cooked sausages – Jenni Hultman – Applied and Environmental Microbiology

Microbial Ecology

An Economic Framework of Microbial Trade – Joshua Tasoff – PLOS ONE

Review: Historical Contingency in Community Assembly: Integrating Niches, Species Pools, and Priority Effects – Tadashi Fukami – Annual Review of Ecology, Evolution, and Systematics

Microbes in the news

These Bizarre Fungi Resemble Corpse Fingers, UFOs, Tongues – Liz Langley – National Geographic

Alarming survey of NYC subway bacteria gets corrected – CBS News

WHO and Sailing Body Seek Virus Tests in Rio Olympic Venues – Stephen Wade – ABC News

Grocers Are Taking Their Anti-Antibiotic Stance to the High Seas:Costco will buy more farmed salmon from Norway, which is raised with far fewer drugs than Chilean fish. – Willy Blackmore – Take Part

There may be a complex market living in your gut: Researchers apply economic concepts to explore the mysteries of the microbial world – Science Daily

Alum helps ASU microbiology students realize their dreams – Arizona State University

India’s Youngest PG To Do Doctorate In Environmental Microbiology – Tehelka

Bacteria pieces in Royal Jelly: No shot needed, bees vaccinate their babies naturally – Arizona State University

Science, publishing, and career

The silent revolution in peer review – The Loop – Frontiers

Bik’s Picks

Women’s immune system genes operate differently from men’s – Stanford Medicine

Study Shows Plants Exhibit ‘Animal-Like’ Signals Despite Lack Of Nervous System – Rhodi Lee – Tech Times

Florida’s giant snails prove to be a slippery foe: Plant detectives and Sierra, the lab, are on their trail – AFP News

August 1, 2015

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So many new papers, so here is another Saturday installment of The Digest. Several papers on microbiome during pregnancy or the first months of life, ear infections, having older siblings, rhizosphere on volcanic islands, and aquatic fungal communities.

General human microbiome

A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota – David J. Roach – PLOS Genetics

Opinion: The human–microbe metaorganism, evolution and extraterrestrial colonization – Leonard A Mermel – Future Microbiology

Frailty and the Microbiome – Meehan C.J. – Frailty in Aging

Pregnancy and birth microbiome

Secretor Status Is Strongly Associated with Microbial Alterations Observed during Pregnancy – Himanshu Kumar – PLOS ONE

Longitudinal Survey of Microbiota in Hospitalized Preterm Very Low Birth Weight Infants – Patel, Aloka L. – Journal of Pediatric Gastroenterology & Nutrition

Lactation and Intestinal Microbiota: How Early Diet Shapes the Infant Gut
Felicia Goldsmith – Journal of Mammary Gland Biology and Neoplasia

DGGE: Distinctive Intestinal Lactobacillus Communities in Six-Month-Old Infants From Rural Malawi and South-Western Finland – Aakko, Juhani – Journal of Pediatric Gastroenterology & Nutrition

Early Gut Colonization with Lactobacilli and Staphylococcus in Infants: the Hygiene Hypothesis Extended – Salminen, Seppo – Journal of Pediatric Gastroenterology & Nutrition

Association between positive urine cultures and necrotizing enterocolitis in a large cohort of hospitalized infants – Leslie C. Pineda – Early Human Development

Human oral microbiome

Strains of Enterococcus faecalis differ in their ability to coexist in biofilms with other root canal bacteria – L. E. Chávez de Paz – International Endodontic Journal

Human respiratory microbiome

Pediatric Cystic Fibrosis Sputum Can Be Chemically Dynamic, Anoxic, and Extremely Reduced Due to Hydrogen Sulfide Formation – Elise S. Cowley – mBio

Human skin and ear microbiome

The microbiome of otitis media with effusion in Indigenous Australian children – Jake Jervis-Bardy – International Journal of Pediatric Otorhinolaryngology

Review: Probiotics in personal care products – Mei-Chiung Jo Huang – Microbiology Discovery

Human gut microbiome

Having older siblings is associated with gut microbiota development during early childhood – Martin Frederik Laursen – BMC Microbiology

Serum Trimethylamine-N-Oxide is Elevated in CKD and Correlates with Coronary Atherosclerosis Burden – Jason R. Stubbs – Journal of the American Society of Nephrology

Probiotics modify human intestinal mucosa-associated microbiota in patients with colorectal cancer – Zhiguang Gao – Molecular Medicine Reports

A Survey on the Developmental Intestinal Microbiota Research in China: the history, funding, and frontiers of gut bacteria – Hui Min Chen – Journal of Digestive Diseases

Review: Gut microorganisms as promising targets for the management of type 2 diabetes – Nathalie M. Delzenne – Diabetologia

Microbiome models

Systems Modeling of Interactions between Mucosal Immunity and the Gut Microbiome during Clostridium difficile Infection – Andrew Leber – PLOS ONE

Evaluation of mucositis induced by irinotecan after microbial colonization in germ-free mice – Silvia H S P Pedroso – Microbiology

Animal microbiome

Exploring the microbial diversity of the distal intestinal lumen and mucosa of farmed rainbow trout Oncorhynchus mykiss (Walbaum) using next generation sequencing (NGS) – Philip P. Lyons – Aquaculture Research

Plant, root, and soil microbiome

Rhizosphere on volcanic islands: Metagenomic analysis of soil fungal communities on Ulleungdo and Dokdo Islands – Yoon-Jong Nam – The Journal of General and Applied Microbiology

Effect of Agricultural Amendments on Cajanus cajan (Pigeon Pea) and Its Rhizospheric Microbial Communities – A Comparison between Chemical Fertilizers and Bioinoculants – Rashi Gupta – PLOS ONE

Vulnerability of Soil and Its Associated Organic Matter to Degradation in a Subtropical Region: A Study From São Paulo State, Brazil – Alexandre Marco da Silva – Environment Quality Management

Effects of historical logging on soil microbial communities in a subtropical forest in southern China – Piao Song – Plant and Soil

Effects of rotifers, copepods and chironomid larvae on microbial communities in peatlands – Tomasz Mieczan – European Journal of Protistology

Methanogenic microbial community of the Eastern Paris Basin: Potential for energy production from organic-rich shales – Margaux Meslé – International Journal of Coal Geology

All ecosystems potentially host electrogenic bacteria – Nicolas Chabert – Bioelectrochemistry

Phylogenetic structure of arbuscular mycorrhizal community shifts in response to increasing soil fertility – Yongjun Liu – Soil Biology and Biochemistry

Water and extremophile microbiome

Phytoplankton–bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge – Erin M. Bertrand – PNAS

Effects of hydrostatic pressure on yeasts isolated from deep-sea hydrothermal vents – Gaëtan Burgaud- Research in Microbiology

Identification of Habitat-Specific Biomes of Aquatic Fungal Communities Using a Comprehensive Nearly Full-Length 18S rRNA Dataset Enriched with Contextual Data – Katrin Panzer – PLOS ONE

Metaproteomics of aquatic microbial communities in a deep and stratified estuary – David Colatriano – Proteomics

Waste treatment microbiology

Review: Meta-omics approaches to understand and improve wastewater treatment systems – Elisa Rodríguez – Reviews in Environmental Science and Bio/Technology

Metagenomics and bioinformatics

Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples – Tal Korem – Science

Spaced seeds improve k-mer-based metagenomic classification – Karel Břinda – Bioinformatics

Microbial Ecology

Resource pulses can alleviate the biodiversity–invasion relationship in soil microbial communities – Cyrus A. Mallon – Ecology

Not sure if I like this term: Tritagonist as a new term for uncharacterised microorganisms in environmental systems – Florian M Freimoser – ISME Journal

Microbes in the news

Bacteria on chicken, turkey, pork linked to bladder infections – Lynne Terry – Oregon Live

Byproduct of intestinal bacteria may jeopardize heart health in kidney disease patients – Medical Xpress

Oregon architecture researchers to study indoor air quality in 72 homes – EurekAlert

Research spotlights a previously unknown microbial ‘drama’ playing in the Southern Ocean – Science Daily

Government of Canada Invests in New Western Canadian Microbiome Centre – Sys-Con Media

A Video of the destruction can be seen here: Wood-Decay Fungus Identified as Culprit Consuming Pomona Family’s Home – LA Testing

Microbes and Art

Don’t Be Grossed Out, The Bacteria On These Petri Dish Plates Is Art – Andrew Liszewski – Gizmodo

Call for Entries! ASM’s 2015 Agar Art Contest: Submit your work by September 3th – MicrobeWorld

Bik’s Picks: drought edition

Puget Sound sweltering from the drought and Blob – Department of Ecology – Courier Herald

Extreme Droughts Weaken Trees’ Ability to Soak Up Carbon – William R L Anderegg – Gizmodo

It’s Raining Spiders! Weirdest Effects of California Drought – Tia Ghose – Live Science

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July 30, 2015

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Correct vocabulary of microbiome research, microbiome during mosquito development, microbes on Granada’s Royal Chapel stone, and microbes in Atacama desert.

General microbiome

About the proper use of “16S”, “microbiome”, and “microbiota”, and why “microflora” is not correct. Note Elies: But “microbiota” is a plant too!
The vocabulary of microbiome research: a proposal – Julian R. Marchesi – Microbiome

Human oral microbiome

Host response mechanisms in periodontal diseases – Nora Silva – Journal of Applied Oral Science

Human respiratory microbiome

The airway microbiome in patients with severe asthma: Associations with disease features and severity – Yvonne J. Huang – The Journal of Allergy and Clinical Immunology

Human gastric microbiome

The Evolution of Stomach Acidity and Its Relevance to the Human Microbiome – DeAnna E. Beasley – PLOS ONE

Microbiome models

Network analysis of temporal functionalities of the gut induced by perturbations in new-born piglets – Nirupama Benis – BMC Genomics

Animal microbiome

Developmental succession of the microbiome of Culex mosquitoes – Dagne Duguma – BMC Microbiology

Review: The Microbiome: The Trillions of Microorganisms That Maintain Health and Cause Disease in Humans and Companion Animals – A. Rodrigues Hoffmann – Veterinary Pathology

Plant, root, and soil microbiome

Arbuscular mycorrhizal fungi affect plant community structure under various nutrient conditions and stabilize the community productivity – Gaowen Yang – Oikos

Complementarity in both plant and mycorrhizal fungal communities are not necessarily increased by diversity in the other – Cameron Wagg – Journal of Ecology

Diversity of endophytic and rhizoplane bacterial communities associated with exotic Spartina alterniflora and native mangrove using Illumina amplicon sequencing –
Youwei Hong – Canadian Journal of Microbiology

Genetic analysis reveals diversity and genetic relationship among Trichoderma isolates from potting media, cultivated soil and uncultivated soil – Abdullah M. Al-Sadi – BMC Microbiology

Mineralogy: Geochemical evidence of microbial activity within ooids – Mara R. Diaz – Sedimentology

Phylogenetic Diversity of Diazotrophs along an Experimental Nutrient Gradient in Mangrove Sediments – Isabel C. Romero – Journal of Marine Science and Engineering

Inexplicable Arsenic: Human Dimensions of Soil, Water, Food and Microbial
Resources – Ramakrishnan B – Journal of Environmetnal and Analytical Toxicology

Water microbiome

Structure of the archaeal community in the Black Sea photic zone – A. Y. Merkel – Microbiology

Review: Bridging the gap between omics and earth system science to better understand how environmental change impacts marine microbes – Thomas Mock – Global Change Microbiology

Extremophiles

Bacterial Diversity in Microbial Mats and Sediments from the Atacama Desert – Maria Cecilia Rasuk – Microbial Ecology

Thesis: Microbial Ecology, Biogeochemistry, and Signatures of Life at Low Temperature in Arctic Thermokarst Lake Sediments and High Sierra Snow Fields – Matheus Carnevali, Paula B – University of Nevada, Reno

Waste and built environment microbiology

Temporal and Spatial Stability of Ammonia-Oxidizing Archaea and Bacteria in Aquarium Biofilters – Samik Bagchi – PLOS ONE

Molecular Tools for Monitoring the Ecological Sustainability of a Stone Bio-Consolidation Treatment at the Royal Chapel, Granada – Fadwa Jroundi – PLOS ONE

Seasonal Variation on Microbial Community and Methane Production during Anaerobic Digestion of Cattle Manure in Brazil – Juliana Alves Resende – Microbial Ecology

Metagenomics and bioinformatics

deFUME: Dynamic exploration of functional metagenomic sequencing data – Eric van der Helm – BMC Research Notes

Microbial Ecology

An Economic Framework of Microbial Trade – Joshua Tasoff – PLOS ONE

Microbes in the news

Kingdoms are so 20th century: The tree of life gets a makeover: Schoolroom kingdoms are taking a backseat to life’s supergroups – Susan Milius – Science News

Soil-Dwelling Fungus Rode Joplin Tornado to Unexpected Human Home – Jennifer Frazer – Scientific American

Agave extracts show ability to shift gut microbiota: Ingredion study – Stephen DANIELLS – Nutraingredients

Bacterial Find Sheds Light on Digestive Issues, Diabetes, Obesity – American Crystallographic Association

Water At Some Olympic Venues In Rio de Janeiro Reportedly Contain Virus Levels On Par With Raw Sewage – Brad Brooks and Jeny Barchfield – Huffington Post

LASA students developing bacteria to improve carbon monoxide detectors – Calily Bien – KXAN

Bik’s Picks

A tragic death leaves just four northern white rhinos living and little hope for the species – Rachel Feltman – Washington Post

‘Once in a Blue Moon’ Happens on Friday — Why? – Geoff Gaherty – Discovery

How did you get that job: designing a parachute for NASA’s Mars rover – Elizabeth Lopatto – The Verge

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July 28, 2015

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A review of the human hand microbiome, microbiome and anxiety in mouse models, diabetes, bacteria in thrombolites, how plants recruits microbial symbionts, towards a standard in microbial genome annotation, and an article about the lab of Jill Banfield.

Microbiome of pregnancy and birth

Prevalence of oral Candida in the first year of life – C. Stecksén-Blicks – Mycoses

Cross-colonization of infants with probiotic organisms in a neonatal unit – L. Hickey – Journal of Hospital Infection

Human oral microbiome

Periodontal microbiota and phospholipases: The Oral Infections and Vascular Disease Epidemiology Study (INVEST) – Adrien Boillot – Atherosclerosis

Review: Alterations of the oral microbiota and oral clinical findings in dry mouth – Y. Hayashi – Journal of Oral Biosciences

Human skin and eye microbiome

Review of Human Hand Microbiome Research – Sarah L. Edmonds-Wilson – Journal of Dermatological Research

Correspondence: Harnessing the microbiome in glaucoma and uveitis – Ankur Gupta – Medical Hypotheses

Human respiratory microbiome

High diversity of non-sporulating moulds in respiratory specimens of immunocompromised patients: should all the species be reported when diagnosing invasive aspergillosis? – Dea Garcia-Hermoso – Mycoses

 

Human gut microbiome

The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment – Xuan Zhang – Nature Medicine

A tough pill to swallow (perspective): Ready for Oral Fecal Microbiota Pill in Clinical Practice? – Timothy Nguyen – The Journal for Nurse Practitioners

Review: The human gut microbiota and virome: potential therapeutic implications – Emidio Scarpellini – Digestive and Liver Disease

Review: Intestinal Immunity and Gut Microbiota as Therapeutic Targets for Preventing Atherosclerotic Cardiovascular Diseases – Tomoya Yamashita – Circulation Journal

Microbiome models

Microbiota and host determinants of behavioural phenotype in maternally separated mice – G. De Palma – Nature Communications

Microbiota regulates type 1 diabetes – Michael P Burrows – PNAS

Gut microbiota facilitates dietary heme-induced epithelial hyperproliferation by opening the mucus barrier in colon – Noortje Ijssennagger – PNAS

Intestinal inhibition of Atg7 prevents tumour initiation through a microbiome-influenced immune response and suppresses tumour growth – Jonathan Lévy – Nature Cell Biology

Lactulose increases bacterial diversity and modulates the swine faecal microbiome as revealed by 454-pyrosequencing – Jong Pyo Chae – Animal Feed Science and Technology

Dynamic Metabonomic and Microbiological Response of Rats to Lincomycin Exposure: An Integrated Microbiology and Metabonomics Analysis – Manna Lin – RSC Advances

Green propolis modulates gut microbiota, reduces endotoxemia and expression of TLR4 pathway in mice fed a high-fat diet – Aline Rissetti Roquetto – Food Research International

Changes in the Swine Gut Microbiota in Response to Porcine Epidemic Diarrhea Infection – Hyeon-Woo Koh – Microbes and Environments

Review: Interrelatedness Between Dysbiosis in the Gut Microbiota Due to Immunodeficiency and Disease Penetrance of Colitis – Avijit Ray – Immunology

Animal microbiome

Experimental studies of microbial populations and incidence of zoonotic pathogens in the faeces of red deer (Cervus elaphus) – Sebastian Gnat – Letters in Applied Microbiology

Yeast microbiota of natural cavities of manatees (Trichechus inunguis and T. manatus) in Brazil and its relevance for animal health and management in captivity – José J.C. Sidrim – Canadian Journal of Microbiology

An Efficient Strategy Developed for Next-Generation Sequencing of Endosymbiont Genomes Performed Using Crude DNA Isolated from Host Tissues: A Case Study of Blattabacterium cuenoti Inhabiting the Fat Bodies of Cockroaches – Yukihiro Kinjo – Microbes and Environments

Prokaryotic microbiota in the digestive cavity of the jellyfish Cotylorhiza tuberculata – Sara Cortés-Lara – Systematic and Applied Microbiology

Plant, root, and soil microbiome

Inner workings of thrombolites: spatial gradients of metabolic activity as revealed by metatranscriptome profiling – J. M. Mobberley – Scientific Reports

Changes in fungal community of Scots pine (Pinus sylvestris) needles along a latitudinal gradient in Sweden – Hanna Millberg – Fungal Ecology

Temporal dynamics of plant-soil feedback and root-associated fungal communities over 100 years of invasion by a non-native plant – Nicola J. Day – Journal of Ecology

Fungal colonization of the rooting system of the early land plant Asteroxylon mackiei from the 407-Myr-old Rhynie Chert (Scotland, UK) – Christine Strullu-Derrien – Botanical Journal of the Linnean Society

Alder trees enhance crop productivity and soil microbial biomass in tea plantations – P.E. Mortimer – Applied Soil Ecology

Perspective: Plant genotype, microbial recruitment and nutritional security – Jai S. Patel – Frontiers in Plant Science

I don’t always have symbionts, but when I do, I prefer alphaproteobacteria: Endemic Mimosa species from Mexico prefer alphaproteobacterial rhizobial symbionts – Cyril Bontemps – New Phytologist

Conference abstract: Changes in rhizosphere microbiome from halotolerant tomato are correlated with physiological and biochemical parameters of oxidative stress in plants – Radu Liviu Sumalan – Journal of Biotechnology

Review: Root associated bacteria – Friends or enemies? A review – Gabriela Mihalache – Memoirs of the Scientific Sections of the Romanian Academy

Analysing the effect of soil organic matter on bacterial communities using T-RFLP fingerprinting: different methods, different stories? – A. Blaud – Biology and Fertility of Soils

Water microbiome

Phospholipids fatty acids of drinking water reservoir sedimentary microbial community: Structure and function responses to hydrostatic pressure and other physico-chemical properties – Bei-bei Chai – Journal of Environmental Biology

Extremophiles

Review: Microbial communities and primary succession in high altitude mountain environments – Sonia Ciccazzo – Annals of Microbiology

Metagenomics and bioinformatics

FastQFS – A tool for evaluating and filtering paired-end sequencing data generated from high throughput sequencing – Rahul Sharma – Mycological Progress

Toward a standard in structural genome annotation for prokaryotes – H. James Tripp – Standards in Genomic Sciences

Development of Novel Random Network Theory-Based Approaches to Identify Network Interactions among Nitrifying Bacteria – Cindy Shi – SciTech Connect

Microbial Ecology

Socially mediated induction and suppression of antibiosis during bacterial coexistence
Monica I. Abrudan – PNAS

Microbes in the news

About work in the lab of Jill Banfield: At Tiny Scales, a Giant Burst on Tree of Life – Kevin Hartnett – Quanta Magazine

Swan song for antibiotics? Can phage therapy and gene editing fill the gap? – Nicholas Staropoli – Genetic Literacy Project

Metagenomic Study Finds Differences in Oral, Gut Microbiomes of Rheumatoid Arthritis Patients – Genome Web

Your Burger Is Full of Living Things, Even If It’s Vegetarian – Maddie Stone – Gizmodo

Title incorrect, it’s a Yersinia, but different species: A Species Of Bacteria That Causes Bubonic Plague And Other Disease In Salmon May Also Be Able To Treat Cancer – Lecia Bushak – Medical Daily

Bacteria in gut profiling secret to healthy weight – Peta Bee – The Australian

Bacteria to protect Appenzeller cheese from fakes – Anand Chandrasekhar – SwissInfo

Grandparents largely to blame for China’s spiking childhood obesity, Microbiota treatment sees dramatic results in obese children – RJ Whitehead – FoodNavigator

Bik’s Picks

Reception of odors and repellents in mosquitoes – Anandasankar Ray – Current Opinion in Neurobiology

570 Sea Turtle Hatchlings Are Released Into Atlantic Ocean – Getty Images

Everything you need to know about lactose intolerance – with maps! – New Scientist

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July 24, 2015

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A review about small molecules produced by human microbiota, layers of microbial life in Dead Sea sediments, fungus making “hair ice”, exploring deep microbial life in the sea, and bacterial diversity at the North Pole.

Events

3rd Microbiome R&D and Business Collaboration Forum: USA, San Diego, September 10-11, 2015

WAO Symposium on Food Allergy & the Microbiome – 5-6 December 2015, Miami, FL

Microbiome reviews

Small molecules from the human microbiota – Mohamed S. Donia, Michael A. Fischbach – Science

Editorial: Microbiota-induced T cells block allergic inflammation – Yvonne Bordon – Nature Reviews Immunology

Perspective: Promise and pragmatism in clinical microbiome research – Nadim J. Ajami – Mini-Reviews in Medicinal Chemistry

Review: The Role of Intestinal Microbiota in Graft versus Host Disease – no authors listed – Mini-Reviews in Medicinal Chemistry

Editorial: Protective role of gut microbial SCFAs – Ellen F. Carney – Nature Reviews Nephrology

Human oral microbiome

In vitro work: Low-dose irradiation affects the functional behavior of oral microbiota in the context of mucositis – Barbara WA Vanhoecke – Experimental Biology and Medicine

Human gut microbiome

Agave Inulin Supplementation Affects the Fecal Microbiota of Healthy Adults Participating in a Randomized, Double-Blind, Placebo-Controlled, Crossover Trial – Hannah D Holscher – Journal of Nutrition

Plant, root, and soil microbiome

Impact of paleoclimate on the distribution of microbial communities in the subsurface sediment of the Dead Sea – C. Thomas – Geobiology

Evidence for biological shaping of hair ice – D. Hofmann – Biogeosciences

Water and extremophile microbiome

Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor – F. Inagaki – Science

Morphological and phylogenetic diversity of thermophilic cyanobacteria in Algerian hot springs – Samia Amarouche-Yala – Extremophiles

Bacterial diversity in snow on North Pole ice floes – Aviaja L. Hauptmann – Extremophiles

Identifying the sources of nitrate contamination of groundwater in an agricultural area (Haean basin, Korea) using isotope and microbial community analyses – Heejung Kim – Science of the Total Environment

Selection Maintains Low Genomic GC Content in Marine SAR11 Lineages – Haiwei Luo – Molecular Biology and Evolution

Built environment microbiome

Microbiological characterization of 3193 French dwellings of Elfe cohort children – S. Rocchi – Science of The Total Environment

Metagenomics and bioinformatics

For plant/animal assemblages, but might be of interest: cati: an R package using functional traits to detect and quantify multi-level community assembly processes – Adrien Taudiere – Ecography

Metabolomics and proteomics

Metaproteomics and metabolomics analyses of chronically petroleum-polluted sites reveal the importance of general anaerobic processes uncoupled with degradation – Rafael Bargiela – Proteomics

Microbes in the news

‘It’s like going to Pluto and seeing McDonald’s: ‘These microbes live more than 2 kilometers below the sea floor off the coast of Japan – Mitch Leslie – Science

It takes a village… to ward off dangerous infections? New microbiome research suggests so – MedicalXpress

Pathogenic microbiome bacteria change shape to adapt to nasopharyngeal environment – American Microbiome Institute

Rotting Fungus Creates Beautiful, Glistening ‘Hair Ice’ – Elizabeth Goldbaum – LiveScience

Not endorsing this one, full of errors and false claims: Discovery of Microbiome “Third Brain” Confirmed by Scientific Research in Japan – BusinessWire

Science, publishing, and career

New life for old bones: inventing ways to apply the DNA sequencing revolution to tissues ravaged by time. – Elizabeth Culotta – Science

Songwriting and science: Pitching songs, however, has taught me a few practical lessons about pitching papers and grant proposals: – C. Neal Stewart Jr. – Science

Bik’s Picks

Comparisons of life-history parameters between free-ranging and captive killer whale (Orcinus orca) populations for application toward species management – Todd R. Robeck – Journal of Mammalogy

Kiwi genome provides insights into evolution of a nocturnal lifestyle – Diana Le Duc – Genome Biology

A medical-toxicological view of tattooing – Peter Laux – The Lancet

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July 23, 2015

Posted on by

Proteobacteria in gut dysbiosis, microbes on seagrass, viral dark matter, metabolic ups and downs in the biofilm, bacteria/whiskey/copper, The Brown Lagoon, and I’ll see you in the gut.

Human gut microbiome

Review: Proteobacteria: microbial signature of dysbiosis in gut microbiota – Na-Ri Shin – Trends in Biotechnology

DGGE: Equol status and changes in faecal microbiota in menopausal women receiving long-term treatment for menopause symptoms with a soy-isoflavone concentrate – Lucía Guadamuro – Frontiers in Microbiology

Microbiome models

Editorial with a clever title. Like. Escaping Negative Selection: ILC You in the Gut – Adam M. Farkas – Immunity

Maraviroc modifies gut microbiota composition in a mouse model of obesity: a plausible therapeutic option to prevent metabolic disorders in HIV-infected patients – Patricia Perez-Matute – Rev Esp Quimioter

Plants, roots, and soil microbiome

Oxalate secretion by ectomycorrhizal Paxillus involutus is mineral-specific and controls calcium weathering from minerals – A. Schmalenberger – Scientific Reports

Cultivation-dependent analysis the microbial diversity associated with the seagrass meadows in Xincun Bay, South China Sea (sic) – Yu-Feng Jiang – Ecotoxicology

Unearthing the genomes of plant-beneficial Pseudomonas model strains WCS358, WCS374 and WCS417 – Roeland L. Berendsen – BMC Genomics

Water microbiome

Microbial communities associated with benthic faunal assemblages at cold seep sediments of the Sonora Margin, Guaymas Basin – Perrine Cruaud – Frontiers in Marine Science

Assessment of Zooplankton Community Composition along a Depth Profile in the Central Red Sea – John K. Pearman – PLOS ONE

Waste and bioreactor microbiology

Functionally redundant but dissimilar microbial communities within biogas reactors treating maize silage in co-fermentation with sugar beet silage – Susanne G. Langer – Microbial Biotechnology

Effects of Calamagrostis epigejos, Chamaenerion palustre and Tussilago farfara on nutrient availability and microbial activity in the surface layer of spoil heaps after hard coal mining – Anna M. Stefanowicz – Ecological Engineering

Degradation of Biofumigant Isothiocyanates and Allyl Glucosinolate in Soil and Their Effects on the Microbial Community Composition – Franziska S. Hanschen – PLOS ONE

Assessing hog lagoon waste contamination in the Cape Fear Watershed using Bacteroidetes 16S rRNA gene pyrosequencing – Ann M. Arfken – Applied Microbiology and Biotechnology

Bacterial community structure and predicted alginate metabolic pathway in an alginate-degrading bacterial consortium – Akihisa Kita – Journal of Bioscience and Bioengineering

Metagenomics and bioinformatics

Viral dark matter and virus-host interactions resolved from publicly available microbial genomes – Simon Roux – eLIFE

Conference abstract: MetaFast: fast reference-free graph-based comparison of shotgun
metagenomic data – Sergey V. Kazakov

Microbial Ecology

Metabolic co-dependence gives rise to collective oscillations within biofilms – Jintao Liu – Nature

Neutral Models of Microbiome Evolution – Qinglong Zeng – PLOS Computational Biology

Fitness cost of antibiotic susceptibility during bacterial infection – Damien Roux – Science Translational Medicine

New Paradigms in Sepsis: From Prevention to Protection of Failing Microcirculation –
J. Hawiger – Journal of Thrombosis and Haemostasis

Helicobacter pylori eradication for the prevention of gastric neoplasia – Alexander C Ford – Cochrane Library

Microbes in the news

Mutations that make bacteria resistant to antibiotics might also make them deadlier – Arielle Duhaime-Ross – The Verge

Bacteria are many things, but selfish isn’t one of them, scientists say – Robert Gebelhoff – Washington Post

Ulcer-causing bacteria may be key to stomach cancer: A combination of antibiotics and a drug reducing the production of gastric acid can eliminate the bacteria – Stephen Feller – UPI

Project aims to use probiotic bacteria to protect algal crops and increase ecosystem resilience – Lawrence Livermore National Laboratory

Bacteria makes copper from whisky waste – Tereza Pultarova – E&T Institution for Engineering and Technology

Bik’s Picks – reptile edition

HT Ed Yong: No Motherhood Yet for 100-Year-Old Turtle – John R. Platt – Scientific American

Turns Out Boa Constrictors Might Not Actually Suffocate Their Prey – Hilary Hanson – Huffington Post

A Fossil Snake With Four Legs – Ed Yong – National Geographic
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