Category Archives: Pregnancy and birth

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 15, 2015

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Here is your Saturday edition of the Digest. Four papers today about Arctic water and soil microbes, oral bacteria in placentas, using hand microbiomes to identify human ethnicities, and machine learning classifiers give insights in bacterial vaginosis.

Pregnancy and birth microbiome

Oral bacteria in placental tissues: Increased molecular detection in pregnant periodontitis patients – Vanessa Blanc – Oral Diseases

Human skin microbiome

Hand bacteria as an identifier: a biometric evaluation – Amanda B. Holbert – Network Modeling Analysis in Health Informatics and Bioinformatics

Minireview: From Head to Toe: Mapping Fungi across Human Skin – Tim Sandle – EC Microbiology

Human respiratory microbiome

Impact of cigarette smoking on the middle meatus microbiome in health and chronic rhinosinusitis – Vijay R. Ramakrishnan – International Forum of Allergy & Rhinology

Human gut microbiome

Metagenomic Analysis of Crohn’s Disease Patients Identifies Changes in the Virome and Microbiome Related to Disease Status and Therapy, and Detects Potential Interactions and Biomarkers – Pérez-Brocal, Vicente – Inflammatory Bowel Diseases

Animal models

SIV-infection-driven changes of pattern recognition receptor expression in mesenteric lymph nodes and gut microbiota dysbiosis – Tiffany W. Glavan – Journal of Medical Primatology

Plant, root, and soil microbiome

Diazotrophic bacilli isolated from the sunflower rhizosphere and the potential of Bacillus mycoides B38V as biofertiliser – A. Ambrosini – Annals of Applied Biology

Relationships between Oak powdery mildew incidence and severity and commensal fungi – E. T. Topalidou – Forest Pathology

The core microbiome bonds the Alpine bog vegetation to a transkingdom metacommunity – Anastasia Bragina – Molecular Ecology

Warming reduces the cover and diversity of biocrust-forming mosses and lichens, and increases the physiological stress of soil microbial communities in a semi-arid Pinus halepensis plantation – Fernando T. Maestre – Frontiers in Microbiology

Microbial Mineral Colonization Across a Subsurface Redox Transition Zone – Brandon Converse – Frontiers in Microbiology

Mutabilis in mutabili: Spatiotemporal dynamics of a truffle colony in soil – Milan Gryndler – Soil Biology and Biochemistry

Water microbiome

Bacterioplankton community shifts associated with epipelagic and mesopelagic waters in the Southern Ocean – Zheng Yu – Scientific Reports

Microbial diversity in a submarine carbonate edifice from the serpentinizing hydrothermal system of the Prony Bay (New Caledonia) over a 6-year period – Anne Poste – Frontiers in Microbiology

Extremophile microbiome: Arctic edition

Microbial activity is not always limited by nitrogen in Arctic tundra soils – Caroline Melle – Soil Biology and Biochemistry

Arctic soil microbial diversity in a changing world – Aimeric Blaud – Research in Microbiology

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

Diversity of planktonic microorganisms in the Arctic Ocean – Carlos Pedrós-Alió – Progress in Oceanography

Waste treatment microbiology

Shotgun metaproteomic profiling of biomimetic anaerobic digestion processes treating sewage sludge – Ariane Bize – Proteomics

Bioinformatics

Machine learning classifiers provide insight into the relationship between microbial communities and bacterial vaginosis – Daniel Beck – BioData Mining

AmpliSAS: a web server for multilocus genotyping using next-generation amplicon sequencing data – Alvaro Sebastian – Molecular Ecology Resources

Science, publishing, and career

My alma mater, Utrecht University was again voted as the best Dutch university! Academic Ranking of World Universities 2015 – Shanghai Ranking

Microbes in the news

The Microbial Discovery Box: a hands-on activity for science teachers – ASM

Young scientists dreaming big: internship presentation competitions – Uganda Virus Research Institute

Infectious Diseases Like It Hot: How Climate Change Helps Cholera and Salmonella Outbreaks – Marlene Cimons – Think Progress

Before an Animal Disease Becomes a Human Epidemic – Cari Romm – The Atlantic

The dangers of eating snakes: Gauteng pastor encouraged his congregation to eat hair and snakes.

Bik’s Picks

Air Problem Is Worse Than You Think – James Fallows – The Atlantic

Georgia court weighs destiny of 18 captured beluga whales – Rich McKay – Reuters

Los Angeles Throws 96M Balls At California’s Drought Problem – Science Daily

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August 13, 2015

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Fecal microbiota transplants also work with frozen stool, rhizobacterial communities on red pepper plants, effect of vaginal ring contraceptives, and the cilantro microbiome.

Pregnancy and birth microbiome

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

Not a microbiome paper, but of interest: Cesarean Section Delivery is not a Risk Factor for Development of IBD: A Population-based Analysis – Charles N. Bernstein – Clinical Gastroenterology and Hepatology

Human gut microbiome

Faecal microbiota transplant for recurrent Clostridium difficile infection using long-term frozen stool is effective: clinical efficacy and bacterial viability data – S. P. Costello – Alimentary Pharmacology & Therapeutics

Review: Colonization Resistance of the Gut Microbiota against Clostridium difficile – Ana Elena Pérez-Cobas – Antibiotics

Review: Microbiome and Asthma: What Have Experimental Models Already Taught Us?
R. Bonamichi-Santos – Journal of Immunology Research

Human reproductive microbiome

Effects of a One Year Reusable Contraceptive Vaginal Ring on Vaginal Microflora and the Risk of Vaginal Infection: An Open-Label Prospective Evaluation – Yongmei Huang – PLOS ONE

Animal models

Lessons from the Drosophila microbiota – Emma L Walton – Biomedical Journal

Studying host-microbiota interactions in Drosophila melanogaster – Jean Kanellopoulos – Biomedical Journal

Impact of Selection for Digestive Efficiency on Microbiota Composition in the Chicken –
Sandrine Mignon-Grasteau – PLOS ONE

Animal microbiome

Deep insights into carbohydrate metabolism in the rumen of mehsani buffalo at different diet treatments – Nidhi R. Parmar – Genomics Data

Metagenomics: Microbiome analyses of pacific white shrimp (Litopenaeus Vannamei) collected from disparate geographical locations – Arun S. Seetharam – Genomics Data

Classifying the bacterial gut microbiota of termites and cockroaches: a curated phylogenetic reference database (DictDb) – Aram Mikaelyan – Systematic and Applied Microbiology

Plant, root, and soil microbiome

Rhizobacterial Communities and Red Pepper (Capsicum annum) Yield under Different Cropping Systems – Byung Kwon Jung – International Journal of Agriculture & Biology

Soil Microbial Community Structure and Metabolic Activity of Pinus elliottii Plantations across Different Stand Ages in a Subtropical Area – Zeyan Wu – PLOS ONE

Microbiomes and potential metabolic pathways of pristine and anthropized Brazilian mangroves – Vanessa L.R. Nogueira – Regional Studies in Marine Science

Phylogenetic Characterization and Community Diversity of Hydrocarbon-Utilizing
Bacteria in Soil Microcosms Enriched with Aromatic Hydrocarbons – Ola Olapade A – Bioremediation & Biodegradation

Review: The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes – Pablo R. Hardoim – Microbiology and Molecular Biology Reviews

Water microbiome

Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake – A. López-Bueno – Molecular Ecology

Causes and consequences of habitat fragmentation in river networks – Matthew R. Fuller – Annals of the New York Academy of Sciences

Capability of the natural microbial community in a river water ecosystem to degrade the drug naproxen – Paola Grenni – Environmental Science and Pollution Research

Food microbiology

Cilantro microbiome before and after nonselective pre-enrichment for Salmonella using 16S rRNA and metagenomic sequencing – Karen G. Jarvis – BMC Microbiology

Changes in the microbial communities of air-packaged and vacuum-packaged common carp (Cyprinus carpio) stored at 4 °C – Yuemei Zhang – Food Microbiology

Metagenomics

An Overview of Genome Organization and How We Got There: from FISH to Hi-C – James Fraser – Microbiology and Molecular Biology Reviews

Microbes in the news

Statistical Advances Help Unlock Mysteries of the Human Microbiome – Infection Control Today

Seeking samples from FIV positive kitties – Holly Ganz – MicroBEnet

NOFA Says ‘Heal the Climate, Heal Ourselves’ – EcoRI news

Guest Post — The Emergent Microbiome: A Revolution for the Life Sciences – Part II, 2015 Patent Trends – Jessica Miles and Anthony D Sabatelli – JDsupra

A Genetically Modified Yeast Turns Sugar Into Painkillers: Stanford scientists have engineered a strain of yeast that can produce opiates on its own – Adam Hoffman – Smithsonian

Science, publishing, and career

What is the future of Science? This guy might know! Podcast with Francis Collins, NIH Director – Michael DL Johnson – Black Science Blog

Bik’s Picks

Longer-term outcome in the prevention of psychotic disorders by the Vienna omega-3 study – G. Paul Amminger – Nature Communications

Music as an aid for postoperative recovery in adults: a systematic review and meta-analysis – Jenny Hole – The Lancet

How can ants tell each other apart? Why, with their crazy refined sense of smell. – Elahe Izadi – Washington Post

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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 8, 2015

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Lung and oral microbiomes in setting of HIV infection, cell biology of the plant–microbe interface, deep see prokaryotes, bacterial succession during grape fermentation, and correcting amplicon errors with Dada2.

Pregnancy and birth microbiome

Is abnormal vaginal microflora a risk factor for intrauterine fetal growth restriction? – Natalija Vedmedovska – Asian Pacific Journal of Reproduction

Multiple Opportunistic Pathogens, but Not Pre-existing Inflammation, May Be Associated with Necrotizing Enterocolitis – Steven T. Leach – Digestive Diseases and Sciences

Review: Nutrient availability, the microbiome and intestinal transport during pregnancy – Stuart Astbury – Applied Physiology, Nutrition, and Metabolism

Human oral and lung microbiome

Multi-center Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals – James M. Beck – American Journal of Respiratory and Critical Care Medicine

Review: Microbial protection and virulence in periodontal tissue as a function of polymicrobial communities: symbiosis and dysbiosis – Frank A. Roberts and Richard P. Darveau – Periodontology 2000

Needs assessment for emerging oral microbiome knowledge in dental hygiene education – R. Constance Wiener – Journal of Epidemiological Research

Human reproductive microbiome

Is abnormal vaginal microflora a risk factor for intrauterine fetal growth restriction? – Natalija Vedmedovska – Asian Pacific Journal of Reproduction

Human gut microbiome

Alterations of mucosal microbiota in the colon of patients with inflammatory bowel disease revealed by real time polymerase chain reaction amplification of 16S ribosomal ribonucleic acid – Jayakanthan Kabeerdoss – Indian J Med Res

An In Vitro Method to Assess Soil Arsenic Metabolism by Human Gut Microbiota: Arsenic Speciation and Distribution – Naiyi Yin – Environmental Science & Technology

Review: Does a low FODMAP diet help IBS? – Drug and Therapeutics Bulletin

Microbiome models

Modulation of intestinal microbiota in mice by kefir administration – Dong-Hyeon Kim – Food Science and Biotechnology

High nutrient availability reduces the diversity and stability of the equine caecal microbiota – Naja C. K. Hansen – Microbial Ecology in Health & Disease

Impact of Dietary Fiber/Starch Ratio in Shaping Cecal Microbiota in Rabbits – YanLi Zhu – Canadian Journal of Microbiology

Animal microbiome

Electrical Retrieval of Living Microorganisms from Cryopreserved Marine Sponges Using a Potential-Controlled Electrode – Sumihiro Koyama – Marine Biotechnology

PhD Thesis: Reproduction, Sex Ratio and Bacterial Communities of the Coffee Berry Borer Hypothenemus Hampei F. (Coleoptera: Curculionidae) – Mariño Cárdenas – Universidad de Puerto Rico

Effect of starch source (corn, oats or wheat) and concentration on fermentation by equine fecal microbiota in vitro – Brittany E. Harlow – Journal of Applied Microbiology

Role of peptidases of the intestinal microflora and prey in temperature adaptations of the digestive system in planktivorous and benthivorous fish – V. V. Kuz’mina – Fish Physiology and Biochemistry

Plant, root, and soil microbiome

Environmental conditions rather than microbial inoculum composition determine the bacterial composition, microbial biomass and enzymatic activity of reconstructed soil microbial communities – Weibing Xun – Soil Biology and Biochemistry

Editorial: Introduction to a Virtual Special Issue on cell biology at the plant–microbe interface – Ralph Panstruga and Hannah Kuhn – New Phytologist

Influence of 34-years of fertilization on bacterial communities in an intensively cultivated black soil in northeast China – Jing Zhou – Soil Biology and Biochemistry

Functional and structural responses of methanogenic microbial communities in Uruguayan soils to intermittent drainage – Yang Ji – Soil Biology and Biochemistry

Effects of pasture management on soil fertility and microbial communities in the semi-arid grasslands of Inner Mongolia – Jun Liu – Journal of Soils and Sediments

Antibiotic resistance differentiates Echinacea purpurea endophytic bacterial communities with respect to plant organs – Alessio Mengoni – Research in Microbiology

Effect of combined microbes on plant tolerance to Zn–Pb contaminations – Anna Ogar – Environmental Science and Pollution Research

From mesophilic to thermophilic digestion: the transitions of anaerobic bacterial, archaeal, and fungal community structures in sludge and manure samples – Weimin Sun – Applied Microbiology and Biotechnology

Water microbiome

Metagenome-based diversity analyses suggest a significant contribution of non-cyanobacterial lineages to carbonate precipitation in modern microbialites – Aurélien Saghaï – Frontiers in Microbiology

Thesis: Geobiological interactions of archaeal populations in acidic and alkaline geothermal springs of Yellowstone National Park, WY, USA – Jacob Preston Beam – Montana State University

Global diversity and biogeography of deep-sea pelagic prokaryotes – Guillem Salazar – ISME Journal

Built environment microbiology

Halophilic microbial communities in deteriorated buildings – Justyna Adamiak – World Journal of Microbiology and Biotechnology

Food microbiology

Insights into the bacterial community and its temporal succession during the fermentation of wine grapes – Hailan Piao – Frontiers in Microbiology

Identification of key microorganisms involved in Douchi fermentation by statistical analysis and their use in an experimental fermentation – Chen Chen – Journal of Applied Microbiology

In vitro fermentation of lupin seeds (Lupinus albus) and broad beans (Vicia faba): dynamic modulation of the intestinal microbiota and metabolomic output – Patricia Gullón – Food & Function

Bioinformatics

DADA2: High resolution sample inference from amplicon data – Benjamin J Callahan

Transcriptomics

Molecular and chemical dialogues in bacteria-protozoa interactions – Chunxu Song – Scientific Reports

Techniques

Methods for Improving Human Gut Microbiome Data by Reducing Variability through Sample Processing and Storage of Stool – Monika A. Gorzelak – PLOS ONE

Microbes in the News

Prestigious Japanese university comes up with cheesecake … made with Gorilla bacteria! – RocketNews

Lambton College research project proves successful in eliminating bacteria in firefighting gear – Lambton College

Where the sausage gets made – Holly Ganz – MicroBEnet

Calgary diseases expert on the importance of studying our guts – The Globe and Mail

Bik’s Picks

Creepers’ peepers: Why animals’ pupils have different shapes – Nicholas St. Fleur – Seattle Times

Venomous frogs discovered during painful scientific mishap: Frogs head-butt enemies with their spines to inject toxic venom – CBC News

ISS Astronauts to Sample Leafy Greens Grown on Space Station – NDTV

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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 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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