Category Archives: Pregnancy and birth

July 20, 2016

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Jobs

Postdoc: Arbuscular mycorrhizal fungi and associated microbiota – Boyce Thompson Institute at Cornell campus (NY) (via ASM)

Pregnancy and birth

Why Don’t All Infants Have Bifidobacteria in Their Stool? – Gerald W. Tannock – Frontiers in Microbiology

Not liking this title: I did not see that coming! It is more than bugs in the bagina – Tamsin Board – Molecular Reproduction and Development

The Probiotics in Pregnancy Study (PiP Study): rationale and design of a double-blind randomised controlled trial to improve maternal health during pregnancy and prevent infant eczema and allergy – Christine Barthow – BMC Pregnancy and Childbirth

Human skin microbiome

Age-related differences in morphological characteristics of residual skin surface components collected from the surface of facial skin of healthy male volunteers – N. E. Chalyk – Skin Research and Technology

Human respiratory microbiome

Metagenome and Metatranscriptome Profiling of Moderate and Severe COPD Sputum in Taiwanese Han Males – Shih-Wei Lee – PLOS ONE

Human gut microbiome

Bacterial and Fungal Microbiota Changes Distinguish C. difficile Infection from Other Forms of Diarrhea: Results of a Prospective Inpatient Study – William Sangster – Frontiers in Microbiology

Effects of Arabinoxylan and Resistant Starch on Intestinal Microbiota and Short-Chain Fatty Acids in Subjects with Metabolic Syndrome: A Randomised Crossover Study – Stine Hald – PLOS ONE

Review: Intestinal microbiota and chronic constipation – Ying Zhao – Springer Plus

Animal experiments

Intestinal Microbiota Promotes Psoriasis-Like Skin Inflammation by Enhancing Th17 Response – Zuzana Zákostelská – PLOS ONE

Animal microbiome

Effects of 16S rDNA sampling on estimates of the number of endosymbiont lineages in sucking lice – Julie M. Allen – PeerJ

Plant, root, and soil microbiome

Patterns of natural fungal community assembly during initial decay of coniferous and broadleaf tree logs – Annemieke van der Wal – Ecosphere

Bioinformatics

CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community – Thomas Richard Connor – bioRxiv

More microbiology

Synchronized cycles of bacterial lysis for in vivo delivery – M. Omar Din – Nature

Press: Self-destructing bacteria are engineered to kill cancer cells – Sally Adee – New Scientist

Microbes in the news

Algae are melting away the Greenland ice sheet. ‘Black and Bloom’ project explores how microorganisms help to determine the pace of Arctic melting – Alexandra Witze – Nature

Science, publishing, and career

Featuring Bik’s Picks! Scientific literature: Information overload – Esther Landhuis – Nature

The unsung heroes of CRISPR. The soaring popularity of gene editing has made celebrities of the principal investigators who pioneered the field — but their graduate students and postdocs are often overlooked – Heidi Ledford – Nature

2016 Raymond and Beverly Sackler Prize in Convergence Research: QnAs with Stephen Quake – Prashant Nair – PNAS

Bik’s Picks

5 Questions: Randall Stafford advocates a plant-based diet – INterview with Randall Stafford – Stanford Medicine

July 18, 2016

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Gut bacteria in the lung in case of sepsis or ARDS, metagenomics along a depth gradient, and microbes in peanut processing plants.

Pregnancy and birth

Screening of vulvovaginal infections during pregnancy in resource constrained settings: Implications on preterm delivery – Chaitanya Tellapragada – Journal of Infection and Public Health

Human respiratory microbiome/ Animal experiments

Enrichment of the lung microbiome with gut bacteria in sepsis and the acute respiratory distress syndrome – Robert P. Dickson

Human gut microbiome

Impact of Cranberries on Gut Microbiota and Cardiometabolic Health: Proceedings of the Cranberry Health Research Conference 2015 – Jeffrey B Blumberg – Advances in Nutrition

Review: On the pathogenesis of insulin-dependent diabetes mellitus: the role of microbiota – Elena Gianchecchi – Immunologic Research

Plant, root, and soil microbiome

Arbuscular mycorrhizal fungi induced changes in rhizosphere, essential oil and mineral nutrients uptake in dill/common bean intercropping system – W. Weisany – Annals of Applied Biology

Water and extremophile microbiome

Comparative metagenomics unveils functions and genome features of microbialite-associated communities along a depth gradient – Aurélien Saghaï – Environmental Microbiology

Comparative Analysis of Microbial Communities in Iron-Dominated Flocculent Mats in Deep Sea Hydrothermal Environments – Hiroko Makita – Applied and Environmental Microbiology

Food production microbiology

Microbiological contamination in peanut confectionery processing plants – Joyce de Almeida Carminati – Journal of Applied Microbiology

Microbes in the news

First virus-hunter in space will test DNA-decoding device – STATnews

Microbe of the month: Nanopusillus acidilobi, an archaeon found in Yellowstone National Park – Jennifer Tsang – The Microbial Menagerie

Sewage in the Saluda deserves more attention, politicians, river advocates say – Sammy Fretwell – The State

Science, publishing, and career

The 7 biggest problems facing science, according to 270 scientists – Julia Belluz – Vox

5 health and medicine issues to watch for at the GOP convention – David Nather – STATnews

 

July 16, 2016

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Bacterial translocation in Crohn’s disease, full length sequencing of mouse microbiome, drinking water and IBD, NanoSIMS, and molecular interactions.

Events
Meet your microbes: The surprising world inside you – New Scientist / UNSW Science – August 13, 2016, Kensington, Australia. Speakers: Elisa Hill and Gabrielle Belz.

Pregnancy and birth / vaginal microbiome

Identification of a novel human papillomavirus by metagenomic analysis of vaginal swab samples from pregnant women – Zhijian Liu – Virology Journal

Human skin microbiome

Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare – Kern Rei Chng – Nature Microbiology

Human oral microbiome

Bacterial diversity and community structure of supragingival plaques in adults with dental health or caries revealed by 16S pyrosequencing – Cuicui Xiao – Frontiers in Microbiology

Profile of bacteria colonizing the exposed bone of patients with anti-osteoclastic drug-related osteonecrosis of the jaws – Zaher Jabbour – Canadian Journal of Microbiology

Human respiratory microbiome

Review: The Lung Microbiome in HIV. Getting to the HAART of the Host–Microbe Interface – Leopoldo N. Segal – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

Environmental Factors Associated with Altered Gut Microbiota in Children with Eczema: A Systematic Review – Carmen W. H. Chan – International Journal of Molecular Sciences

Fecal Microbiota and Diet of Children with Chronic Constipation – Joyce Gomes de Moraes – International Journal of Pediatrics

The predominant site of bacterial translocation across the intestinal mucosal barrier occurs at the advancing disease margin in Crohn’s disease – Rodrick J. Chiodini – Microbiology

Review: May the Force Be With You: The Light and Dark Sides of the Microbiota–Gut–Brain Axis in Neuropsychiatry – Eoin Sherwin – CNS Drugs

Animal experiments

Gut Microbial Alterations Associated With Protection From Autoimmune Uveitis – Yukiko K. Nakamura – Investigative Ophthalmology & Visual Science

Animal microbiome

Isolation of an antimicrobial compound produced by bacteria associated with reef-building corals – PeerJ Preprint

Evidence of a bacterial core in the stored products pest Plodia interpunctella: The influence of different diets – Matteo Montagna – Environmental Microbiology

Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing – 
Jongoh Shin – Scientific Reports

Comparative phylogenetic analysis of bacterial associates in Pyrrhocoroidea and evidence for ancient and persistent environmental symbiont reacquisition in Largidae (Hemiptera: Heteroptera) – Eric Robert Lucien Gordon – bioRxiv

Plant, root, and soil microbiome

Strong linkage between plant and soil fungal communities along a successional coastal dune system – Alice Roy-Bolduc – FEMS Microbiology Ecology

Biodiversity of green algae covering artificial hard substrate surfaces in a suburban environment: A case study using molecular approaches – Christine Hallmann – Journal of Phycology

Bacterial selection by mycospheres of Atlantic Rainforest mushrooms – Joshua Andrew Halsey – Antonie van Leeuwenhoek

Bacterial Community Structure at the Microscale in Two Different Soils – Rory Michelland – Microbial Ecology

Diversity of Cultivated Fungi Associated with Conventional and Transgenic Sugarcane and the Interaction between Endophytic Trichoderma virens and the Host Plant – Aline Silva Romão-Dumaresq – PLOS ONE

Water and extremophile microbiome

Genomic and transcriptomic resolution of organic matter utilization among deep-sea bacteria in Guaymas Basin hydrothermal plumes – Meng Li – Frontiers in Microbiology

Microbiome profiling of drinking water in relation to incidence of inflammatory bowel disease – Jessica D. Forbes – Canadian Journal of Microbiology

Viruses and phages

The feral swine virome is dominated by single stranded DNA viruses and contains a novel orthopneumovirus which circulates both in feral and domestic swine – Ben M. Hause – Journal of General Virology

Techniques

Review: Tracking microbial interactions with NanoSIMS – Niculina Musat – Current Opinion in Biotechnology

Other microbiology

Review: Decoding molecular interactions in microbial communities – Nicole A. Abreu – FEMS Microbiology Reviews

Functional Comparison of Bacteria from the Human Gut and Closely Related Non-Gut Bacteria Reveals the Importance of Conjugation and a Paucity of Motility and Chemotaxis Functions in the Gut Environment – Dragana Dobrijevic – PLOS ONE

Verification of an automated, digital dispensing platform for at-will broth microdilution antimicrobial susceptibility testing – Kenneth P. Smith – Journal of Clinical Microbiology

Press: Simple method tests hard-to-treat bacteria’s susceptibility to different antibiotics – Science Codex

Nice or nasty: Protein translocation between bacteria and the different forms of response – Daniel Unterweger – PNAS

Editorial: Resource competition: When communities collide – Jason Merritt – eLIFE

Community-level cohesion without cooperation – Mikhail Tikhonov – eLIFE

Microbes in the news

Overselling the Microbiome Award for @nytimes on thumb sucking, nail biting protecting from allergy – Jonathan Eisen – The Tree of Life

Study to explore microbes attached to floating plastic – Holly Ganz – MicroBE.net

Gut reaction: How bacteria in the belly may affect the heart – Harvard Health

You scratch my back… the beneficial (and not so beneficial) relationships between organisms – Andrew Taylor-Robinson – The Conversation

Viruses Have Guided the Path of Human Evolution – Nathaniel Scharping – Discover Magazine

Antarctica: A Center for Climate Change and Microbiology Research – Latin America Herald Tribune

Science, publishing, and career

Where are the female science professors? A personal perspective – Shina Caroline Lynn Kamerlin – F1000Research

Bik’s Picks

Carl Zimmer’s Game Of Genomes: Episode 1 to 5 – STATnews

July 14, 2016

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Gut microbes and diabetes risk, llama sausages, urban greenness, and the sea turtle microbiome.

Pregnancy and birth

The Infant Gut Bacterial Microbiota and Risk of Pediatric Asthma and Allergic Diseases – Christine Cole Johnson – Translational Research

Human gut microbiome

Human gut microbes impact host serum metabolome and insulin sensitivity – Helle Krogh Pedersen – Nature

Press: Gut bacteria imbalance increases diabetes risk – EurekAlert
Gut bacteria imbalance increases diabetes risk – BioMed Central blog

Effects of Gut Microbiota Manipulation by Antibiotics on Host Metabolism in Obese Humans: A Randomized Double-Blind Placebo-Controlled Trial – Dorien Reijnders – Cell Metabolism

The Gut Microbiota from Lean and Obese Subjects Contribute Differently to the Fermentation of Arabinogalactan and Inulin – Marisol Aguirre – PLOS ONE

Review: The esophageal microbiota in health and disease – Vincenzo Di Pilato – Annals of the New York Academy of Sciences

Review: Colon microbiota fermentation of dietary prebiotics towards short-chain fatty acids and their roles as anti-inflammatory and antitumour agents: A review – Javier Fernández – Journal of Functional Foods

Animal and other experiments

Microbial Mat Functional and Compositional Sensitivity to Environmental Disturbance –
Eva Christine Preisner – bioRxiv

Gut microbiota directs PPARγ-driven reprogramming of the liver circadian clock by nutritional challenge – Mari Murakami – EMBO Reports

Preview: Microbially Produced Acetate: A “Missing Link” in Understanding Obesity? – Chad M. Trent – Cell Metabolism

Plant, root, and soil microbiome

Glyphosate and aminomethylphosphonic acid chronic risk assessment for soil biota – Georg von Mérey – Environmental Toxicology and Chemistry

Zonal Soil Type Determines Soil Microbial Responses to Maize Cropping and Fertilization – Mengxin Zhao – mSystems

Built environment microbiome

Urban greenness influences airborne bacterial community composition – Gwynne Mhuireach – Science of The Total Environment

Research Watch: Dirty environment for adult life: the bad, the good, the unknown – Jun Sun – Genes & Diseases

Food microbiology

Microbial ecology involved in the ripening of naturally fermented llama meat sausages. A focus on lactobacilli diversity – Fontana Cecilia – International Journal of Food Microbiology

Metabolomics

Free eBook: Metabolomics – A Key Technology for Microbiome Research – Kirk Beebe – Metabolon

Techniques

Evaluation of VITEK matrix-assisted laser desorption ionization–time of flight mass spectrometry for identification of anaerobes – Zheng Xiao – Microbiology and Immunology

Fungal identification biases in microbiome projects – Leho Tedersoo – Environmental Microbiology Reports

Rapid and Selective Detection of Pathogenic Bacteria in Bloodstream Infection with Aptamer-based Recognition – Haijing Shen – Applied Materials and Interfaces

Microbes in the news

Project to study sea turtle microbiomes in captivity and in the wild – Holly Ganz – MicroBEnet

Gonorrhea may soon become resistant to all antibiotics and untreatable – Helen Branswell – STAT news

Bacteriophage Therapy Grows as Alternative to Antibiotics – Michael McGrady – Heartland

Getting to the guts: Studying the gut microbiome to manage pain – Shay Stowell – Missouri State University

Career

Men cite themselves more than women do. The apparent trend has been on the rise over the past two decades – Dalmeet Singh Chawla – Nature

Bik’s non-microbiology Picks

A Gathering of Giants. A photographer slips into the ocean to swim among hundreds of sperm whales – witnessing a rarely seen social spectacle – Tony Wu – Biographic

The people who don’t get ‘Eleanor Rigby’. Happy music and sad sounds are not universal. – Nature

July 13, 2016

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So many great new papers that it’s hard to choose! Liver quickly clears bacteria from blood, microbiology of death, mobile genes in human microbiomes from Fiji and the USA, Splenda makes fly more hungry, feather degrading bacilli, underwater microscopy, and what is being transferred in a stool transplant.

Events and jobs

Annual Meeting of the Microbial Ecology Division – November 4, 2016, Nijmegen, The Netherlands

Senior/Tenure Track scientists for the Department of Marine Microbiology and Biochemistry – NIOZ The Netherlands

Microbiome of Death

“Biology of Death” Special Issue – Current Biology
Microbiology of death – Jessica L. Metcalf
Also read (non-microbiology but sadly beautiful): Death and the octopus – Florian Maderspacher

Also appropriate in this category is this video protocol: Removal of Exogenous Materials from the Outer Portion of Frozen Cores to Investigate the Ancient Biological Communities Harbored Inside – Robyn A. Barbato – JOVE

Pregnancy and birth

Early Life Antibiotic Exposure and Weight Development in Children – Catherine A. Mbakwa – The Journal of Pediatrics

Preview: Tummy Time: The Infant Microbiota–IgA Connection – Tyler A. Rice – Cell Host & Microbe

Review: The microbiome in early life: implications for health outcomes – Sabrina Tamburini – Nature Medicine

Special issue with abstracts from the 3rd International Congress on Pre- and Probiotics
in Journal of Pediatric Gastroenterology and Nutrition

A Prebiotic Formula Improves the Gastrointestinal Bacterial Flora in Toddlers – Ya-Ling Chen – Gastroenterology Research and Practice

Human blood “microbiome”

Editorial: Fast-Track Clearance of Bacteria from the Liver – Cristina Llorente – Cell Host & Microbe
Dual-Track Clearance of Circulating Bacteria Balances Rapid Restoration of Blood Sterility with Induction of Adaptive Immunity – Steven P. Broadley – Cell Host & Microbe
CRIg Functions as a Macrophage Pattern Recognition Receptor to Directly Bind and Capture Blood-Borne Gram-Positive Bacteria – Zhutian Zeng – Cell Host & Microbe

Human skin microbiome

What if scalp flora was involved in sensitive scalp onset? – A. Guichard – International Journal of Cosmetic Science

Human gut microbiome

Mobile genes in the human microbiome are structured from global to individual scales – I. L. Brito – Nature

Press: Microbiome ‘social network’ revealed by gene swaps
Movement of genes across and between microorganism species could influence humans’ susceptibility to disease – Peter Andrey Smith – Nature News

Fecal Transplants: What Is Being Transferred? – Diana P. Bojanova – PLOS Biology

Press: Poo transplants transfer much more than bacteria. Viruses, fungi – even sloughed colon cells – may affect how well a faecal transplant works – Belinda Smith – Cosmos

Animal experiments

Sucralose Promotes Food Intake through NPY and a Neuronal Fasting Response – Qiao-Ping Wang – Cell Metabolism

Press: Artificial sweeteners trick flies into thinking they’re starving – Lindzi Wessel – STAT News

Investigation into Host Selection of the Cecal Acetogen Population in Rabbits after Weaning – Chunlei Yang – PLOS ONE

Animal microbiome

Genome evolution in the obligate but environmentally active luminous symbionts of flashlight fish – Tory A. Hendry – Genome Biology and Evolution

Deep divergence and rapid evolutionary rates in gut-associated Acetobacteraceae of ants – Bryan P. Brown – BMC Microbiology

Feather-degrading bacilli in the plumage of wild birds: Prevalence and relation to feather wear – Cody M. Kent – The Auk Ornithological Advances

Press: Feather-munching bacteria damage wild bird plumage – EurekAlert

Multi-scale ecological filters shape the crayfish microbiome – James Skelton – PeerJ Preprint

Plant, root, and soil microbiome

Rapid response of arbuscular mycorrhizal fungal communities to short-term fertilization in an alpine grassland on the Qinghai-Tibet Plateau – Xingjia Xiang – PeerJ

High-throughput sequencing of 16S rRNA Gene Reveals Substantial Bacterial Diversity on the Municipal Dumpsite – Kilaza Samson Mwaikono – BMC Microbiology

Temporal and Spatial Variation of Soil Bacteria Richness, Composition, and Function in a Neotropical Rainforest – Stephanie N Kivlin – PLOS ONE

Land use intensification in the humid tropics increased both alpha and beta diversity of soil bacteria – Teotonio Soares de Carvalho = Ecology

The role of arbuscular mycorrhizal fungi in plant uptake, fractions, and speciation of antimony – Yuan Wei – Applied Soil Ecology

Review: Bidirectional Interaction between Phyllospheric Microbiotas and Plant Volatile Emissions – Gerard Farré-Armengol – Trends in Plant Science

Water microbiome

Underwater microscopy for in situ studies of benthic ecosystems – Andrew D. Mullen – Nature Communications

Press: Underwater microscope provides new views of ocean-floor sea creatures in their natural setting – Jules Jaffe – The Conversation

Identifying the key taxonomic categories that characterize microbial community diversity using full-scale classification: a case study of microbial community in the sediments of Hangzhou Bay – Tianjiao Dai – FEMS Microbiology Ecology

Novel acsF gene primers revealed a diverse phototrophic bacterial population including Gemmatimonadetes in the Lake Taihu – Yili Huang – Applied and Environmental Microbiology

Allelopathic interactions involving benthic phototrophic microorganisms – Joey L. Allen – Environmental Microbiology Reports

Metagenomics and bioinformatics

Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond – Satoshi Hiraoka – Microbes and Environments

Metabolites

Research Highlight: Keeping microbial metabolites at bay – Andrea Du Toit – Nature Reviews Microbiology

Techniques

New Primers for Discovering Fungal Diversity Using Nuclear Large Ribosomal DNA – Asma Asemaninejad – PLOS ONE

Not sure what is new here, but: Multiplex amplicon sequencing for microbe identification in community-based culture collections – Jaderson Silveira Leite Armanhi – Scientific Reports

Applying CRISPR–Cas9 tools to identify and characterize transcriptional enhancers – Rui Lopes – Nature Reviews Molecular Cell Biology

Phages and viruses

Perspective: Piggyback-the-Winner in host-associated microbial communities – Cynthia B Silveira – NPJ Biofilms

Microbes in the news

Fill Your House With Microbes and Live With an Animal, Say Yale Researchers – Drake Baer

Unfortunately, no update from his DIY stool transplant with Hadza feces: The Human Microbiome as Road Kill in the Age of the Anthropocene – Jeff Leach – Human Food Project

Studies find that manipulating gut microbes may reverse the negative effect of a high fat – EurekAlert

Archaea: Breakthrough in Reconstruction of Warm Climate Phases – Marine Technology News

Alarming Antibiotic-Resistant Superbug Discovered In NYer’s Bacteria Sample – Miranda Katz – Gothamist

How bacteria can help prospectors find oil – Fram Dinshaw – The Chronicle Herald

With link to video: Tiny ‘racetracks’ show how bacteria get organized – EurekAlert

Microbes and Money

uBiome and University of Oxford Investigate the Relationship Between the Human Microbiome and Personality – PR web

Commercializing the Microbiome: No Guts, No Glory – Michael Darcy – DRG

Evelo and Epiva Merge to Become a Leading Immuno-Microbiome Platform Company – BioSpace

Merck to open new Cambridge facility for microbiome research this year – Boston Business Journal

Science, publishing, and career

How Australia fails mid-career scientists – Catherine Osborne – ABC Australia

How President Obama could really lead on open access – Michael Eisen – it is NOT junk

Where are all the award winning women scientists? – Tenure, she wrote

Bik’s Picks

Organ delivery by 1,000 drones – Michael Francisco – Nature Biotechnology

 

July 9, 2016

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

Pregnancy and birth

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

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

Human oral microbiome

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

Human respiratory microbiome

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

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

Human gut microbiome

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

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

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

Animal experiments

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

Animal microbiome

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

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

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

Plants, roots, and soil microbiome

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

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

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

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

Water and extremophile microbiome

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

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

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

Built environment microbiome

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

Bioreactors

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

Biofilms

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

Bioinformatics and metagenomics

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

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

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

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

Proteomics

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

Bik’s Picks

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

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

 

 

July 7, 2016

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Genetic variation and airway microbiome, Thai vegetarians, social wasps carry local yeast strains, classifying infections by host response, profiling of arbuscular mycorrhizal fungi.

Pregnancy and birth

Research Highlight: First steps in the infant gut microbiota – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Human respiratory microbiome

Host genetic variation in mucosal immunity pathways influences the upper airway microbiome – Catherine Igartua – bioRxiv

Human gut microbiome

A Disease-associated Microbial and Metabolomics State in Relatives of Pediatric Inflammatory Bowel Disease Patients – Jonathan P. Jacobs – CMGH Cellular and Molecular Gastroenterology and Hepatology

Microbial community of healthy Thai vegetarians and non-vegetarians, their core gut microbiota and pathogens risk – Supatjaree Ruengsomwong – Journal of Microbiology and Biotechnology

Animal experiments

Personality composition alters the transmission of cuticular bacteria in social groups – Carl N. Keiser – Biology Letters

Oat products modulate the gut microbiota and produce anti-obesity effects in obese rats – Ji-lin Dong – Journal of Functional Foods

Animal microbiome

Social wasp intestines host the local phenotypic variability of Saccharomyces cerevisiae strains – Leonardo Dapporto – Yeast

Spatial and temporal investigation of the microbiome of the Caribbean octocoral Erythropodium caribaeorum – Erin P McCauley – FEMS Microbiology Ecology

Bacterial and fungal symbionts of parasitic Dendroctonus bark beetles – Loïc Dohet – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Active microorganisms in forest soils differ from the total community yet are shaped by the same environmental factors: the influence of pH and soil moisture – Karl J. Romanowicz – FEMS Microbiology Ecology

High-resolution community profiling of arbuscular mycorrhizal fungi – Klaus Schlaeppi – New Phytologist

Mycorrhizal associations and soil properties of native Allanblackia stuhlmannii stands in the Eastern Usambara Mountains, Tanzania – P. Fransson – Annals of Applied Biology

Hierarchical neighbor effects on mycorrhizal community structure and function – Holly V. Moeller – Ecology and Evolution

Review: The role of plant-microbiome interactions in weed establishment and control – F. Trognitz – FEMS Microbiology Ecology

Water and extremophile microbiome

Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya – Anne Kelly Kambura – BMC Microbiology

Spatial distribution of aquatic marine fungi across the western Arctic and sub-arctic – Brandon T. Hassett – Environmental Microbiology

Metagenomics and bioinformatics

Metagenome Mining: A Sequence Directed Strategy for the Retrieval of Enzymes for Biocatalysis – Jack W. E. Jeffries – Chemistry Select

Reaching saturation in 16S rRNA sequences: After All, Only Millions? – Rudolf Amann – mBio

More microbiology

Robust classification of bacterial and viral infections via integrated host gene expression diagnostics – Timothy E. Sweeney – Science Translational Medicine

Press: A Blood Test To Determine When Antibiotics Are Warranted: Scientists can assay gene activity to distinguish between bacterial and viral infections – Alison F. Takemura – The Scientist

Editorial: Linking Ecosystem Function to Microbial Diversity – Anne E. Bernhard – Frontiers in Microbiology

Microbes in the news

Meet Angus, the C. difficile-sniffing dog trained to detect superbugs – CBC News

Researchers, farmers collaborate to prevent E. coli – Science Daily

How the bacterial protective shell is adapted to challenging environments – Phys.org

Could E.Coli be used to fight disease? Bacteria could transport next-generation vaccines, experts reveal – Daily Mail

Single microbe may restore social behaviors in mice – Ann Griswold – Spectrum

High Demand For Antibiotics Leads To Growth In Microbiology Culture Industry In United States – MedGadget

Discovery of new bacterium brings laurels to Palamuru University – The Hindu

July 1, 2016

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NIH’s Lita Proctor writes about the Human Microbiome Project, oral microbiome among Cheyenne and Arapaho, Cystic Fibrosis, responses to resistant starch, the Swan Goose, sugarcane, litter decomposition.

General microbiome

Review: The National Institutes of Health Human Microbiome Project – Lita M. Proctor – Seminars in Fetal and Neonatal Medicine

Pregnancy and birth

Early-Life Events, Including Mode of Delivery and Type of Feeding, Siblings and Gender, Shape the Developing Gut Microbiota – Rocio Martin – PLOS ONE

Human oral microbiome

Oral microbiome diversity among cheyenne and arapaho individuals from Oklahoma – Andrew T. Ozga – American Journal of Physical Anthropology

Human respiratory microbiome

Pyrosequencing Unveils Cystic Fibrosis Lung Microbiome Differences Associated with a Severe Lung Function Decline – Giovanni Bacci – PLOS ONE

Human skin microbiome

The skin microbiome is different in pediatric versus adult atopic dermatitis –
Baochen Shi – Journal of Allergy and Clinical Immunology

Just colony counts: Chlorhexidine avoids skin bacteria recolonization more than triclosan – Juan H. Macias – American Journal of Infection Control

Human gut microbiome

Variable responses of human microbiomes to dietary supplementation with resistant starch – A. Venkataraman – Microbiome

Duodenal bacteria from patients with celiac disease and healthy subjects distinctly affect gluten breakdown and immunogenicity – Alberto Caminero – Gastroenterology

Predominance of Lactobacillus spp. among patients who do not acquire multidrug-resistant organisms – Rafael Araos – Clinical Infectious Diseases

Nutrition and the Microbiome: Special Edition of the Annals of the New York Academy of Sciences
Review: Nutrition and the microbiome – Karin Moelling
Review: Nutrition meets the microbiome: micronutrients and the microbiota – Hans K. Biesalski

Letter: Microbiota and Alcoholic Liver Disease – Peng Chen – Alcoholism: Clinical and Experimental Research

Animal experiments

Sex differences and hormonal effects on gut microbiota composition in mice – Elin Org – Gut Microbes

Animal microbiome

Distinctive gut microbial community structure in both the wild and farmed Swan goose (Anser cygnoides) – Wen Wang – Journal of Basic Microbiology

The gut microbiome of the sea urchin, Lytechinus variegatus from their natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles – Joseph A. Hakim – FEMS Microbiology Ecology

Analysis of microbiota on abalone (Haliotis discus hannai) in South Korea for improved product management – Min-Jung Lee – International Journal of Food Microbiology

Bacterial endosymbionts protect aphids in the field and alter parasitoid community composition – Lukas Rothacher – Ecology
Midgut fungal and bacterial microbiota of Aedes triseriatus and Aedes japonicus shift in response to La Crosse virus infection – Ephantus J. Muturi – Molecular Ecology

Plant, root, and soil microbiome

The importance of C, N and P as driver for bacterial community structure in German beech dominated forest soils – Fabian Bergkemper – Journal of Plant Nutrition and Soil Science

Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome – Rafael Soares Correa de Souza – Scientific Reports

Life in leaf litter: novel insights into community dynamics of bacteria and fungi during litter decomposition – Witoon Purahong – Molecular Ecology

Endophytic microbial diversity of the halophyte Arthrocnemum macrostachyum across plant compartments – M. del R. Mora-Ruiz – FEMS Microbiology Ecology

Conference abstract: High diversity of enzymes in plant-associated microbiomes – Christina A. Müller – New Biotechnology

Review: Plant-Mediated Systemic Interactions Between Pathogens, Parasitic Nematodes, and Herbivores Above- and Belowground – Arjen Biere – Annual Review of Phytopathology

Unearthed! The Amazing Microbiome Exposed: Editor’s Note – Stephen L. Young – Bulletin of the Ecological Society of America
Unearthed! The Amazing Microbiome Exposed: The Arising Researcher – Marnie E. Rout
Unearthed! The Amazing Microbiome Exposed: The Established Researcher – John Klironomos

Water microbiome

Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments – Benjamin J. Tully – Applied and Environmental Microbiology

Built environment microbiome

Evidence of Avian and Possum Fecal Contamination in Rainwater Tanks as Determined by Microbial Source Tracking Approaches – W. Ahmed – Applied and Environmental Microbiology

Factors Influencing Bacterial Diversity and Community Composition in Municipal Drinking Waters in the Ohio River Basin, USA – Lee F. Stanish – PLOS ONE

Microbes in space

Review: Venturing into new realms? Microorganisms in space – Christine Moissl-Eichinger – FEMS Microbiology Reviews

Techniques

Simultaneous purification of DNA and RNA from microbiota in a single colonic mucosal biopsy – Aina E. F. Moen – BMC Research Notes

Microbes in the news

The North American Beaver: Castor canadensis : A look at our local Canadian friend’s microbes – Megan McGrath – Genotek’s The Microbiome Snapshot

Human Microbiome Market : Growth, Development, and Outlook 2014 – 2020 – SB Wire

uBiome Completely Re-Imagines Microbiome Experimentation with New Launch – PR Web

Bacteria prevents mosquitoes from spreading Zika, UW-Madison study says – Wisconsin State Journal

Study sheds more light on how bacteria rapidly causes infectious diseases – News Medical

Gut bacteria spotted eating brain chemicals for the first time – Andy Coghlan – New Scientist

Large Grant to Research on Bacteria in the Nose – Statens Serum Institute

Science, publishing, and career

Great and funny read: Some things you need to know about Google Scholar – Mark Dingemans – Ideophone

June 28, 2016

Posted on by

A fundraiser to study the turtle microbiome, multiple sclerosis, generalists inside specialist, and visualizing translational activity.

Events

IndieGoGo campaign: TurtleTracts: Study Microbes to Save Sea Turtles – Aubrey Tauer

Also see this blog post: Sneak Peak at our Sea Turtle Microbiome Initiative – Aubrey Tauer

Pregnancy and birth

Gut bacteria and late-onset neonatal bloodstream infections in preterm infants – Phillip I. Tarr – Seminars in Fetal and Neonatal Medicine

Human respiratory microbiome

Commentary: Mode of delivery to the brave new (microbial) world: a defining moment for the respiratory microbiome? – Georgios D. Kitsios – EBioMedicine

Human gut microbiome

Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls – Jun Chen – Scientific Reports

Press: Link between gut bacteria, MS discovered. MS patients show lower levels of good bacteria – Science Daily

Review: Microbiota as Therapeutic Targets – Xavier R.J. – Digestive Diseases

Animal microbiome
The Generalist Inside the Specialist: Gut Bacterial Communities of Two Insect Species Feeding on Toxic Plants Are Dominated by Enterococcus sp. – Cristina Vilanova – Frontiers in Microbiology

Review: The gut microbiome as a virtual endocrine organ with implications for farm and domestic animal endocrinology – T.F. O’Callaghan – Domestic Animal Endocrinology

Plant, root, and soil microbiome
Systemic enrichment of antifungal traits in the rhizosphere microbiome after pathogen attack – Jan-Hendrik Dudenhöffer – Journal of Ecology

A multi-biological assay approach to assess microbial diversity in arsenic (As) contaminated soils – S.R. Stazi – Geomicrobiology Journal

Effects of two fungicide formulations on microbial and macroinvertebrate leaf decomposition under laboratory conditions – Adria A. Elskus – Environmental Toxicology and Chemistry

Book: Plant, Soil and Microbes – Editors: Khalid Rehman Hakeem, Mohd Sayeed Akhtar – Springer

Water and extremophile microbiome

Metagenomics-Guided Mining of Commercially Useful Biocatalysts from Marine Microorganisms – A.R. Uria – Advances in Food and Nutrition Research

Lessons learned from thirty years of geomicrobiological studies of Río Tinto – Ricardo Amils – Research in Microbiology

Metabolic diversity and adaptive mechanisms of iron- and/or sulfur-oxidizing autotrophic acidophiles in extremely acidic environments – Xian Zhang – Environmental Microbiology Reports

Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill – Nina Dombrowski – Nature Microbiology

News and views: Marine microbiology: Community clean up – Rachel Mackelprang – Nature Microbiology

Assessing viral taxonomic composition in benthic marine ecosystems: reliability and efficiency of different bioinformatic tools for viral metagenomic analyses – M. Tangherlini – Scientific Reports

Marine phage genomics: the tip of the iceberg – Blanca Perez Sepulveda – Microbiology Letters

Metabolic networks and proteomics

MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota – Xu Zhang – Microbiome

The use of propidium monoazide in conjunction with qPCR and Illumina sequencing to identify and quantify live yeasts and bacteria – Mansak Tantikachornkiata – International Journal of Food Microbiology

Protocol: Constructing and Analyzing Metabolic Flux Models of Microbial Communities – José P. Faria – Springer Protocols

Viruses and phages

Opinion: The Janus-Face of Bacteriophages across Human Body Habitats – Adam Wahida – PLOS Pathogens

Review: Research on the human virome: where are we and what is next – Shimian Zou – Microbiome

Microbial ecology and techniques

Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia – Roland Hatzenpichler – PNAS

Press: See and sort: Developing novel techniques to visualize uncultured microbial cell activity – Science Daily

High functional diversity stimulates diversification in experimental microbial communities – Alexandre Jousset – Science Advances

Measuring the biodiversity of microbial communities by flow cytometry – Ruben Props – Methods in Ecology and Evolution

Highlight: A timely reminder of technical limitations – James I. Prosser – Microbial Biotechnology

Species-sorting and mass-transfer paradigms control managed natural metacommunities – Susanne Günther – Environmental Microbiology

Microbes in the news

Slimy clumps of bacteria kill thousands. Scientists are fighting back – Usha Lee McFarling – STAT News

Why everyone’s suddenly talking about gut bacteria – Laura Entis – Fortune

Scientists find link between makeup of individual’s microbiome and head and neck cancer – News Medical

June 27, 2016

Posted on by

A short Monday post. Bronchiolitis and virome milestones in infants, and playing drums.

Pregnancy and birth

The Fecal Microbiota Profile and Bronchiolitis in Infants – Kohei Hasegawa – Pediatrics

Editorial: Do Bacteria in the Gut Set the Stage for Who Gets Viral Bronchiolitis and Its Severity? – Patrick C. Seed – Pediatrics

Research Highlight: Distinct Fecal Microbiota Pattern Associated with Infant Bronchiolitis – Christine Judge – NEJM Journal Watch

The Bacterial Microbiome and Virome Milestones of Infant Development – Efrem S. Lim – Trends in MIcrobiology

More microbiology

Is there an Infection Risk when Playing Drums Contaminated with Bacillus anthracis? –
A M Bennett – Journal of Applied Microbiology

Microbes in the news

UI researcher finds link between gut bacteria and MS. MS patients show lower levels of good bacteria – EurekAlert

Microbes in extreme heat and cold hold lessons about life on Earth, and beyond – Don Cowan – The Conversation

Olympic rowers unveil special suits to combat bacteria in Rio – WHEC

Pineapples Can Stop Harmful Bacteria In The Gut – Diane Palmer – Parent Herald