Category Archives: Human respiratory

July 28, 2016

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Maternal HIV status and infant microbiome development, nose bacteria producing antibiotics, gases produced by gut microbes, microbial mats in Hawaiian lava caves.

Pregnancy and birth

Maternal HIV infection influences the microbiome of HIV-uninfected infants – Jeffrey M. Bender – Science Translational Medicine

Press: Maternal HIV status may disrupt normal microbiome development in uninfected infants – Medical Xpress

Human respiratory microbiome

Human commensals producing a novel antibiotic impair pathogen colonization – Alexander Zipperer – Nature

Press: Scientists are looking everywhere, and we mean everywhere, for new antibiotics – Katherine Ellen Foley – Quartz
Nose-Dwelling Bacteria Could Be Antibiotic Factories, Study Says – Robert Lee Hotz – Wall Street Journal

Human vaginal microbiome

Desialylation of Neisseria gonorrhoeae Lipooligosaccharide by Cervicovaginal Microbiome Sialidases: The Potential for Enhancing Infectivity in Men – Margaret R. Ketterer – Journal of Infectious Diseases

Does the cervicovaginal microbiome facilitate transmission of Neisseria gonorrhoeae from women to men? Implications for understanding transmission of gonorrhea and advancing vaccine development – William M. Shafer – Journal of Infectious Diseases

Human gut microbiome

Review: Neuromodulatory effects and targets of the SCFAs and gasotransmitters produced by the human symbiotic microbiota –  Alexander V. Oleskin – Microbial Ecology in Health and Disease

Press: Explosive new findings: Farting shown to play a role in regulating your brain and behavior – Kelly Hodgkins – Yahoo Tech

Review: Progress in Our Understanding of the Gut Microbiome: Implications for the Clinician – Sara Iqbal – Current Gastroenterology Reports

 
Animal microbiome

Testosterone levels are positively correlated with cloacal bacterial diversity and the relative abundance of Chlamydiae in breeding male rufous-collared sparrows – Camilo Escallón – Functional Ecology

Review: The rich somatic life of Wolbachia – Jose E. Pietri – MicrobiologyOpen

Plant, root, and soil microbiome

Diversity of root-associated arbuscular mycorrhizal fungal communities in a rubber tree plantation chronosequence in Northeast Thailand – Laetitia Herrmann – Mycorrhiza

Bromeliad tanks are unique habitats for microbial communities involved in methane turnover – Franziska B. Brandt – Plant and Soil

Soil compartment is a major determinant of the impact of simulated rainfall on desert microbiota – Shazia N. Aslam – Environmental Microbiology

Assessing Fungal Population in Soil Planted with Cry1Ac and CPTI Transgenic Cotton and Its Conventional Parental Line Using 18S and ITS rDNA Sequences over Four Seasons – Xiemin Qi – Frontiers in Plant Science

Systems-level proteomics of two ubiquitous leaf commensals reveals complementary adaptive traits for phyllosphere colonization – Daniel B. Müller – Molecular and Cellular Proteomics

Water and extremophile microbiome

(PDF) Microbial mat communities in Hawaiian lava caves – Michael N. Spilde – International Symposium on Vulcanospeleology

Poster, abstract only: Microbial Diversity of Culinary Salts – Galen Muske – Utah Space Grant Consortium

Built environment microbiome

Influence of carbon sources and concrete on microbially induced corrosion of carbon steel in subterranean groundwater environment – Pauliina Rajala – Corrosion

Bioinformatics and metagenomics

MBMC: An Effective Markov Chain Approach for Binning Metagenomic Reads from Environmental Shotgun Sequencing Projects – Wang Ying – OMICS: A Journal of Integrative Biology

Scalable metagenomics alignment research tool (SMART): a scalable, rapid, and complete search heuristic for the classification of metagenomic sequences from complex sequence populations – Aaron Y. Lee – BMC Bioinformatics

Review: Computational Biology in the 21st Century: Scaling with Compressive Algorithms – Bonnie Berger – Communications of the ACM

Microbes in the news

Five new studies will examine how the trillions of tiny organisms that call our bodies home can impact health – University at Buffalo

NASA releases ‘Microbiomics: The Living World In and On You’ – Video highlights Twins Study microbiome investigation – EurekAlert

The Olympians can leave. Brazil’s poor live with filthy, reeking water every day – Melissa Bailey – STAT News

Bizarre bacteria causing major cattle disease named by researchers – Pajaroellobacter abortibovis causes “foothill abortion disease” –  Science Daily

Bik’s non-microbiology Picks

From Impossible Foods, co-founded by Patrick Brown, a former Stanford professor: Impossible burger: New York’s latest food craze is a veggie burger that bleeds – Amanda Holpuch – The Guardian

July 26, 2016

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The last common ancestor, pika gut microbiome, fire-fighting chemicals and soil microbiome, improved Illumina-compatible 18S rRNA primers.

Jobs

Verily (Google-associated) is looking for a Microbiome Research Associate

Pregnancy and birth

Probiotic properties of lactic acid bacteria isolated from human milk – N.A. Reis – Journal of Applied Microbiology

Human oral microbiome

High Throughput Quantitative Method for Assessing Coaggregation among Oral Bacterial Species – Elizabeth Levin-Sparenberg – Letters in Applied Microbiology

Periodontal infectogenomics: systematic review of associations between host genetic variants and subgingival microbial detection – Luigi Nibali – Journal of Clinical Periodontology

Human respiratory microbiome

Upper airway viruses and bacteria and clinical outcomes in children with cough – Kerry-Ann F. O’Grady – Pediatric Pulmonology

Human skin microbiome

Hypothesis: The skin microbiome: Is it affected by UV-induced immune suppression? – Vijaykumar Patra – Frontiers in Microbiology

Human gut microbiome

Gut microbiota-host interactions and juvenile idiopathic arthritis – Miika Arvonen – Pediatric Rheumatology

Designing fecal microbiota transplant trials that account for differences in donor stool efficacy – Scott W. Olesen – bioRxiv

Probiotics and the Microbiome in Celiac Disease: A Randomised Controlled Trial – Joanna Harnett – Evidence-Based Complementary and Alternative Medicine

Review: Links Between the Microbiome and Bone – Christopher J Hernandez – Journal of Bone and Mineral Research

Human vaginal microbiome

More Easily Cultivated Than Identified: Classical Isolation With Molecular Identification of Vaginal Bacteria – Sujatha Srinivasan – The Journal of Infectious Diseases

The Effects of Hormones and Vaginal Microflora on the Glycome of the Female Genital Tract: Cervical-Vaginal Fluid – Bernard J. Moncla – PLOS ONE

Review: New Systems for Studying Intercellular Interactions in Bacterial Vaginosis – Melissa M. Herbst-Kralovetz – The Journal of Infectious Diseases

Animal experiments

Lactulose differently modulates the composition of luminal and mucosal microbiota in C57BL/6J mice – Bingyong Mao – Journal of Agricultural and Food Chemistry

American Ginseng Attenuates Colitis Associated Colon Carcinogenesis in Mice: Impact on Gut Microbiota and Metabolomics – Chong-Zhi Wang – Cancer Prevention Research

Alterations of Gut Microbiota After Roux-en-Y Gastric Bypass and Sleeve Gastrectomy in Sprague-Dawley Rats – Yikai Shao – Obesity Surgery

Animal microbiome

Diet diversity is associated with beta but not alpha diversity of pika gut microbiota – Huan Li – Frontiers in Mcrobiology

The Microbial Signature Provides Insight into the Mechanistic Basis of Coral Success across Reef Habitats – Alejandra Hernandez-Agreda – mBio

Perspective: Hominid superorganisms – Julia A. Segre – Science

Plant, root, and soil microbiome

Long-term response of soil microbial communities to fire and fire-fighting chemicals –
A. Barreiro – Biology and Fertility of Soils

Desert Perennial Shrubs Shape the Microbial-Community Miscellany in Laimosphere and Phyllosphere Space – Varsik Martirosyan – Microbial Ecology

Lichen-associated Fungal Community in Hypogymnia hypotrypa (Parmeliaceae, Ascomycota) Affected by Geographic Distribution and Altitude – Yanyan Wang – Frontiers in Microbiology

Water management impacts rice methylmercury and the soil microbiome – Sarah E. Rothenberg – Science of the Total Environment

Ecological restoration of a copper polluted vineyard: Long-term impact of farmland abandonment on soil bio-chemical properties and microbial communities – Luciano Cavani – Journal of Environmental Management

Review: Soil C and N models that integrate microbial diversity – Benjamin P. Louis – Environmental Chemistry Letters

Water and extremophile microbiome

Genomes of Abundant and Widespread Viruses from the Deep Ocean – Carolina Megumi Mizuno – mBio

Microbial communities associated with Antarctic snow pack and their biogeochemical implications – Runa Antony – Microbiological Research

Novel chytrid lineages dominate fungal sequences in diverse marine and freshwater habitats – André M. Comeau – Scientific Reports

Metabolomics

Review: Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health – Pamela Vernocchi – Frontiers in Microbiology

Functional foods

Review: Fermented Foods: Are They Tasty Medicines for Helicobacter pylori Associated Peptic Ulcer and Gastric Cancer? – Mydhily R. B. Nair – Frontiers in Microbiology

Bioinformatics

A novel alignment-free method for detection of lateral genetic transfer based on TF-IDF – Yingnan Cong – Scientific Reports
Exploring lateral genetic transfer among microbial genomes using TF-IDF – Yingnan Cong – Scientific Reports

Techniques

Design and Evaluation of Illumina MiSeq Compatible Primers for the 18S rRNA Gene for Improved Characterization of Mixed Microalgal Communities – Ian M. Bradley – Applied and Environmental Microbiology

More microbiology

Are multi-omics enough? – Cristina Vilanova – Nature Microbiology

Review: Bacterial Communities: Interactions to Scale – Reed M. Stubbendieck – Frontiers in Microbiology

The physiology and habitat of the last universal common ancestor – Madeline C. Weiss – Nature Microbiology

Press: Scientists find Luca, a single-cell, bacterium-like organism that is the common ancestor of all life on Earth – Andrew Griffin – Independent
Behold LUCA, the Last Universal Common Ancestor of Life on Earth – Jason Daley – Smithsonian
Our last common ancestor inhaled hydrogen from underwater volcanoes – Robert F. Service – Science
Meet Luca, the Ancestor of All Living Things – Nicholas Wade – New York Times

Microbes in the news

What your gut microbiome may be telling you – Katrina Clarke – The Record

Healthy microbiome supports antibiotic-free production – World Poultry

Charlottesville Lab to Test Microbiology of Local Breweries – NBC29

Nanostructured bacterial film makes new mortar resistant to water uptake – NanoWerk

Bik’s non-microbiology Picks

The Dutchies are still holding the top positions! A century of trends in adult human height – NCD Risk Factor Collaboration (NCD-RisC) – eLIFE

July 22, 2016

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

Jobs

Research scientists to engineer microbiome engineering therapies – Eligo Bioscience

General microbiome

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

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

Pregnancy and birth microbiome

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

Human mouth microbiome

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

Human respiratory microbiome

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

Human vaginal microbiome

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

Human gut microbiome

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

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

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

Animal experiments

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

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

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

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

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

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

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

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

Animal microbiome

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

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

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

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

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

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

Plant, root, and soil microbiome

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

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

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

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

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

Water and extremophile microbiome

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

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

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

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

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

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

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

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

Bioinformatics and metagenomics

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

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

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

Microbes in the news

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

Janet Jansson Among Nine Authors of Nature Review Article – PNNL

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

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

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

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

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

Microbes and money

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

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

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

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

July 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 11, 2016

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Poor oral health associated with decreased chance of developing IBD, thumb-sucking associated with decreased chance of developing atopic sensitization, and the core actinobacteriome of rice plants.

Jobs

Senior Scientist intestinal health – Wageningen UR Livestock Research, The Netherlands

Human oral microbiome (sort of)

Inverse Association Between Poor Oral Health and Inflammatory Bowel Diseases – Weiyao Yin – Clinical Gastroenterology and Hepatology

Thumb-Sucking, Nail-Biting, and Atopic Sensitization, Asthma, and Hay Fever – Stephanie J. Lynch – Pediatrics

Human respiratory microbiome

Review: Airway Microbiota and the Implications of Dysbiosis in Asthma – Juliana Durack – Current Allergy and Asthma Reports

Review: Understanding the role of the microbiome in chronic obstructive pulmonary disease: principles, challenges, and future directions – Yvonne J. Huang – Translational Research

Human gut microbiome

Review: Communicating systems in the body: how microbiota and microglia cooperate – Daniel Erny – Immunology

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

Animal and bioreactor experiments

Dietary silver nanoparticles can disturb the gut microbiota in mice – Sybille van den Brule – Particle and Fibre Toxicology

Modelling Longitudinal Metabonomics and Microbiota Interactions in C57BL/6 mice fed a high fat diet – Ivan Montoliu – Analytical Chemistry

High-fiber and high-protein diets shape different gut microbial communities, which ecologically behave similarly under stress conditions, as shown in a gastrointestinal simulator – Massimo Marzorati – Molecular Nutrition & Food Research

Plant, root, and soil microbiome

Plant and insect microbial symbionts alter the outcome of plant-herbivore-parasitoid interactions: implications for invaded, agricultural and natural systems – Alison E Bennett – Journal of Ecology

Influences of plant type on bacterial and archaeal communities in constructed wetland treating polluted river water – Yan Long – Environmental Science and Pollution Research

Illumina-based analysis of core actinobacteriome in roots, stems, and grains of rice – Wenfeng Wang – Microbiological Research

Water microbiome

Comparative metagenome of a stream impacted by the urbanization phenomenon – Julliane Dutra Medeiros – Brazilian Journal of Microbiology

Drinking water systems

A modified weighted mixture model for the interpretation of spatial and temporal changes in the microbial communities in drinking water reservoirs using compositional phospholipid fatty acid data – I. Stanimirova – Talanta

Bioinformatics

An automated system for evaluation of the potential functionome: MAPLE version 2.1.0 – Hideto Takami – DNA Research

Microbes in the news

You Can Contract Fatal Bacteria Just By Sniffing – Angela Chen – Gizmodo
Deadly bug strikes in a day – New pathway discovered for bacteria – EurekAlert

Tiny bacteria-powered ‘windfarm’ for your phone? – Science Daily
Scientists show how bacteria can power micro-machines – Indiana Express

Antibiotic resistance discovered in the guts of ancient mummies – Andy Coghlan – New Scientist

Antibiotic-resistant bacteria have been around for centuries – Karen Graham – Digital Journal

Seres initiates first clinical trial of synthetic microbiome therapy for C. difficile – Healio

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 8, 2016

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The highly anticipated microbiome statistical workflow from the Holmes lab at Stanford, lichen planus, chronic lung disease, and the beneficial microbes of buildings.

Bioinformatics

Preprint, awaiting peer review: Bioconductor workflow for microbiome data analysis: from raw reads to community analyses  – Ben J. Callahan – F1000 Research

Human oral microbiome

The presence of bacteria within tissue provides insights into the pathogenesis of oral lichen planus – Yun Sik Choi – Scientific Reports

Human respiratory microbiome

The microbiota in bronchoalveolar lavage from young children with chronic lung disease includes taxa present in both the oropharynx and nasopharynx – R. L. Marsh – Microbiome

Review: Commensal–Pathogen Interactions along the Human Nasal Passages – Silvio D. Brugger – PLOS Pathogens

Animal experiments

Structural Change in Microbiota by a Probiotic Cocktail Enhances the Gut Barrier and Reduces Cancer via TLR2 Signaling in a Rat Model of Colon Cancer – Eugene Dogkotenge Kuugbee – Digestive Diseases and Sciences

Adaptive immunity against gut microbiota enhances apoE-mediated immune regulation and reduces atherosclerosis and western-diet-related inflammation – Diego Saita – Scientific Reports

Animal microbiome

The Fecal Microbial Communities of Dairy Cattle Shedding Shiga Toxin–Producing Escherichia coli or Campylobacter jejuni – Dong Hee-Jin – Foodborne Pathogens and Disease

Press: Microbiology of cattle poop – Doug Powell – BarfBlog

Characterization of the microbial communities along the gastrointestinal tract of sheep by 454 pyroseqencing analysis – Jin Wang – Asian-Australasian Journal of Animal Sciences

Microbial Composition in Different Gut Locations of Weaning Piglets Receiving Antibiotics – Kaifeng Li – Asian-Australasian Journal of Animal Sciences

Plant, root, and soil microbiome

Source–sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities – James P. J. Hall – PNAS

Built environment microbiome

Review: Buildings, Beneficial Microbes, and Health – Jordan Peccia – Trends in Microbiology

Press: Invite good bacteria into home: scientists – MSN
Should architecture take our microbial health into account? – Coby McDonald – Popular Science

Microbes in the news

Gut Bacteria Are Different in People With Chronic Fatigue Syndrome – Nicholas Bakalar – NY Times

An Algorithm To Predict Which Bacteria Are Good For You. For a more targeted microbiome fix than a fecal transplant – Alexandra Ossola – Vocativ

Purdue students hope new bacteria stops toxic algae blooms – Washington Times

Japanese and Chinese scientists team up against infectious diseases – Tetsuya Abe – Nikkei Asian Review

The Microbiome’s New Frontier: The Rest of the Animal Kingdom – Conservation Magazine

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