Category Archives: Built Environment Microbiology

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 27, 2016

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Gut microbiome in men with pelvic pain, zebrafish stomach motility and bacterial competition, microbiomes of indoor environments, and the Microbial Olympics.

Human gut microbiome

Analysis of Gut Microbiome Reveals Significant Differences between Men with Chronic Prostatitis/Chronic Pelvic Pain Syndrome and Controls – Daniel A. Shoskes – Journal of Urology

Press: Gut Microbiome Diversity Lower in Chronic Pelvic Pain Syndrome – Medical Xpress

Animal and bioreactor experiments

Host Gut Motility Promotes Competitive Exclusion within a Model Intestinal Microbiota – Travis J Wiles – PLOS Biology

Press: Real-time imaging of fish gut ties bacterial competition to gut movements – Science Daily

Microbial Communities are Well Adapted to Disturbances in Energy Input – Nuria Fernandez-Gonzalez – bioRxiv

Built environment microbiome

What Have We Learned about the Microbiomes of Indoor Environments? – Brent Stephens – mSystems

Bioinformatics

Cloud Computing in Bioinformatics: current solutions and challenges – Barbara Calabrese – PeerJ preprint

More microbiology

Discovery of a sesamin-metabolizing microorganism and a new enzyme – Takuto Kumano – PNAS

Microbes in the news

The Microbial Olympics 2016 – Michaeline B. Nelson – Nature Microbiology

New method improves accuracy of microbiome measurement – University of Minnesota

How To Control Eczema? With Fierce Bacterial Competition – Daniel Soo – Asian Scientist

How Miraculous Microbes Help Us Evolve Better, Faster, Stronger – Ed Yong – Smithsonian

Could this household chemical mess with your body’s microbiome? – Brian Mastroianni – CBS News

Research team uses nanoparticles to break up plaque and prevent cavities – Katherine Unger Baillie

This smells promising: Nasal bacteria pump out a new antibiotic that kills MRSA – Anna Vlasits – STAT News

July 24, 2016

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Songbird, soil nitrogen-cycling around the world, and parasites on an ancient butt-wipe stick.

Pregnancy and birth

Dysfunctional gut microbiota and relative co-abundance network in infantile eczema – Heping Wang – Gut Pathogens

Human oral microbiome

Review: From focal sepsis to periodontal medicine: A century of exploring the role of the oral microbiome in systemic disease – Purnima S Kumar – The Journal of Physiology

Human gut microbiome

Review: The Role of the Gut Microbiome on Chronic Kidney Disease – B. Sampaio-Maia – Advances in Applied Microbiology

Review: The Microbiota, Immunoregulation, and Mental Health: Implications for Public Health – Christopher A. Lowry – Current Environmental Health Reports

Animal and other experiments

Insulin resistance, microbiota and fat distribution changes by a new model of vertical sleeve gastrectomy in obese rats – Nicola Basso – Diabetes

Establishment of microbiota in larval culture of Pacific oyster, Crassostrea gigas – Katia Asmani – Aquaculture

Changes in the structure of the microbial community associated with Nannochloropsis salina following treatments with antibiotics and bioactive compounds – Haifeng Geng – Frontiers in Microbiology

Animal microbiome
Social environment has a primary influence on the microbial and odor profiles of a chemically signaling songbird – Danielle J. Whittaker – Frontiers in Ecology and Evolution

16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife – Maxime Galan – mSystems

Plant, root, and soil microbiome

Global biogeography of microbial nitrogen-cycling traits in soil – Michaeline B. Nelson – PNAS

Mammalian engineers drive soil microbial communities and ecosystem functions across a disturbance gradient – David J Eldridge – Journal of Animal Ecology

Biogeochemical drivers of microbial community convergence across actively retreating glaciers – Sarah C. Castle – Soil Biology and Biochemistry

The structure of bacterial communities along two vertical profiles of a deep colluvial soil – Marketa Sagova-Mareckova – Soil Biology and Biochemistry

Silver nanoparticles, ions and shape governing soil microbial functional diversity: nano shapes micro – Yujia Zhai – Frontiers in Microbiology

Water microbiome

Metagenomic signatures of a tropical mining-impacted stream reveal complex microbial and metabolic networks – Mariana P. Reis – Chemosphere

Effects of Copper, Nickel, and Sulphate from the Smelters at Sudbury, Ontario (Canada) on Microbial Communities in Lakes – Togwell A. Jackson – Geomicrobiology Journal

Archeological microbes

Early evidence for travel with infectious diseases along the Silk Road: Intestinal parasites from 2000 year-old personal hygiene sticks in a latrine at Xuanquanzhi Relay Station in China – Hui-Yuan Yeh – Journal of Archaeological Science: Reports

Press: Ancient Faeces Provide Earliest Evidence of Infectious Disease Being Carried on Silk Road – SciCasts
Ancient bottom wipers yield evidence of diseases carried along the Silk Road – Maev Kennedy – The Guardian

Built environment microbiome

Microorganisms associated with corrosion of structural steel in diverse atmospheres – Laura L. Machuca – International Biodeterioration & Biodegradation

More microbes

Individuals hospitalized with acute mania have increased exposure to antimicrobial medications – Robert Yolken – Bipolar Disorders

Metagenomics and bioinformatics

Multiplexed Metagenomic Deep Sequencing To Analyze the Composition of High-Priority Pathogen Reagents – Michael R. Wilson – mSystems

Microbes in the news

Everyday chemicals may be messing up our microbiomes—but we don’t know – Beth Mole – Ars Technica
The jury is still out on whether antibacterial chemical impacts microbiome or causes resistance – Bob Yirka – Medical Xpress

Some Microbes Have Been With Us Since Before We Existed. Certain gut bacteria have evolved in parallel with apes, so that their family tree perfectly mirrors our own. – Ed Yong – The Atlantic

Plants have a microbiome just like humans — and it could transform how our food is produced – Ariel Schwartz – Tech Insider

New book: The Human Superorganism: How the Microbiome Is Revolutionizing the Pursuit of a Healthy Life – Rodney Dietert
Your Microbes, Yourself. In his new book, Rodney Dietert argues that it’s time to re-configure our relationship with germs: – Louise Fabiani – Pacific Standard

Science, publishing, and career

The Women and the Science
Rachel Ignotofsky tells the stories of 50 women in science in her fantastic new science art book – Scientific American
Women in Science: An Illustrated Who’s Who – Julie Leibach – Science Friday

Women in Science: An Illustrated Who’s Who

July 19, 2016

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Gut microbial translocation and liver cirrhosis, cockatiel microbiome, human thanatomicrobiome, and the Pokémon microbiome.

Human gut microbiome

Gut microbial translocation corrupts myeloid cell function to control bacterial infection during liver cirrhosis – Carl-Philipp Hackstein – Gut

Press: Fighting life-threatening bacteria without antibiotics. Researchers discover the cause of infections in patients with cirrhosis of the liver – Science Daily

Review: Emerging Technologies for Gut Microbiome Research – Jason W. Arnold – Trends in Microbiology

Review: Gut Microbiome and Liver Disease – Naga S. Betrapally – Translational Research

Human vaginal microbiome

Review:  Does the vaginal microbiota play a role in the development of cervical cancer? –
Maria Kyrgiou – Translational Research

Animal experiments

Arsenic Dysbiosis to the Zebrafish Microbiome: An Ecological or Physiological Response?
Jonathan Michael Von Reusner – Bard College

Commensal Bacteria Aid Mate-selection in the Fruit Fly, Bactrocera dorsalis – Kamala Jayanthi Pagadala Damodaram – Microbial Ecology

Animal microbiome

Cockatiel (Nymphicus hollandicus) gut microbiomes, bacterial inhabitants of a worldwide distributed pet – Luis David Alcaraz – PeerJ Preprint

Plant, root, and soil microbiome

Long-term effects of imbalanced fertilization on the composition and diversity of soil bacterial community – Jinu Eo – Agriculture, Ecosystems & Environment

Built environment microbiome

Protocol: Protocols for Investigating the Microbial Communities of Oil and Gas Reservoirs – Nicolas Tsesmetzis – Springer Protocols Handouts

Thesis: A Metagenomic Analysis of Hurricane Sandy Flood-Borne Bacteria – Isabel Anna Keddy-Hector – Bard College

Microbiome of death

Human Thanatomicrobiome Succession and Time Since Death – Gulnaz T. Javan – Scientific Reports

Techniques

Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition – Berith E Knudsen – bioRxiv

Microbes in the news

Pokébiome: A call for Research Participants – Sea Germ – Megabiome (satire)

Understanding the microbiome of the Boston subway – BioBE

Studies Offer Fresh Hope in Fight Against HIV/AIDS in South Africa. Certain bacteria put some women at greater risk of infection and make treatment less effective – Betsy McKay – The Wall Street Journal
How vaginal bacteria could be stoking HIV cases and blocking prevention – Heather Boerner – PBS Newshour
Vaginal bacteria species can raise HIV infection risk and undermine prevention – Jon Cohen – Science

The Wild Life of Showerheads: Another great #CitizenMicrobiology project from ‏@RobRDunn – Jonathan Eisen – MicroBEnet

How Bacteria May Have Jumpstarted the First Animal Life – Heather Goldstone – Cape and Islands

Scientists grow bacteria that breathe greenhouse gases – Christoph Keuschnig – Science Nordic

QIIME 2 alpha release is now live! – Greg Caporaso – MicroBEnet

Bacteria Hysteria

How much faecal bacteria is on YOUR shopping trolley? Tests reveal unhealthy levels on trolleys and baskets at Coles and Aldi – Daily Mail

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 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 2, 2016

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Colonic transit time, innovations in artificial gut systems, and how the majority of the human gut microbiome members can be cultured.

Human respiratory microbiome

Nasopharyngeal microbiota composition of children is related to the frequency of upper respiratory infection and acute sinusitis – Clark A. Santee – Microbiome

Metagenomics Study of Viral Pathogens in Undiagnosed Respiratory Specimens
and Identification of Human Enteroviruses at a Thailand Hospital – Yanfei Zhou – American Journal of Tropical Medicine and Hygiene

Review: The respiratory microbiome of HIV-infected individuals – MB Lawani – Expert Review of Anti-infective Therapy

Review: A tale of two sites: how inflammation can reshape the microbiomes of the gut and lungs – Brittan S. Scales – Journal of Leukocyte Biology

Human gut microbiome

Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut – Henrik M. Roager – Nature Microbiology

Behind the paper: How we got captivated by colonic transit time – Henrik Munch Roager – Nature Microbiology Community

Datafying microbes: Malnutrition at the intersection of genomics and global health – Amber Benezra – BioSocieties

Several reviews in the July issue of Therapeutic Advances in Gastroenterology:
The interplay between the microbiome and the adaptive immune response in cancer development – Edda Russo
The intestinal microbiome, barrier function, and immune system in inflammatory bowel disease: a tripartite pathophysiological circuit with implications for new therapeutic directions – Stephen M. Vindigni
Role of the gut microbiota in health and chronic gastrointestinal disease: understanding a hidden metabolic organ – Caitriona M. Guinane
Novel perspectives on therapeutic modulation of the gut microbiota – Justin L. McCarville

Review: The Brain-Body-Microbial Communities: A Crosstalk and Stress Exchange
Beyond the “Gut hypothesis” – Afifi Ma – Abnormal and Behavioural Psychology

Review: The Role of the Microbial Metabolites Including Tryptophan Catabolites and Short Chain Fatty Acids in the Pathophysiology of Immune-Inflammatory and Neuroimmune Disease – Gerwyn Morris – Molecular Neurobiology

Animal experiments

Relationship between the microbiota in different sections of the gastrointestinal tract, and the body weight of broiler chickens – Geon Goo Han – Springer Plus

The upper respiratory tract microbiome and its potential role in bovine respiratory disease and otitis media – Svetlana F. Lima – Scientific Reports

Review: Farewell to Animal Testing: Innovations on Human Intestinal Microphysiological Systems – Tae Hyun Kang – Micromachines

Plant, root, and soil microbiome

Effects of Short-Term Warming and Altered Precipitation on Soil Microbial Communities in Alpine Grassland of the Tibetan Plateau – Kaoping Zhang – Frontiers in Microbiology

Bacterial diversity in the rhizosphere of two phylogenetically closely related plant species across environmental gradients – Xiaofan Na – Journal of Soils and Sediments

Soil microbial communities of three major Chinese truffles in Southwest China – Yu Fu – Canadian Journal of Microbiology

Review: Ecology of nitrogen fixing, nitrifying and denitrifying microorganisms in tropical forest soils – Silvia Pajares – Frontiers in Microbiology

Water and extremophile microbiome

Metagenomic analysis of microbial community of an Amazonian geothermal spring in Peru – Sujay Paul – Genomics Data

Characterization of microbial mat microbiomes in the modern thrombolite ecosystem of Lake Clifton, Western Australia using shotgun metagenomics – John G. Warden – Frontiers in Microbiology

Built environment microbiome

Microbes in the Water Infrastructure: Underpinning Our Society – Takashi Narihiro – Microbes and Environments

Techniques / Metabolomics

Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling – Jennifer T. Lau – Genome Medicine

A Microbiome DNA Enrichment Method for Next-Generation Sequencing Sample Preparation – Erbay Yigit – Current Protocols in Molecular Biology

Sample preparation optimization in fecal metabolic profiling – Olga Deda – Journal of Chromatography B

Viruses and phages

Survival studies of a temperate and lytic bacteriophage in bovine faeces and slurry – Sepo Nyambe – Journal of Applied Microbiology

Microbes in the news

Conference report: Machine Learning Method Differentiates Between Healthy Male, Female Microbiomes: Topological Data Analysis – UC San Diego

A New Role for Marine Archaea. Researchers discover acetogenesis in archaea, suggesting an important role for these little-studied organisms in generating organic carbon below the seafloor – Catherine Offord – The Scientist

Stop worrying about GMOs; it’s that organic granola bar that could make you sick: Listeria – Henry I. Miller – LA Times

USM marine microbiologist Jay Grimes weighs in on vibrio vulnificus – WDAM

Chesterfield Royal scientists send ripples around the NHS – Andy Done-Johnson – Derbyshire Times

Efficiency in the pathology lab: Friend or Foe; the probiotic power of helminths can prevent Crohn’s Disease – Anouk Gouvras – BioMedCentral blog

Supplement may switch off cravings for high-calorie foods – Stephen Feller – UPI
Cravings for high-calorie foods may be switched off by new food supplement – Kate Wighton – Imperial College London

Science, publishing, and career

“He Thinks He’s Untouchable”: Michael Katze, famous for his studies of Ebola and the flu, ran a lab at the University of Washington where intoxication and sexual harassment went unchecked – Azeen Ghorayshi – Buzzfeed

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