Category Archives: Metabolomics

August 26, 2015

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Microbes in household dust, oropharynx microbiome in schizophrenia, pneumonia in foals, metabolic footprint of bacteria on plant leaves, and Mozzarella cheese.

Human mouth / respiratory microbiome

Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls – Eduardo Castro-Nallar​ – PeerJ

Human vaginal microbiome

Unravelling the Bacterial Vaginosis-Associated Biofilm: A Multiplex Gardnerella vaginalis and Atopobium vaginae Fluorescence In Situ Hybridization Assay Using Peptide Nucleic Acid Probes – Liselotte Hardy – PLOS ONE

Human gut microbiome

Gut feelings of safety: Tolerance to the microbiota mediated by innate immune receptors – Bartlomiej Swiatczak – Microbiology and Immunology

Animal and bioreactor models

The colonic mucus protection depends on the microbiota – Ana M Rodríguez-Piñeiro – Gut Microbes

Sialic acid catabolism drives intestinal inflammation and microbial dysbiosis in mice –
Yen-Lin Huang – Nature Communications

Differential responses of gut microbiota to the same prebiotic formula in oligotrophic and eutrophic batch fermentation systems – Wenmin Long – Scientific Report

Animal microbiome

Composition and Diversity of the Fecal Microbiome and Inferred Fecal Metagenome Does Not Predict Subsequent Pneumonia Caused by Rhodococcus equi in Foals – Canaan M. Whitfield-Cargile – PLOS ONE

Plant, root, and soil microbiome

Metabolic footprint of epiphytic bacteria on Arabidopsis thaliana leaves – Florian Ryffel – The ISME Journal

Diversity of Arbuscular Mycorrhizal Fungi in a Brazilian Atlantic Forest Toposequence – Joice Andrade Bonfim – Microbial Ecology

Native root-associated bacteria rescue a plant from a sudden-wilt disease that emerged during continuous cropping – Rakesh Santhanam – PNAS

Water microbiome

Marine amoebae with cytoplasmic and perinuclear symbionts deeply branching in the Gammaproteobacteria – Frederik Schulz – Scientific Reports

Built environment microbiome

The ecology of microscopic life in household dust – Albert Barberán – Proceedings B

A Pilot Study on Integrating Videography and Environmental Microbial Sampling to Model Fecal Bacterial Exposures in Peri-Urban Tanzania – Timothy R. Julian – PLOS ONE

Food microbiology

Metabolomics and microbiological profile of Italian mozzarella cheese produced with buffalo and cow milk – Maria Barbara Pisano – Food Chemistry

Microbes in the news

What I Learned From Sequencing the Bacteria in My Apartment – Sarah Zhang – Wired

Thousands of microbes found in house dust – Rebecca Morelle – BBC

Household Dust Packed With Thousands of Microbes – Jennifer Viegas – Discovery

Waikiki Water Tested for Bacteria After Sewage Spill – Caleb Jones – ABC News

Methanotrophs: Could bacteria help protect our environment? – EurekAlert
Is our love affair with antibiotics slowly killing us? – Ailin Quinlan – Independent

Science, publishing, and career

In brief, papers with shorter titles get more citations, study suggests – Dalmeet Singh Chawla

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August 18, 2015

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New paper from our lab about human microbiota during pregnancy, association between obesity and cervical microflora, Argentina soil metagenomes, proteomics library, and microbiology during mozzarella cheese making.

Events and conferences

ECCMID: 26th European Congress of Clinical Microbiology and Infectious Diseases: April 2016, Istanbul, Turkey

General microbiome

Review: Fulfilling the Promise of Microbiomics to Revolutionize Medicine – Traci L Testerman – J Microbiol Exp

Review: Cross-kingdom similarities in microbiome functions – Rodrigo Mendes – ISME Journal

Pregnancy and birth microbiome

From our lab: Temporal and spatial variation of the human microbiota during pregnancy – Daniel B. DiGiulio – PNAS

Maternal group B Streptococcus and the infant gut microbiota – A. E. Cassidy-Bushrow – Journal of Developmental Origins of Health and Disease

The stool microbiota of insulin resistant women with recent gestational diabetes, a high risk group for type 2 diabetes – Marina Fugmann – Scientific Reports

Human reproductive tract microbiome

Relationship of Specific Bacteria in the Cervical and Vaginal Microbiotas With Cervicitis – Linda M. Gorgos – Sexually Transmitted Diseases

Changes in vaginal microbiota following antimicrobial and probiotic therapy – Jean M. Macklaim – Microbial Ecology in Health and Disease

Association between obesity and cervical microflora dominated by Lactobacillus iners in Korean women – Hea Young Oh – Journal of Clinical Microbiology

Distribution of human papillomavirus (HPV) genotypes and bacterial vaginosis presence in cervical samples from Paraguayan indigenous – Pamela Mongelos – International Journal of Infectious Diseases

The most common isolated microorganisms and its clinical manifestation in hospitalised women suffering from urogenital diseases in Latvia – Anatolijs Naumčiks – International Journal of Reproduction, Contraception, Obstetrics and Gynecology

Human respiratory microbiome

Conference abstract: Profiling of lung microbial communities in lung cancer and chronic obstructive pulmonary disease patients – Yanhong Liu – Cancer Research

Human oral microbiome

Conference abstract: 16S rRNA saliva analysis unveils differences in the head and neck squamous cell carcinoma microbiome before and after surgical resection – Rafael E. Guerrero-Preston – Cancer Research

Human gut microbiome

Variable alterations of the microbiota, without metabolic or immunological change, following faecal microbiota transplantation in patients with chronic pouchitis – J. Landy – Scientific Reports

Review: Systematic Review of the Relation Between Intestinal Microbiota and Toll-Like Receptors in the Metabolic Syndrome: What Do We Know So Far? – José Pedro Portela-Cidade – GE Portuguese Journal of Gastroenterology

Review: Commensal Microbiome Promotes Resistance to Local and Systemic Infections – Nan Zhang – Chinese Medical Journal

Animal microbiome

High diversity of viable bacteria isolated from lymph nodes of slaughter pigs and its possible impacts for food safety – Evelyne Mann – Journal of Applied Microbiology

Geographic patterns in the bacterial microbiome of the glassy-winged sharpshooter, Homalodisca vitripennis (Hemiptera: Cicadellidae) – E. W. Welch – Symbiosis

Plant, root, and soil microbiome

Using direct amplification and next-generation sequencing technology to explore foliar endophyte communities in experimentally inoculated western white pines – Lorinda S. Bullington – Fungal Ecology

Maize lines with different nitrogen use efficiency select bacterial communities with different β-glucosidase-encoding genes and glucosidase activity in the rhizosphere – Shamina I. Pathan – Biology and Fertility of Soils

Fire severity shapes plant colonization effects on bacterial community structure, microbial biomass, and soil enzyme activity in secondary succession of a burned forest – Joseph E. Knelman – Soil Biology and Biochemistry

Diversity of hydrolases from hydrothermal vent sediments of the Levante Bay, Vulcano Island (Aeolian archipelago) identified by activity-based metagenomics and biochemical characterization of new esterases and an arabinopyranosidase – Antonio Placido – Applied Microbiology and Biotechnology

Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe – Jonathan W. Leff – PNAS

Soil Metagenomes from Different Pristine Environments of Northwest Argentina – Christina B. McCarthy – Genome Announcements

Relationships between the density and activity of microbial communities possessing arylsulfatase activity and soil sulfate dynamics during the decomposition of plant residues in soil – Séverine Piutti – European Journal of Soil Biology

Food microbiology

Microbial changes of natural milk cultures for mozzarella cheese during repeated propagation cycles – Angela Guidone – LWT – Food Science and Technology

No paper, just abstract, no pathogens appear to have been found: Culture-independent Pathogenic Bacterial Communities in Bottled Mineral Water – Hamdy A. Hassan – Renewable Energy & Sustainable Development

A diagnosis of the microbiological quality of dehydrated bee-pollen produced in Brazil – Adriane Alexandre Machado De-Melo – Letters in Applied Microbiology

Metagenomics and bioinformatics

HipMer: An Extreme-Scale De Novo Genome Assembler – Evangelos Georganas

Functional metagenomic discovery of bacterial effectors in the human microbiome and isolation of commendamide, a GPCR G2A/132 agonist – Louis J. Cohen – PNAS

Proteomics and metabolomics

The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity – Samuel H. Payne – Scientific Data

Monitoring microbial metabolites using an inductively coupled resonance circuit – Daniil Karnaushenko – Scientific Reports

Extremophiles

Biotechnological applications of extremophiles, extremozymes and extremolytes – Noura Raddadi – Applied Microbiology and Biotechnology

Microbes in the news

Mothers facing C-sections look to vaginal ‘seeding’ to boost their babies’ health – Aimee Molloy – The Guardian

Bacterial community in pregnant women linked to preterm birth, study finds – Erin Digitale – Stanford Medicine
Stanford preterm birth study counters Detroit findings – Karen Bouffard – The Detroit News
Microbe Mix May Play Role In Preterm Birth Risk – Rob Stein – NPR

Biologist investigates how gene-swapping bacteria evade antibiotics – University of Texas at Dallas – EurekAlert

Methane and Climate Change: Arctic Bacteria Might Eat Methane? – Nature World News

How beneficial bacteria protect intestinal cells – Quinn Eastman – Emory News Center

Researchers Identify Metaproteomic Differences between Obese, Non-Obese Individuals – Adam Bonislawski – Genomeweb

How does Cincinnati Children’s Hospital use the microbiome to study lupus? A look inside with Diana Taft – Megan McGrath – DNA Genotek

Science, publishing, and career

A Scientific Look at Bad Science – Bourree Lam – The Atlantic

Bik’s Picks

Photos: Ancient Flowering Plant May Have Lived with Dinosaurs – Live Science

First-Ever Salamander in Amber Found in Caribbean – Richard Farrell – Discovery

Nasa awards $200,000 grant to a research project aimed at turning astronaut poo into food – Independent

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August 16, 2015

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So many new papers, that I need to do a Sunday post as well. Human nose microbiota changes during rhinovirus infection. tsrimethylamine and human gut microbiome, gut microbiota in sloths, and effect of timber harvesting on forest soils.

Human oral microbiome

Long-term evaluation of the antimicrobial susceptibility and microbial profile of subgingival biofilms in individuals with aggressive periodontitis – Talita Gomes Baêta Lourenco – Brazilian Journal of Microbiology

The human oral metaproteome reveals potential biomarkers for caries disease – Pedro Belda-Ferre – Proteomics

Human respiratory microbiome

Changes in microbiota during experimental human Rhinovirus infection – J. J. Hofstra – BMC Infectious Disease

Human gut microbiome

The Microbiome and Osteosarcopenic Obesity in Older Individuals in Long-Term Care Facilities – Julia E. Inglis – Current Osteoporosis Reports

Review: Microbiology Meets Big Data: The Case of Gut Microbiota–Derived Trimethylamine – Gwen Falony – Annual Review of Microbiology

Review: Gut microbiota modulate the immune effect against hepatitis B virus infection – D. Xu – European Journal of Clinical Microbiology & Infectious Diseases

Microbiome models

Osteopontin Deficiency Accelerates Spontaneous Colitis in Mice with Disrupted Gut Microbiota and Macrophage Phagocytic Activity – Takahiko Toyonaga – PLOS ONE

Prolonged antibiotic treatment induces a diabetogenic intestinal microbiome that accelerates diabetes in NOD mice – Kirsty Brown – ISME Journal

Prebiotic effects of diet supplemented with the cultivated red seaweed Chondrus crispus or with fructo-oligo-saccharide on host immunity, colonic microbiota and gut microbial metabolites – Jinghua Liu – BMC Complementary and Alternative Medicine

Animal microbiome

Metagenome Sequencing of the Greater Kudu (Tragelaphus strepsiceros) Rumen Microbiome – Anita N. Dube – Genome Announcements

Diet specialization selects for an unusual and simplified gut microbiota in two- and three-toed sloths – Kimberly A. Dill-McFarland – Environmental Microbiology

Microbiome Variation Across Amphibian Skin Regions: Implications for Chytridiomycosis Mitigation Efforts – Arnaud Bataille – Microbial Ecology

Plant, root, and soil microbiome

Molecular screening of microbial communities for candidate indicators of multiple metal impacts in marine sediments from Northern Australia – Alyssa M. Cornall – Environmental Toxicology and Chemistry

Response of Archaeal and Bacterial Soil Communities to Changes Associated with Outdoor Cattle Overwintering – Alica Chroňáková – PLOS ONE

Long-term effects of timber harvesting on hemicellulolytic microbial populations in coniferous forest soils – Hilary T C Leung – ISME Journal

Microbial Community Composition and Extracellular Enzyme Activities Associated with Juncus roemerianus and Spartina alterniflora Vegetated Sediments in Louisiana Saltmarshes – Anthony J. Rietl – Microbial Ecology

Water microbiome

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time-series and global field samples – Alma Parada – Environmental Microbiology

Diversity of Synechococcus at the Martha’s Vineyard Coastal Observatory: Insights from Culture Isolations, Clone Libraries, and Flow Cytometry – Kristen R. Hunter-Cevera – Microbial Ecology

Built environment microbiome

The Effectiveness of Three Home Products in Cleaning and Disinfection of S. aureus and E. coli on Home Environmental Surfaces – Nancy Goodyear – Journal of Applied Microbiology

Geochemical influences and mercury methylation of a dental wastewater microbiome – Asha Rani – Scientific Reports

Metagenomics

Research Highlights: An encrypted growth signature – Naomi Attar – Nature Reviews Microbiology

Archaea / Metabolomics

Untargeted metabolomics studies employing NMR and LC–MS reveal metabolic coupling between Nanoarcheum equitans and its archaeal host Ignicoccus hospitalis – Timothy Hamerly – Metabolomics

Microbes in the news

Toxoplasma parasite’s greedy appetite may be its downfall – University of Melbourne – EurekAlert

Let’s hope the stock photo was not related to the techniques used in this study:
Computerized ‘fishing expedition’ hooks 12,500 virus genomes – Brooks Hays – UPI

New Beach Act aims for faster results on bacteria tests – Dan Radel – APP.com

Swedish infant infects four others with resistant bacteria – New Straits Times

What’s lurking in your lungs? Surprising findings emerge from U-M microbiome research – Health Canal

Science, publishing, and career

Fixing the Leaky Bucket: What Tech Companies Must Do to Retain Their Best Female Talent – Belle Beth Cooper – Huffington Post

Bik’s Picks

Here’s How To Call The International Space Station – Gizmodo

Playing Tetris for 3 minutes could reduce your worst cravings – IBN Live

Teenagers are making themselves DIY braces and it is horrifying – Amy Willis – Metro.co.uk

How the internet of things is having an impact in Africa – HTXT Africa

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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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July 31, 2015

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Microbiome antibodies prevented an HIV vaccine from working, effect of antibiotics during rhinosinusitis, microbiome and tuberculosis, how mussels get colonized, and a fruit based nutrient bar’s effect on human metabolism.

Human respiratory microbiome

The Microbiome at the Pulmonary Alveolar Niche: How It Affects the Human Innate Response against Mycobacterium tuberculosis – Alexander J. Adami – Tuberculosis

The effect of antibiotics on the microbiome in acute exacerbations of chronic rhinosinusitis – Mark A. Merkley – International Forum of Allergy & Rhinology

Review: Microbiome influences on allergy in mice and humans – Benjamin J Marsland – Current Opinion in Immunology

Human gut microbiome

Diversion of HIV-1 vaccine-induced immunity by gp41-microbiota cross-reactive antibodies – Wilton B. Williams – Science

Not microbiota, but of interest: Go with the Flow: Regional gastrointestinal transit and pH studied in 215 healthy volunteers using the wireless motility capsule: influence of age, gender, study country and testing protocol – Y. T. Wang – Alimentary Pharmacology & Therapeutics

Commentary: You Lose Some, You Win Some: Weight Loss Induces Microbiota and Metabolite Shifts – Elisabeth M. Bik – EBioMedicine

Review: The role of the gut microbiota in metabolic health – Aafke W. F. Janssen and Sander Kersten – The FASEB Journal

Microbiome models

MyD88 Adaptor-Dependent Microbial Sensing by Regulatory T Cells Promotes Mucosal Tolerance and Enforces Commensalism – Sen Wang – Immunity

Commentary: A Toolbox for Microbiome Engineering – Mohamed S. Donia – Cell Systems

Animal microbiome

The nasopharyngeal microbiota of feedlot cattle that develop bovine respiratory disease – Devin B. Holman – Veterinary Microbiology

Adapted to change: the rapid development of symbiosis in newly settled, fast-maturing chemosymbiotic mussels in the deep sea – Laming Sven R – Marine Environmental Research

Plant, soil, and root microbiology

Roots from distinct plant developmental stages are capable of rapidly selecting their own microbiome without the influence of environmental and soil edaphic factors – Jun Yuan – Soil Biology and Biochemistry

Environmental Filtering of Microbial Communities in Agricultural Soil Shifts with Crop Growth – Sarah K. Hargreaves – PLOS ONE

Interactions between a plant growth-promoting rhizobacterium and smoke-derived compounds and their effect on okra growth – Heino B. Papenfus – Journal of Plant Nutrition and Soil Science

Food microbiology

Diversity and dynamics of antibiotic-resistant bacteria in cheese as determined by PCR denaturing gradient gel electrophoresis – Ana Belén Flórez – International Journal of Food Microbiology

Proteomics and metabolomics

A human gut metaproteomic dataset from stool samples pretreated or not by differential centrifugation – Alessandro Tanca – Data in Brief

A multicomponent nutrient bar promotes weight loss and improves dyslipidemia and insulin resistance in the overweight/obese: chronic inflammation blunts these improvements – Joyce C. McCann – The FASEB Journal

Microbes in the news

Gut microbiome may have interfered with experimental HIV vaccines – Rachel Tompa – Fred Hutch

Vacation souvenirs can be crappy, but rarely are they actual crap: Ilana Brito, the Biologist Who Flew to Fiji for Feces – Rachel Becker – Ozy

Science, publishing, and career

Why not have a life? I only stay late if I’m actually doing an experiment – Gary McDowell – Science

Bik’s Picks

Deadly Fungus Could Threaten U.S. Salamanders – Stephanie Pappas – Discover / LiveScience

Plants send out stress signals just like animals, scientists find – Robert Gebelhoff – Washington Post

Vaccine Success Holds Hope For End To Deadly Scourge Of Ebola – Kate Kelland – Huffington Post

The world’s best whiskey is being sent into space for the sake of science – Gabriel Fisher – Quartz

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July 29, 2015

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Pack hunting by soil amoeba, microbiota of meconium and uterus, transcriptomics of oral phages, no differences in antibiotic resistance gene content in organic or regular pigs, and effects of IBD associated microbes on mouse physiology.

General microbiome

Editorial: News Feature: Microbes on the mind – Helen H. Shen – PNAS

Microbiome of pregnancy and birth

Note: just one sample was PCR positive: First-Pass Meconium Samples from Healthy Term Vaginally-Delivered Neonates: An Analysis of the Microbiota – Richard Hansen – PLOS ONE

Understanding the Biologic Therapies of Probiotics, Prebiotics, and Synbiotics: Exploring Current Evidence for Use in Premature Infants for the Prevention of Necrotizing Enterocolitis – Asmerom, Mussie – Journal of Perinatal & Neonatal Nursing

Human oral microbiome

Transcriptome analysis of bacteriophage communities in periodontal health and disease – Tasha M. Santiago-Rodriguez – BMC Genomics

Human respiratory microbiome

Paired analysis of the microbiota of surface mucus and whole-tissue specimens in patients with chronic rhinosinusitis – Raymond J.T. Kim – International Forum of Allergy & Rhinology

Human genital microbiome

Characterisation of the human uterine microbiome in non-pregnant women through deep sequencing of the 16S rRNA gene – Hans Verstaelen – PeerJ

Human skin microbiome

Review: Regulation of T cell immunity in atopic dermatitis by microbes: the Yin and Yang of cutaneous inflammation – Tilo Biedermann – Frontiers in Immunology

Human gut microbiome

Ruminococcal cellulosomes: molecular Lego to deconstruct microcrystalline cellulose in human gut – Gurvan Michel – Environmental Microbiology

Influence of galacto-oligosaccharide mixture (B-GOS) on gut microbiota, immune parameters and metabonomics in elderly persons – Jelena Vulevic – British Journal of Nutrition

Review: Microbiome influences on allergy in mice and humans – Benjamin J Marsland – Current Opinion in Immunology

Editorial: Gut microbiota: Microbiota and neuroimmune signalling—Metchnikoff to microglia – John F. Cryan & Timothy G. Dinan

Review: 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

Editorial: Stool microbiome changes in VEGF-TKI-induced diarrhoea – Nature Reviews Urology

Models of microbiome research

Microorganisms linked to inflammatory bowel disease-associated dysbiosis differentially impact host physiology in gnotobiotic mice – Thomas W Hoffmann – ISME Journal

The Role of Curcumin in Modulating Colonic Microbiota During Colitis and Colon Cancer Prevention – Rita-Marie McFadden – Inflammatory Bowel Diseases

Intestinal microbiota of mice influences resistance to Staphylococcus aureus pneumonia –
Stefanie Gauguet – Infection and Immunity

Oral Administration of P. gingivalis Induces Dysbiosis of Gut Microbiota and Impaired Barrier Function Leading to Dissemination of Enterobacteria to the Liver – Mayuka Nakajima – PLOS ONE

Fecal microbiota transplantation and bacterial consortium transplantation have comparable effects on the re-establishment of mucosal barrier function in mice with intestinal dysbiosis – Ming Li – Frontiers in Microbiology

Symbiotic maple saps minimize disruption of the mice intestinal microbiota after oral antibiotic administration – Riadh Hammami – International Journal of Food Sciences and Nutrition

Animal microbiome

Characterization of Antibiotic Resistance Gene Abundance and Microbiota Composition in Feces of Organic and Conventional Pigs from Four EU Countries – Lenka Gerzova – PLOS ONE

Symbiotic bacteria enable olive fly larvae to overcome host defences – Michael Ben-Yosef – Royal Society Open Science

Plant, root, and soil microbiome

Not sure where to file this one under, but pretty cool: Pack hunting by a common soil amoeba on nematodes – Stefan Geisen – Environmental Microbiology

Anaerobic degradation pathway of the novel chiral insecticide Paichongding and its impact on bacterial communities in soils – Zhiqiang Cai – Journal of Agricultural and Food Chemistry

Metagenomics and bioinformatics

Exploiting topic modeling to boost metagenomic reads binning – Ruichang Zhang – BMC Bioinformatics

Metabolomics and Proteomics

Effects of Dietary Different Doses of Copper and High Fructose Feeding on Rat Fecal Metabolome – Xiaoli Wei – Journal of Proteome Research

Science, publishing, and career

Let’s Make Gender Diversity in Data Science a Priority Right from the Start – Francine D. Berman – PLOS Biology

Microbes in the news

What are ‘eye crusties’ made of? uBiome asking for participants to use their eye kit

Bacteria Hysteria

Germaphobes look away! Your gym bag might contain high levels of bacteria usually found in faeces – Irish Examiner

Bik’s Picks

A Skeleton, a Catholic Relic, and a Mystery About American Origins – Adrienne Lafrance – The Atlantic

The confounding case of the missing carbon – Michael Casey – CBS News

Washington Is Finally Getting What It Deserves As It Sinks Into The Sea – Kate Sheppard – Huffington Post

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July 25, 2015

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Extracting DNA from the soil under a cadaver, metabolomics of periodontitis, HLA haplotypes and microbiome, and microbes using ancient carbon from melting permafrost.

Microbiome of pregnancy and health

Gut Bifidobacterium microbiota in one-month-old Brazilian newborns – Łukasz Grześkowiak – Anaerobe

Microbiome of death

Assessment of microbial DNA extraction methods of cadaver soil samples for criminal investigations – Sheree J. Finley – Australian Journal of Forensic Sciences

Human oral microbiome

Editorial: Targeting specific bacteria in the oral microbiome – Jorge Frias-Lopez – Trends in Microbiology

The human salivary microbiome exhibits temporal stability in bacterial diversity – Simon J. S. Cameron – FEMS Microbiology Ecology

Association of Synergistetes and Cyclodipeptides with Periodontitis – J.T. Marchesan – Journal of Dental Research

Human urinary tract microbiome

Article in Russian: Microbial communities on kidney stones – YM Romanova – Mol Gen Mikrobiol Virusol

Human gut microbiome

The Influence of the Autoimmunity-Associated Ancestral HLA Haplotype AH8.1 on the Human Gut Microbiota: A Cross-Sectional Study – Johannes R. Hov – PLOS ONE

Clostridium amazonense sp. nov. an obliqately anaerobic bacterium isolated from a remote Amazonian community in Peru – Lindsey O’Neal – Anaerobe

Crohn-associated microbial communities from colonic mucosal biopsies in patients of the western Mediterranean – Roberto Vidal – Systematic and Applied Microbiology

Human eye microbiome

Bacteria Colonizing the Ocular Surface in Eyes With Boston Type 1 Keratoprosthesis: Analysis of Biofilm-Forming Capability and Vancomycin Tolerance – Sarmad H. Jassim – Investigative Ophthalmology & Visual Science

Microbiome models

Persistent hyperglycemia modulates gut immune function and microbiota in rats – Katsuya Mori – Journal of Intensive Care

Animal microbiome

16S rDNA analysis of archaea indicates dominance of Methanobacterium and high abundance of Methanomassiliicoccaceae in rumen of Nili-Ravi buffalo – S.S. Paul – Anaerobe

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

Plant, root, and soil microbiome

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

Soils, microbes, and forest health: A qualitative analysis of social and institutional factors affecting genomic technology adoption – Sara E. Crann – Technology in Society

Assessment of microbial DNA extraction methods of cadaver soil samples for criminal investigations – Sheree J. Finley – Australian Journal of Forensic Sciences

Water microbiome

Spatial patterns of benthic bacterial communities in a large lake – Li-Xiang Liu – International Review of Hydrobiology

Extremophile microbiome

Utilization of ancient permafrost carbon in headwaters of Arctic fluvial networks – Paul J. Mann – Nature Communications

Waste water and bioreactor microbiology

Determination of the archaeal and bacterial communities in two-phase and single-stage anaerobic systems by 454 pyrosequencing – Yogananda Maspolim – Journal of Environmental Sciences

Influence of co-substrate on textile wastewater treatment and microbial community changes in the anaerobic biological sulfate reduction process – Kashif Rasool – Journal of Hazardous Materials

Metabolic networks

Metabolic interactions in microbial communities: untangling the Gordian knot – Olga Ponomarova – Current Opinion in Microbiology

Association of Synergistetes and Cyclodipeptides with Periodontitis – J.T. Marchesan – Journal of Dental Research

Microbes in the news

If the sea is dirty, the sand is worse. Beach sand contains more fecal bacteria than seawater – Megan Scudellari – Boston Globe

Bacteria Hysteria

The Best Way To Clean Your Purse From All That Dirty Bacteria – Madelyn Chung – Huffington Post Canada

Breast milk containing bacteria for sale on Craigslist in Upstate – Gabrielle Komorowski – WYFF4

Bik’s Picks

What San Diego Scientists Are Discovering About Dolphins And Diabetes – Megan Burke – KPBS

Bid to save dolphins in polluted Ganges – Nirmala Ganapathy – Straits Times

 

The SnotBot: Patrick Stewart Backs Drones That Collect Whale Snot – Keith Wagstaff – NBC News

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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 21, 2015

Posted on by

Microbiome of a dead pig in the snow, two papers on oral microbiome in HIV infection, sweetener consumption and microbiome, proteomics of preterm infant colonization, sequencing platform and primer choices, and including microbial ecology in Pre-med programs.

Microbiology of death

Using Bacterial and Necrophagous Insect Dynamics for Post-Mortem Interval Estimation during Cold Season: Novel Case Study in Romania – Lavinia Iancu – Forensic Science International

Pregnancy and birth / Proteomics

Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant – Brandon Brooks

Human oral microbiome

The Oral Microbiome in HIV-positive Individuals – James O. Kistler – Journal of Medical Microbiology

Exploring salivary microbiota in AIDS patients with different periodontal statuses using 454 GS-FLX Titanium pyrosequencing – Fang Zhang – Frontiers in Cellular and Infection Microbiology

Review: Bacteria and Archaea Paleomicrobiology of the Dental Calculus: a Review – Hong T.T. Huynh – Molecular Oral Microbiology

Human urinary tract microbiome

Review: Intracellular Bacterial Communities: A Potential Etiology for Chronic Lower Urinary Tract Symptoms – Victoria C.S. Scott – Urology

Human gut microbiome

High-intensity sweetener consumption and gut microbiome content and predicted gene function in a cross-sectional study of adults in the United States – Cara L. Frankenfeld – Annals of Epidemiology

Pomegranate extract induces ellagitannin metabolite formation and changes stool microbiota in healthy volunteers – Zhaoping Li – Food & Function

Models of microbiome

Neutrophil gelatinase-associated lipocalin regulates gut microbiota of mice – Katsuya Mori – Journal of Gastroenterology and Hepatology

Effect of Dietary Protein Levels on Composition of Odorous Compounds and Bacterial Ecology in Pig Manure – Sungback Cho – Asian Australas. J. Anim. Sci

Animal microbiome

Shotgun Metagenomic Sequencing Reveals Functional Genes and Microbiome Associated with Bovine Digital Dermatitis – Martin Zinicola – PLOS ONE

Diversity and composition of the bacterial community in Amphioxus feces – Minming Pan – Journal of Basic Microbiology

Isolation, characterization, and antibiotic resistance of Vibrio spp. in sea turtles from Northwestern Mexico – Alan A. Zavala-Norzagaray – Frontiers in Microbiology

Microbial Infections Are Associated with Embryo Mortality in Arctic-Nesting Geese – Cristina M. Hansen – Applied and Environmental Microbiology

An insight into the functional role of thioredoxin reductase, a selenoprotein, in maintaining normal native microbiota in the Gulf Coast tick (Amblyomma maculatum) – K. Budachetri – Insect Molecular Biology

Chemotaxis by natural populations of coral reef bacteria – Jessica Tout – The ISME Journal

Review: Exploring the avian gut microbiota: current trends and future directions – David W. Waite – Frontiers in Microbiology

Plant, root, and soil microbiome

Lactic acid bacteria are endophytic components of durum wheat plant following the whole life cycle from plant to flour – Fabio Minervini – Applied and Environmental Microbiology

Application of mesotrione at different doses in an amended soil: Dissipation and effect on the soil microbial biomass and activity – Eva Pose-Juan – Science of The Total Environment

Plant species richness does not attenuate responses of soil microbial and nematode communities to a flood event – Daniela Wagner – Soil Biology and Biochemistry

Declined soil suppressiveness to Fusarium oxysporum by rhizosphere microflora of cotton in soil sickness – Xiaogang Li – Biology and Fertility of Soils

Water / extremophile microbiome

Diversity of methanogens and sulfate-reducing bacteria in the interfaces of five deep-sea anoxic brines of the Red Sea – Yue Guan – Research in Microbiology

Analysis of virus genomes from glacial environments reveals novel virus groups with unusual host interactions – Christopher M. Bellas – Frontiers in Microbiology

A Paleoarchean coastal hydrothermal field inhabited by diverse microbial communities: the Strelley Pool Formation, Pilbara Craton, Western Australia – K. Sugitani – Geobiology

Predicting the response of the deep-ocean microbiome to geochemical perturbations by hydrothermal vents – Daniel C Reed – The ISME Journal

Waste and bioreactor microbiology

GeoChip-based analysis of microbial community of a combined nitritation-anammox reactor treating anaerobic digestion supernatant – Jian Zhao – Water Research

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

Microbial ecology

Review: Ecological speciation in bacteria: reverse ecology approaches reveal the adaptive part of bacterial cladogenesis – Florent Lassalle – Research in Microbiology

Microbiology and Ecology Are Vitally Important to Premedical Curricula – Val H. Smith – Evolution, Medicine, and Public Health

Bioinformatics and metagenomics
MCaVoH: A toolkit for Mining, Classification and Visualization of Human Microbiota –
Maryum Nisar – Journal of Microbiological Methods

An intriguing new bacterial phylum – Naomi Attar – Nature Reviews Microbiology

Metabolic networks

A biosynthetic pathway for a prominent class of microbiota-derived bile acids – A Sloan Devlin – Nature Chemical Biology

Methanogenic food web in the gut contents of methane-emitting earthworm Eudrilus eugeniae from Brazil – Kristin Schulz – The ISME Journal

Auxotrophy and intra-population complementary in the ‘interactome’ of a cultivated freshwater model community – Sarahi L Garcia – Molecular Ecology

Techniques

Primer and platform effects on 16S rRNA tag sequencing – Julien Tremblay – Frontiers in Microbiology

Microbes in the news

Programming Bacteria to Kill Cancer Cells – Lecia Bushak – Newsweek

Scientists keep finding more evidence that bacteria in your stomach are connected to your mood – Kevin Loria – Business Insider

#BacteriaHysteria: The even grosser cause behind gross smelling feet – Stephanie Bell-Flynt

Bik’s Picks
One Migration from Siberia Peopled the Americas: Study – Discovery

Study: Women With Mild Memory Problem Worsen Faster Than Men – Lauran Neergaard – ABC News

Marijuana helps broken bones heal, says Israeli scientific team – Ruth Schuster – Haaretz

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