Category Archives: Built Environment Microbiology

September 12, 2016

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Individual response of gut microbiota to diet (in mice), appendicitis, adaptive evolution of goose with its microbiome, fungi in rubber plantations.

Events

Storify of days 1-2 of the 6th ASM Beneficial Microbes Meeting, Sept 9-12, Seattle, WA.

Pregnancy and birth

Urinary Microbiota Associated with Preterm Birth: Results from the Conditions Affecting Neurocognitive Development and Learning in Early Childhood (CANDLE) Study – Nicholas J. Ollberding – PLOS ONE

Review: The role of the bacterial microbiota on reproductive and pregnancy health – Deborah B. Nelson – Anaerobe

Human skin microbiome

Skin microbiome prior to development of atopic dermatitis: early colonization with commensal staphylococci at 2 months is associated with a lower risk of atopic dermatitis at 1 year – Elizabeth A. Kennedy – Journal of Allergy and Clinical Immunology

Human respiratory microbiome (and Methods)

Note that 2 different amplification strategies were performed, so IMHO this is more reflection of primer differences than sequencing differences: Different next generation sequencing platforms produce different microbial profiles and diversity in cystic fibrosis sputum – Andrea Hahn – Journal of Microbiological Methods

Human gut microbiome

Evaluation of the microbiome in children’s appendicitis – Martin Salö – International Journal of Colorectal Disease

Review: Food: a new form of personalised (gut microbiome) medicine for chronic diseases? – Tess Pallister – Journal of the Royal Society of Medicine

Review: Linking the Microbiota, Chronic Disease, and the Immune System – Timothy W. Hand – Trends in Endocrinology & Metabolism

Animal and bioreactor experiments

From the Sonnenburg lab @Stanford: Individualized Responses of Gut Microbiota to Dietary Intervention Modeled in Humanized Mice – Samuel A. Smits – mSystems

An In Vitro Approach to Study Effects of Prebiotics and Probiotics on the Faecal Microbiota and Selected Immune Parameters Relevant to the Elderly – Yue Liu – PLOS ONE

Animal microbiome

Genome and metagenome analyses reveal adaptive evolution of the host and interaction with the gut microbiota in the goose – Guangliang Gao – Scientific Reports

Hold off on the orange oil: Characterization of Antibacterial Activities of Eastern Subterranean Termite, Reticulitermes flavipes, against Human Pathogens – Yuan Zeng – PLOS ONE

Use of MALDI-TOF MS and culturomics to identify mosquitoes and their midgut microbiota – Fatalmoudou Tandina – Parasites & Vectors

Plant, root, and soil microbiome

Drought history affects grassland plant and microbial carbon turnover during and after a subsequent drought event – Lucia Fuchslueger – Journal of Ecology

Effect of organic matter enrichment on the fungal community in limestone cave sediments – ELS Marques – Genetics and Molecular Research

Contrasting elevational diversity patterns for soil bacteria between
two ecosystems divided by the treeline – Guixiang Li – Science China Life Sciences

Review: Diversity and ecology of soil fungal communities in rubber plantations – Jutamart Monkai – Fungal Biology Reviews

Illumina sequencing reveals a rhizosphere bacterial community associated with foxtail millet smut disease suppression – Yansha Han – Plant and Soil

Water and extremophile microbiome

Viruses-to-mobile genetic elements skew in the deep Atlantis II brine pool sediments – Mustafa Adel – Scientific Reports

Built environment microbiome

Review: The Microbiome of the Built Environment and Human Behavior: Implications for Emotional Health and Well-Being in Postmodern Western Societies – C.E. Stamper – International Review of Neurobiology

Microbes in the news

The Bacteria on Your Skin Are Safer Than These Two Chemicals the FDA Just Banned From Your Soap – Jill Richardson – Truth Digg

DNA in London Grave May Help Solve Mysteries of the Great Plague – Roff Smith – National Geographic

Bik’s Non-Microbiology Picks

This paper was discussed on Twitter this weekend because of a conflict of interest of one of the authors (Deepak Chopra) and the design and interpretation of the study:

Identification of Altered Metabolomic Profiles Following a Panchakarma-based Ayurvedic Intervention in Healthy Subjects: The Self-Directed Biological Transformation Initiative (SBTI) – Christine Tara Peterson – Scientific Reports

September 10, 2016

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Bifidobacteria and ulcerative colitis, the pollen microbiome, busting the 5-second rule, resistance genes in 23,000 microbial genomes, and a cool video of evolution of bacterial resistance.

Events

Gut health, microbiota & probiotics throughout the lifespan – Metabolic & Brain function 2016 – Sept 15-16, Harvard Medical School, Boston, MA

Human oral microbiome

Deep sequencing reveals microbiota dysbiosis of tongue coat in patients with liver carcinoma – Haifeng Lu – Scientific Reports

Human respiratory microbiome

Review: The microbiome in asthma – Magali Noval Rivas – Current Opinion Pediatrics

Human gut microbiome

Elucidating the gut microbiome of ulcerative colitis: bifidobacteria as novel microbial biomarkers – Sabrina Duranti – FEMS Microbiology Ecology

Review: Gut Microbiota, Inflammation, and Colorectal Cancer – Caitlin A. Brennan – Annual Review of Microbiology

Review: Microbiota—myeloid cell crosstalk beyond the gut – Sayeh Gorjifard – Journal of Leukocyte Biology

Four reviews in Current Pharmaceutical Design in the category “Could the gut microbiota perhaps be involved in disease X?” – with 4 different X’s. 

Animal models

Antibiotic Treatment Induces Long-lasting Changes in the Fecal Microbiota that Protect Against Colitis – Naomi L. Ward – Inflammatory Bowel Diseases

Differences In CD8αα And Cecal Microbiome Community During Proliferation And Late Cytolytic Phases Of Marek’s Disease Virus (MDV) Infection Are Associated With Genetic Resistance To Marek’s Disease – Sudeep Perumbakkam – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Bacterial microbiota associated with flower pollen is influenced by pollination type, and shows a high degree of diversity and species-specificity – Binoy Ambika Manirajan – Environmental Microbiology

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

Small-scale spatial heterogeneity of ecosystem properties, microbial community composition and microbial activities in a temperate mountain forest soil – Martina Štursová – FEMS Microbiology Ecology

Extremophile microbiome

Seasonal dynamics of extremely halophilic microbial communities in three Argentinian salterns – Leonardo Di Meglio – FEMS Microbiology Ecology

Built environment microbiome

screen-shot-2016-09-10-at-10-44-32-am

Christin Lola / Fotolia (via Science Direct)

Longer Contact Times Increase Cross-Contamination of Enterobacter aerogenes from Surfaces to Food – Robyn C. Miranda – Applied and Environmental Microbiology

Researchers debunk ‘five-second rule’: Eating food off the floor isn’t safe. Sometimes bacteria transfer in less than a second – Science Daily

Forget the ‘five-second rule’: Food dropped on the floor picks up bacteria in just ONE second – David Gardner – Daily Mail

Antimicrobial Chemicals Are Associated with Elevated Antibiotic Resistance Genes in the Indoor Dust Microbiome – Erica M. Hartmann – Environmental Science & Technology

Antibiotic Resistance Genes in Indoor Dust – Technology Networks

Metagenomics and bioinformatics

The transfer network of bacterial mobile resistome connecting animal and human microbiome – Yongfei Hu – Applied and Environmental Microbiology

Catalog of Mobile Antibiotic Resistance Genes Helps Explain Transfer to Human Pathogens – Genome Web

Chinese investigators characterize the world of resistance gene exchange among bacteria – Phys.org

Phages and viruses

Bacteriophages in clinical samples can interfere with microbiological diagnostic tools – Maryury Brown-Jaque – Scientific Reports

Techniques

Absolute quantification of microbial taxon abundances – Ruben Props – The ISME Journal

Microbes in the news

Jo Handelsman of White House Office of Science and Technology to Speak Monday – University of Tennessee

WATCH: Bacteria Invade Antibiotics And Transform Into Superbugs – Angus Chen – NPR
This might be the coolest visualization of evolution ever. Watch these bacteria evolve antibiotic resistance in just 12 days – Brian Resnick – Vox

These researchers would like you to mail them your gut bacteria – Katherine Lindemann – Research Gate Blog

Hepatitis A Outbreak Linked to Strawberries at Smoothie Chain – Daniel Victor – New York Times

Bacteria Hysteria

M&S becomes first supermarket to offer anti-bacterial shopping bags to banish bugs such as E. coli –  Katie Morley – The Telegraph

Bik’s non-microbiology Picks

Microbiome analysis, please! Giraffes aren’t just giraffes. Turns out there are four species – Rachel Feltman – Washington Post

Flatworm parasite named after Barack Obama: Is that a compliment? – Rowena Lindsay Christian Science Monitor

 

September 9, 2016

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Microbiome and tuberculosis, mangoes, lessons from amphibians, and the microbiome of buildings.

Human gut microbiome

Oral, frozen fecal microbiota transplant (FMT) capsules for recurrent Clostridium difficile infection – Ilan Youngster – BMC Medicine

Review: Microbiome Changes during Tuberculosis and Antituberculous Therapy – Bo-Young Hong – Clinical Microbiology Reviews

No consensus on how the microbiome affects tuberculosis, review finds – Science Daily

Animal models

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Mango, “hedgehog” style – Wikipedia

Mango Supplementation Modulates Gut Microbial Dysbiosis and Short-Chain Fatty Acid Production Independent of Body Weight Reduction in C57BL/6 Mice Fed a High-Fat Diet – Babajide Ojo – Journal of Nutrition

Mango and the Microbiota: New Research Reveals Potential Role of this Superfruit in Maintaining Gut Health – National Mango Board – PR Newswire

Antibiotics Suppress Activation of Intestinal Mucosal Mast Cells and Reduce Dietary Lipid Absorption in Sprague-Dawley Rats – Hirokazu Sato – Gastroenterology

Press (with ugly title): The influence of fat when gut bacteria is reduced by antibioticsm – Science Daily

Animal microbiome

Harnessing the Microbiome to Prevent Fungal Infections: Lessons from Amphibians – Jenifer B. Walke – PLOS Pathogens

Built environment microbiome

Ten questions concerning the microbiomes of buildings – Rachel I. Adams – Building and Environment

The hot new 10 questions concerning the microbiomes of buildings will surprise you – Jonathan Eisen – MicroBEnet

Microbes in the news

“I’ll never let go, Jack I promise”
Titanic expected to disappear by 2030 thanks to hungry bacteria – Matthew Humphries – Geek.com
Video: Will Bacteria Completely Destroy The Titanic’s Remains? – MSN Video

Scientists find deadly scrub typhus bacteria in South America – Reuters

Mount Sinai Beth Israel Says Legionella Bacteria Found in Several Areas of Hospital – NY1.com

Mood, mind and memory: can gut bacteria meddle with the brain? – Dyani Lewis – Cosmos Magazine
Bugs as drugs – medicine’s next frontier – Dyani Lewis – Cosmos Magazine

Driving Microbiome Science: PKU and Probiotics – Raredr

Experts urge a defensive stance in efforts against antimicrobial resistance – EurekAlert

Microbes and money

Microban Opens Microbiology Testing Services to Non-Partners – Genevieve Scarano – Sourcing Journal

Science, publishing, and career

Your toughest experiment: taking the lead in the lab. Eight scientists share the secrets of being a successful PI – Times Higher Education

September 6, 2016

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Tongue diagnostics and bacterial communities, microbiome and ALS, flowers and bees sharing microbes, and CRISPR assembly.

Events

4th World Congress on Targeting Microbiota is organized at Institut Pasteur, Paris, France – October 17-19, 2016

How the Indoor Microbiome Influence Health, with Jack A. Gilbert – October 27, 2016 at British International School of Chicago – Lincoln Park in Chicago

Human oral microbiome

Bacillus as a potential diagnostic marker for yellow tongue coating – Juan Ye – Scientific Reports

Human skin microbiome

Redefining the Chronic-Wound Microbiome: Fungal Communities Are Prevalent, Dynamic, and Associated with Delayed Healing – Lindsay Kalan – mBio

Human respiratory tract microbiome

Review: Development of the respiratory tract microbiota in cystic fibrosis – Emma M. de Koff – Current Opinion in Pulmonary Medicine

Human urinary tract microbiome

Commentary: “Urinary tract infection” and the microbiome – Thomas E. Finucane – The American Journal of Medicine

Human gut microbiome

Pitfalls in Inferring Human Microbial Dynamics from Temporal Metagenomics Data – Hong-Tai Cao – bioRxiv

Evaluation of the microbial diversity in amyotrophic lateral sclerosis using high-throughput sequencing – Xin Fang – Frontiers in Microbiology

Review: Beyond 16S rRNA community profiling: intra-species diversity in the gut microbiota – Kirsten M. Ellegaard – Frontiers in Microbiology

Review: Epigenetic mechanisms in microbial members of the human microbiota: current knowledge and perspectives – Natacha Cureau – Future Medicine

Microbiology and immunology

Perspective: Autoimmunity and the microbiome: T-cell receptor mimicry of “self” and microbial antigens mediates self tolerance in holobionts – Robert Root-Bernstein – BioEssays

Animal models of microbiome research

Ketogenic diet modifies the gut microbiota in a murine model of autism spectrum disorder – Christopher Newell – Molecular Autism

Animal microbiome

Disentangling a holobiont – recent advances and perspectives in Nasonia wasps – Jessica Dittmer – Frontiers in Microbiology

Review: The terrestrial isopod microbiome: An all-in-one toolbox for animal-microbe interactions of ecological relevance – Didier Bouchon – Frontiers in Microbiology

Plant, root, and soil microbiome

Microbial communities in passive remediation systems at three abandoned coal mine sites in the United Kingdom – Carmen Falagán – Proceedings IMWA 2016, Freiberg

Primary Succession of Nitrogen Cycling Microbial Communities Along the Deglaciated Forelands of Tianshan Mountain, China – Jun Zeng – Frontiers in Microbiology

Flowers and Wild Megachilid Bees Share Microbes – Quinn S. McFrederick – Microbial Ecology

Triclosan Resistome from Metagenome Reveals Diverse Enoyl Acyl Carrier Protein Reductases and Selective Enrichment of Triclosan Resistance Genes – Raees Khan – Scientific Reports

Water and extremophile microbiome

Oligotrophic Lagoons of the South Pacific Ocean Are Home to a Surprising Number of Novel Eukaryotic Microorganisms – Eunsoo Kim – Environmental Microbiology

Upstream freshwater and terrestrial sources are differentially reflected in the bacterial community structure along a small Arctic river and its estuary – Aviaja L. Hauptmann – Frontiers in Microbiology

Built environment microbiology

Review: Emerging Investigators Series: Sewer surveillance for monitoring antibiotic use and prevalence of antibiotic resistance: urban sewer epidemiology – Nicole Fahrenfeld – Environmental Science: Water Research & Technology

Food microbiology

High-throughput identification of the microbial biodiversity of cocoa bean fermentation by MALDI-TOF MS – S. Miescher Schwenninger – Letters in Applied Microbiology

Bioinformatics and metagenomics

Assemble CRISPRs from metagenomic sequencing data – Jikai Lei – Bioinformatics

Contig annotation tool CAT robustly classifies assembled metagenomic contigs and long sequences – Diego D. Cambuy – bioRxiv

Techniques

High throughput sequencing of multiple amplicons for barcoding and integrative taxonomy – Perrine Cruaud – bioRxiv

Microbes in the news

Podcast (12 min) with Stephen Pointing: Protecting the Earth’s Microbiome – Jesse Mulligan – Radio NZ

Biochemists’ discovery could lead to vaccine against ‘flesh-eating’ bacteria – Science Daily

Enzyme from oral bacteria could be potential therapy for celiac disease – News Medical

Bik’s Non-Microbiology Picks

Bizarre ant colony discovered in an abandoned Polish nuclear weapons bunker – Annalee Newitz – ArsTechnica

September 1, 2016

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Bedouins, urban Saoudis and monkeys, a subglacial lake, and the oldest microbial fossils.

Events

Alfred P. Sloan Foundation Workshop on Viruses to be Held in Singapore, January 2017 – David Coil – MicroBEnet

Human respiratory microbiome

News: Does barnyard dust protect Amish children from asthma? – Bryant Furlow – The Lancet

Human gut microbiome

Gut microbiome and dietary patterns in different Saudi populations and monkeys – Emmanouil Angelakis – Scientific Reports

Fecal Microbiota Transplantation is Safe and Efficacious for Recurrent or Refractory Clostridium difficile Infection in Patients with Inflammatory Bowel Disease – Monika Fischer

Animal experiments

High fat diet drives obesity regardless the composition of gut microbiota in mice – Sylvie Rabot – Scientific Reports

Gut Microbiota Promote Angiotensin II–Induced Arterial Hypertension and Vascular Dysfunction – Susanne H. Karbach – Hypertension

Plant, root, and soil microbiome

Forest area and connectivity influence root-associated fungal communities in a fragmented landscape – Rachel L. Vannette – Ecology

Review: Comparative phylogenomics of symbiotic associations – Pierre-Marc Delaux – New Phytologist

Water and extremophile

Microbial Community Structure of Subglacial Lake Whillans, West Antarctica – Amanda M. Achberger – Frontiers in Microbiology

Dust microbiome

Poultry houses: DNA from dust: comparative genomics of large DNA viruses in field surveillance samples – Utsav Pandey – bioRxiv

Techniques

Direct 16S rRNA-seq from bacterial communities: a PCR-independent approach to simultaneously assess microbial diversity and functional activity potential of each taxon – Riccardo Rosselli – Scientific Reports

More microbiology

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Geological map and location of microbial structures

Rapid emergence of life shown by discovery of 3,700-million-year-old microbial structures – Allen P. Nutman – Nature

Press: Life thrived on young Earth: scientists discover 3.7-billion-year-old fossils – Science Daily
The World’s Oldest Fossils Are 3.7 Billion Years Old. The newly discovered rocks suggest that life arose very quickly after the Earth was formed – Ed Yong – The Atlantic

Microbes in the news

Microbial genomics and the future of food microbiology – Julie Wolf – American Society for Microbiology

Space Microbiome? Yes Please! and I’ll take a minION sequencer as well if you don’t mind – Ben Libberton – NPJ Biofilms Community

Multitalented microbiology student is highly lauded for her scholarship – Western Michigan University

Manuka honey makes bacteria less resistant to antibiotics – Rowena Jenkins – The Conversation

Changes in Gut microflora – early warning of Equine Metabolic Syndrome (EMS)? – Jackie Bellamy-Zions – Harness Link

uBiome Hires New Vice President of Research and Development: Dr. Audrey Goddard Joins from Genomic Health and Genentech – PR Web

Samorost 3’s fairy tale of microbiology is now on iPhone – Chris Priestman – Kill Screen

Science, publishing, and career

How to Motivate Your Employees: Give Them Compliments and Pizza – Melissa Dahl – New York Magazine

Opinion: Fixing Science’s Human Bias. It’s time to accelerate the conversation about why the research community is still not diverse – Edward Courchaine and Sarah Smaga – The Scientist

Thanks to the glass ceiling breakers – Yarrow Axford – Science

Peer review

HT: Tomer Altman: Stupid Patent of the Month: Elsevier Patents Online Peer Review – Electronic Frontier Foundation

Research Integrity

OMICS vs. The FTC: Plagiarism at a Predatory Publisher – Neuroskeptic – Discover

 

August 26, 2016

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MRI scans of colonic contents in setting of diet or defaecation, fecal transplants, the microbiome of ambulances, and a core taxa tool.

Pregnancy and birth

Longitudinal study on clinical and microbial analysis of periodontal status in pregnancy – Fernanda Campos Machado – Brazilian Oral Research

Review: Role of microbiota function during early life and children neurodevelopment – Tomás Cerdó – Trends in Food Science & Technology

Human oral microbiome (also see above)

Evaluation of oral microbiota in undernourished and eutrophic children using checkerboard DNA-DNA hybridization – M. Testa – Anaerobe

Review: Human neutrophils and oral microbiota: a constant tug-of-war between a harmonious and a discordant coexistence – Silvia M. Uriarte – Immunological Reviews

Human skin microbiome

Temporal stability in chronic wound microbiota is associated with poor healing – Michael Loesche – Journal of Investigative Dermatology

Human gut microbiome

Colonic content: effect of diet, meals, and defecation – R. A. Bendezú – Neurogastroenterology & Motility

Gut microbiota associated with HIV infection is significantly enriched in bacteria tolerant to oxygen – Grégory Dubourg – BMJ Open Gastroenterology

Prevalence and genetic diversity of Blastocystis in family units living in the United States – Pauline D. Scanlan – Infection, Genetics and Evolution

Nitrogen fixation and nifH diversity in human gut microbiota – Katsura Igai – Scientific Reports

Letter: Intestinal Microbiota and Health of Adults Who Were Born by Cesarean Delivery – James J. Goedert – JAMA Pediatrics

Opinion: The microbiome, microbial generated pro-inflammatory neurotoxins, and Alzheimer’s disease – Walter J. Lukiw – Journal of Sport and Health Science

Review: Estrogen and Microbiota Crosstalk: Should We Pay Attention? – Karen L. Chen – Trends in Endocrinology & Metabolism

Review: Gender, aging and longevity in humans: an update of an intriguing/neglected scenario paving the way to a gender-specific medicine – Rita Ostan – Clinical Science

Fecal transplants

Estimating the risks of faecal transplants – K. Patel – The Journal of Hospital Infection

Effect of Fecal Microbiota Transplantation on Recurrence in Multiply Recurrent Clostridium difficile Infection: A Randomized Trial – Colleen R. Kelly – Annals of Internal Medicine

Plant, root, and soil microbiome

Arbuscular mycorrhizal fungi communities from tropical Africa reveal strong ecological structure – Susana Rodríguez-Echeverría – New Phytologist

Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria – Edward W. Davis II – PeerJ

Water microbiome

Structure and function of methanogenic microbial communities in sediments of Amazonian lakes with different water types – Yang Ji – Environmental Microbiology

Built environment microbiome

Detection and characterization of surface microbial contamination in emergency ambulances – Aketza Varona-Barquin – American Journal of Infection Control

Fitness and recovery of bacterial communities and antibiotic resistance genes in urban wastewaters exposed to classical disinfection treatments – Andrea Di Cesare – Environmental Science & Technology

Bioinformatics and metagenomics

PhyloCore: A phylogenetic approach to identifying core taxa in microbial communities – Tiantian Ren – Gene

Microbes in the news

Gut reaction: the surprising power of microbes – Ed Yong – The Guardian

Want to feel better? Be kind to your bugs. Ed Yong’s new book will give you a positive outlook on your body’s trillions of bacteria – Kate Womersley – The Spectator

The world’s largest bacterial study of baby poo – MedicalXpress

What’s in Your Poo? The nonmicrobial components of feces may have important consequences as we try to grapple with microbiome research – Kevin Bonham – Scientific American

Solving a 48-year-old mystery: scientists succeed at growing noroviruses in human intestinal cell cultures in the lab – Graciela Gutierrez – Baylor College of Medicine

MSU researchers spread the buzz about bee viruses – Marshall Swearingen – Montana State University

Science, publishing, and career

Family ties ‘help scientists to get ahead’ in some countries. Levels of nepotism in scientific publishing have been revealed by report – Jack Grove  – Times Higher Education

Supervisors can do a lot more to support PhD students. Many doctoral candidates feel poorly looked after. More awareness and empathy from academics can help fight that – Geoffrey Cantor – Times Higher Education

New leader of NIH’s research watchdog faces staff revolt – Jocelyn Kaiser – Science

August 25, 2016

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Microbiome of the Graduate Student Gut, allergic cats, tree phyllosphere, milk tanker trucks, and microbes of soda lakes.

Pregnancy and birth

Review: Role of microbiota function during early life and children neurodevelopment – Tomás Cerdó – Trends in Food Science & Technology

General microbiome

Now published after preprint earlier this year and article in Cell: Revised Estimates for the Number of Human and Bacteria Cells in the Body – Ron Sender – PLOS Biology

Enemies and brothers in arms: Candida albicans and gram-positive bacteria – Toni M. Förster – Cellular Microbiology

Human respiratory microbiome

General antibiotic exposure is associated with increased risk of developing chronic rhinosinusitis – Alice Z. Maxfield – The Laryngoscope

Evidence and Role for Bacterial Mucin Degradation in Cystic Fibrosis Airway Disease – Jeffrey M. Flynn – PLOS Pathogens

Human gut microbiome

Master Thesis: Characterizing Microbiome Changes in the Graduate Student Gut – Justin Roy Lund – University of Oklahoma

Altered Fecal Microbiota Correlates with Liver Biochemistry in Nonobese Patients with Non-alcoholic Fatty Liver Disease – Baohong Wang – Scientific Reports

Prosteatotic and Protective Components in a Unique Model of Fatty Liver: Gut Microbiota and Suppressed Complement System – Long Liu – Scientific Reports

Is there a role for stool metabolomics in cystic fibrosis? – Nadeem O Kaakoush – Pediatrics International

Animal microbiome

Allergic to humans? Characterization of the cutaneous mycobiota in healthy and allergic cats using next generation sequencing – Courtney Meason-Smith – Veterinary Dermatology

Fish: The influence of weight and gender on intestinal bacterial community of wild largemouth bronze gudgeon (Coreius guichenoti, 1874) – Xuemei Li – BMC Microbiology

Plant, root, and soil microbiome

Tree phyllosphere bacterial communities: exploring the magnitude of intra- and inter-individual variation among host species – Isabelle Laforest-Lapointe – PeerJ

Long-Term Recovery of Microbial Communities in the Boreal Bryosphere Following Fire Disturbance – Nick A. Cutler – Microbial Ecology

Autochthonous Microbiota in Arsenic-Bearing Technosols from Zemianske Kostoľany (Slovakia) and Its Potential for Bioleaching and Biovolatilization of Arsenic – Alexandra Šimonovičová – Water, Air, & Soil Pollution

Built environment microbiology

Fungi and Bacteria in Indoor Cultural Heritage Environments: Microbial-related Risks for Artworks and Human Health – Enza Di Carlo – Environment and Ecology Research

Fitness and recovery of bacterial communities and antibiotic resistance genes in urban wastewaters exposed to classical disinfection treatments – Andrea Di Cesare – Environmental Science & Technology

Bacterial diversity and antibiotic resistances of abundant aerobic culturable bacteria in input and output samples of fifteen German biogas plants – Thorsten Schauss – Journal of Applied Microbiology

Food microbiology

The Core and Seasonal Microbiota of Raw Bovine Milk in Tanker Trucks and the Impact of Transfer to a Milk Processing Facility – Mary E. Kable – mBio

Water and extremophile microbiome

Microbial community diversity and composition varies with habitat characteristics and biofilm function in macrophyte-rich streams – Peter S. Levi – Oikos

Evaluation of Alternative High-Throughput Sequencing Methodologies for the Monitoring of Marine Picoplanktonic Biodiversity Based on rRNA Gene Amplicons – Isabel Ferrera- Frontiers in Marine Science

Book Chapter: Bacteria, Archaea and Viruses of Soda Lakes – William D. Grant – Soda Lakes of East Africa

Bioinformatics and metagenomics

ResistoMap – online visualization of human gut microbiota antibiotic resistome – Konstantin Yarygin – bioRxiv

Techniques

Protocols.io: Virtual Communities for Protocol Development and Discussion – Leonid Teytelman – PLOS Biology

More microbiology

The Ecology and Evolution of Microbial Competition – Melanie Ghoul – Trends in Microbiology

Microbes in the news

How Designers and Scientists Are Using Bees to Map NYC’s Microbes – Liz Stinson – Wired

Graphic novel about World War I depicts gross realities of dysentery – Carolyn Webb – The Age Victoria

The newest food trend: fermentation – Ted Weesner – Boston Globe

 

 

August 16, 2016

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Gut microbiome and drug metabolism, bacteria and concrete, transposons in metagenomes.

Note: My lab does not longer allow me to run this blog under work hours, so I will do all my literature searches in my free time from now on. 😦 Not sure how this will affect the contents and frequency, but this is such a sad development. My sincere apologies! I will still strive to have a good representation of the new literature in the microbiome field, even it this means I will have to prepare this post at 1 AM (as I do now)

Pregnancy and birth

Review: The human gut microbiota in perinatology and neonatology – Josef Neu – Seminars in Fetal and Neonatal Medicine

Human oral microbiome

PCR-based detection of composite transposons and translocatable units from oral metagenomic DNA – Supathep Tansirichaiya – FEMS Microbiology Letters
Animal microbiome

Insights into Symbiont Population Structure among Three Vestimentiferan Tubeworm Host Species at Eastern Pacific Spreading Centers – Maëva Perez – Applied and Environmental Microbiology

Human gut microbiome

Review: Gut Microbiome Interactions with Drug Metabolism, Efficacy and Toxicity – Ian D. Wilson – Translational Research

Plant, root, and soil microbiome

Methyl Mercury Formation in Hillslope Soils of Boreal Forests: The Role of Forest Harvest and Anaerobic Microbes – Rose-Marie Kronberg – Environmental Science & Technology

Divergent habitat filtering of root and soil fungal communities in temperate beech forests – Kezia Goldmann – Scientific Reports

Extremophile microbiome

First insight into microbial diversity and ion concentration in the Uyuni salt flat, Bolivia – Cesar A. Perez-Fernandez – Caribbean Journal of Science

Built environment microbiome

Analysis of bacterial communities in and on concrete – Julia A. Maresca – Materials and Structures

Metagenomics

Exploring divergent antibiotic resistance genes in ancient metagenomes and discovery of a novel beta-lactamase family – Nicolás Rascovan – Environmental Microbiology Reports

Microbes in the news

Book Review: Multitudes of Praises for Ed Yong’s “I Contain Multitudes” – Anne Estes – Mostly Microbes

The Slow Growth Movement – Or Why Microbiologists May Have Been Doing it All Wrong – Jeffrey Marlow – Discover Magazine

Discharge pipe could be source of bacteria at Oxford treatment plant – Zach Tyler – The Anniston Star

August 6, 2016

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Airwair microbiome at birth, fungi on strawberries, molds in a library.

Pregnancy and birth

The Airway Microbiome at Birth – Charitharth Vivek Lal – Scientific Reports

Press: Discovery of Infants’ Airway Microbiomes May Help Predict Lung Disease
A newborn’s airway — once thought to be sterile until after birth — is colonized by bacteria– University of Alabama at Birmingham
Discovery of infants’ airway microbiomes may help predict lung disease – Jeff Hansen – Medical Xpress

Gestational Diabetes is associated with changes in Placental Microbiota and Microbiome – Judit Bassols – Pediatric Research

Human respiratory microbiome (also see Pregnancy and Birth)

Characterizing human lung tissue microbiota and its relationship to epidemiological and clinical features – Guoqin Yu – Genome Biology

High Frequency and Diversity of Antimicrobial Activities Produced by Nasal Staphylococcus Strains against Bacterial Competitors – Daniela Janek – PLOS Pathogens

Human ear microbiome

Molecular microbiological profile of chronic suppurative otitis media – Michel Neeff – Journal of Clinical Microbiology

Human gut microbiome

Antibiotic-Induced Gut Microbiota Disruption Decreases TNF-α Release by Mononuclear Cells in Healthy Adults – Jacqueline M. Lankelma – Clinical and Translational Gastroenterology

Review: Fecal Microbiota Transplantation and Its Usage in Neuropsychiatric Disorders – Alper Evrensel – Clinical Psychopharmacology and Neuroscience

Review: Interactions between the gut microbiome and the central nervous system and their role in schizophrenia, bipolar disorder and depression – Adrian Andrzej Chrobak – Archives of Psychiatry and Psychotherapy

Animal microbiome

Strain diversity and host specificity in a specialized gut symbiont of honey bees and bumble bees – J. Elijah Powell – Molecular Ecology

Flow cytometric enumeration of bacterial in the coral surface mucus layer – Yvan Bettarel – Journal of Microbiological Methods

Worldwide exploration of the microbiome harbored by the cnidarian model, Exaiptasia pallida indicates a lack of bacterial association specificity at a lower taxonomic rank – Tanya Brown – PeerJ Preprint

Plant, root, and soil microbiome

Metagenomic Analysis of Fungal Diversity on Strawberry Plants and the Effect of Management Practices on the Fungal Community Structure of Aerial Organs – Ahmed Abdelfattah – PLOS ONE

The active microbial diversity drives ecosystem multifunctionality and is physiologically related to carbon-availability in Mediterranean semiarid soils – Felipe Bastida – Molecular Ecology

Spatial and successional dynamics of microbial biofilm communities in a grassland stream ecosystem – Allison M. Veach – Molecular Ecology

Review: Phytoremediation: state-of-the-art and a key role for the plant microbiome in future trends and research prospects – Sofie Thijs – International Journal of Phytoremediation

Review: Bacterial pathogenesis of plants: future challenges from a microbial perspective. Challenges in Bacterial Molecular Plant Pathology – Sebastian Pfeilmeier – Molecular Plant Pathology

Review: Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments – Lucie Musilova – Int J Mol Sci

Water and extremophile microbiome

Unexpected biodiversity of ciliates in marine samples from below the photic zone – Jean-David Grattepanche – Molecular Ecology

Meltwater export of prokaryotic cells from the Greenland Ice Sheet – Karen A. Cameron – Environmental Microbiology

Environmental Conditions Outweigh Geographical Contiguity in Determining the Similarity of nifH-Harboring Microbial Communities in Sediments of Two Disconnected Marginal Seas – Haixia Zhou – Frontiers in MIcrobiology

Review: Extremophilic adaptations and biotechnological applications in diverse environments – James Charlesworth – AIMS Microbiology

Built environment microbiome

Detection of volatile metabolites of moulds isolated from a contaminated library – Anna Micheluz – Journal of Microbiological Methods

Review: Shoe soles as a potential vector for pathogen transmission: A systematic review – Tasnuva Rashid – Journal of Applied Microbiology

Bioinformatics and metagenomics
PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories – Victor Hanson-Smith – PLOS Computational BIology

The Phylogenetic LASSO and the Microbiome – Stephen T Rush – arXiv

Microbiome networks: A systems framework for identifying candidate microbial assemblages for disease management – Ravin Poudel – Phytopathology

Techniques

On the study of microbial transcriptomes using second- and third-generation sequencing technologies – Sang Chul Choi – Journal of Microbiology

Microbes in the news

Notre Dame Researcher Explores Bacteria beyond the Ability of Typical Hospital Setting: Gail Weaver – Nina Welding – Engineering

 

August 3, 2016

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Saliva and Polycystic Ovary Syndrome, early colonization of honey bees, hospital air metagenomes, analysis tool for viral metagenomes.

Human oral microbiome

The Salivary Microbiome in Polycystic Ovary Syndrome (PCOS) and its Association with Disease-related Parameters: A Pilot Study – Lisa Lindheim – Frontiers in Microbiology

A novel compound to maintain a healthy oral plaque ecology in vitro – Marleen M. Janus – Journal of Oral Microbiology

Human vaginal microbiome

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

Human skin microbiome

Diverse human skin fungal communities in children converge in adulthood – Jay-Hyun Jo – Journal of Investigative Dermatology

Human gut microbiome

A pleiotropic missense variant in SLC39A8 is associated with Crohn’s disease and human gut microbiome composition – Dalin Li – Gastroenterology

Press: Genetic Variant Newly Linked to Crohn’s Disease Also Associated with Altered Gut Microbiome Composition – PR Web

Gut microbiota associated with HIV infection is significantly enriched in bacteria tolerant to oxygen – Grégory Dubourg – BMJ Open Gastroenterology

Review: A clinical update on the significance of the gut microbiota in systemic autoimmunity – Elizabeth C. Rosser – Journal of Autoimmunity

Review: The human gut microbiome of Latin America populations: a landscape to be discovered – Fabien Magne – Current Opinion in Infectious Diseases

Animal microbiome

Early gut colonizers shape parasite susceptibility and microbiota composition in honey bee workers – Ryan S. Schwarz – PNAS

Another pika paper by the same authors (who killed all pika to obtain gut contents – booh): Pika gut may select for rare but diverse environmental bacteria – Huan Li – Frontiers in Microbiology

Review: Bacterial symbiosis in the fish gut and its role in health and metabolism – Goutam Banerjee – Symbiosis

Plant, root, and soil microbiome

Diverse gene functions in a soil mobilome – Wenting Luo – Soil Biology and Biochemistry

Genetic Diversity and Association Characters of Bacteria Isolated from Arbuscular Mycorrhizal Fungal Spore Walls – Gopal Selvakumar – PLOS ONE

Spatio-temporal variation of core and satellite arbuscular mycorrhizal fungus communities in Miscanthus giganteus – Christopher J. Barnes – Frontiers in Microbiology

DGGE: Impacts of Grazing Intensity and Plant Community Composition on Soil Bacterial Community Diversity in a Steppe Grassland – Tong-bao Qu – PLOS ONE

Book chapter: Calling in the Dark: The Role of Volatiles for Communication in the Rhizosphere – Nicole M. van Dam – Deciphering Chemical Language of Plant Communication

Book Chapter: Truffle-Associated Bacteria: Extrapolation from Diversity to Function – Elena Barbieri – True Truffle (Tuber spp.) in the World

Water and extremophile microbiome

Yeasts from sub-Antarctic region: biodiversity, enzymatic activities and their potential as oleaginous microorganisms – A. Martinez – Extremophiles

First report of microorganisms of Caucasus glaciers (Georgia) – Nicoletta Makowska – Biologia

Species sorting along a subsidy gradient alters bacterial community stability – Mario E. Muscarella – Ecology

Air microbiome / Built environment microbiome

Longitudinal Metagenomic Analysis of Hospital Air Identifies Clinically Relevant Microbes – Paula King – PLOS ONE

Bioinformatics

MetLab: An In Silico Experimental Design, Simulation and Analysis Tool for Viral Metagenomics Studies – Martin Norling – PLOS ONE

MetaCoMET: a web platform for discovery and visualization of the core microbiome – Yi Wang – Bioinformatics

More microbiology

Tempo and mode of genome evolution in a 50,000-generation experiment – Olivier Tenaillon – Nature

Press: Still changing after all these years. Long-term evolution experiment looks at genetic changes in bacteria: Richard Lenski – Science Daily

Review: Survival of the Fittest: How Bacterial Pathogens Utilize Bile To Enhance Infection – Jeticia R. Sistrunk – Clinical Microbiology Reviews

Book: Infective Endocarditis. Epidemiology, Diagnosis, Imaging, Therapy, and Prevention – Editors: Gilbert Habib – Springer

Élie Metchnikoff (1845–1916): celebrating 100 years of cellular immunology and beyond – David M. Underhill – Nature Reviews Immunology

Microbes in the news

Understanding diverse microbial communities: An interview with A. Murat Eren (Meren) – Kelle Freel – The Molecular Ecologist

Back from vacation? Your gut bacteria picked up souvenirs, too – Meredith Knight – Genetic Literacy Project

Evelo, Mayo Clinic team up to use bacteria for cancer immunotherapies – Ben Adams – Fierce Biotech

Plop into Canada’s first poop-themed dessert café next month – Heather Dockray – Mashable
Poop Dessert Cafe to open in Koreatown.Toronto is poised to get its first poop-themed café, set to open in August – The Star
First poo-themed dessert cafe set to open in Canada – Rachael Revesz – The Independent

Council agrees to trial of microbiology treatment – Lici Beveridge – Hattiesburg American

Opinion: Goals and possibilities in microbiology – Andrea Taboada – The Independent Florida Alligator

How Do Microbes Build Resistance to Metals? – Contagion

Bacteria Needed To Save Coral Reef – The Munich Eye

WATCH: Pac-Man Faithfully Recreated with Microbes – Nathaniel Scharping – Discover Magazine