Category Archives: General Microbiome

October 18, 2016

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Vaginal probiotics, forensic analysis of skin bacteria on fabrics, Wolbachia in nematodes, ivy phyllosphere, microbial life in two polar extremes, how to improve the indoor environment, and mass spec analysis of human habitat molecules.

Pregnancy and early life

Vaginal Probiotic Administration in the Management of Preterm Premature Rupture of Membranes – Daskalakis G.J. – Fetal Diagnosis and Therapy

General human microbiome

Review: Health Disparities and the Microbiome – Keisha Findley – Trends in Microbiology

Human respiratory microbiome

Review: Host–Bacterial Crosstalk Determines Staphylococcus aureus Nasal Colonization – Michelle E. Mulcahy – Trends in Microbiology

Human skin and tissue microbiome

Forensic analysis using microbial community between skin bacteria and fabrics – So-Yeon Lee – Toxicology and Environmental Health Sciences

Not a word about extraction controls, so proceed with caution: Bacterial Communities Associated with Atherosclerotic Plaques from Russian Individuals with Atherosclerosis – Elvira E. Ziganshina – PLOS ONE

Human gut microbiome

Construction and Analysis of Functional Networks in the Gut Microbiome of Type 2 Diabetes Patients – Lianshuo Li – Genomics, Proteomics & Bioinformatics

Review: Metabolite and Microbiome Interplay in Cancer Immunotherapy – Caroline H. Johnson – Cancer Research

Review: The gut microbiota and gastrointestinal surgery – Kristina Guyton – Nature Reviews Gastroenterology & Hepatology

Review: Gut Microbiota and Risk of Developing Celiac Disease – Cenit, Maria C. – Journal of Clinical Gastroenterology

Editorial: What’s in Your GI Microbiome? – Martin H. Floch – Journal of Clinical Gastroenterology

Animal and in vitro models

Study of the Ability of Bifidobacteria of Human Origin to Prevent and Treat Rotavirus Infection Using Colonic Cell and Mouse Models – Mélanie Gagnon – PLOS ONE

Farnesoid X Receptor Signaling Shapes the Gut Microbiota and Controls Hepatic Lipid Metabolism – Limin Zhang – mSystems

A mixture of milk and vegetable lipids in infant formula changes gut digestion, mucosal immunity and microbiota composition in neonatal piglets – Isabelle Le Huërou-Luron – European Journal of Nutrition

An Advanced In Vitro Technology Platform to Study the Mechanism of Action of Prebiotics and Probiotics in the Gastrointestinal Tract – Marzorati, Massimo – Journal of Clinical Gastroenterology

Animal microbiome

Sea lions: Protein and RNA extraction from mucosal swabs: a minimally invasive source of ecological data for studies of natural populations – W Espinosa-de Aquino – Methods in Ecology and Evolution

Mycobacteria in aquarium fish: results of a 3-year survey indicate caution required in handling pet-shop fish – D Kušar – Journal of Fish Diseases

Genomic evidence for plant-parasitic nematodes as the earliest Wolbachia hosts – Amanda M. V. Brown – Scientific Reports

Plant, root, and soil microbiome

Disentangling interactions between microbial communities and roots in deep subsoil – Martina I. Gocke – Science of the Total Environment

Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock – Alexandre Bagnoud – Nature Communications

Diversity and hydrocarbon-degrading potential of epiphytic microbial communities on Platanus x acerifolia leaves in an urban area – Isabella Gandolfi – Environmental Pollution

Response of soil bacterial communities to lead and zinc pollution revealed by Illumina MiSeq sequencing investigation – Xihui Xu – Environmental Science and Pollution Research

Impact of urban land use on the bacterial phyllosphere of ivy (Hedera sp.) – Wenke Smets – Atmospheric Environment

Water and extremophile microbiome

Periodic change in coastal microbial community structure associated with submarine groundwater discharge and tidal fluctuation – Eunhee Lee – Limnology and Oceanography

Microbial Community Dynamics in Two Polar Extremes: The Lakes of the McMurdo Dry Valleys and the West Antarctic Peninsula Marine Ecosystem – Jeff S. Bowman – BioScience

Diversity and physiological and biochemical properties of heterotrophic bacteria isolated from Lake Baikal neuston – A. D. Galach’yants – Microbiology

Phylogenetic and functional prokaryotic diversity in the Hoito-Gol mesothermal mineral spring (Eastern Sayan Mountains, Buryat Republic) – E.S. Kashkak – Microbiology

Metagenomic Insights into Effects of Chemical Pollutants on Microbial Community Composition and Function in Estuarine Sediments Receiving Polluted River Water – Xiao-Ming Lu – Microbial Ecology

Built environment microbiome

How do we make indoor environments and healthcare settings healthier? – Jack A. Gilbert – Microbial Biotechnology

Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats – Daniel Petras – Analytical Chemistry

Food microbiology

Raw Ready-to-Eat Seafood Safety: Microbiological Quality of the Various Seafood Species Available at Fishery, Hyper, and Online Market – H.W. Kim – Letters in Applied Microbiology

Bioinformatics and metagenomics

MIxS-HCR: a MIxS extension defining a minimal information standard for sequence data from environments pertaining to hydrocarbon resources – Nicolas Tsesmetzis – Standards in Genomic Sciences

IMG/M: integrated genome and metagenome comparative data analysis system
I-Min A. Chen – Nucleic Acids Research

Review: The present and future of de novo whole-genome assembly – Jang-il Sohn – Briefings in Bioinformatics

Microbes in the news

Soaking A Bunch Of Toads In Their Own Bacteria Could Save Their Lives – Krista Langlois – Five Thirty Eight

Bacteria Hysteria

Why your office could be making you sick: Keyboards ‘contain 20,000 MORE bacteria than a toilet bowl’– Stephen Matthews – Daily Mail

How to clean and disinfect your keyboard and mouse – Ed Rhee – CNET

Science, publishing, and career

A Tale of Two Women and Their Careers in Science – Anna Katie – YouTube

Promoting Responsible Scientific Research – American Society for Microbiology

October 13, 2016

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Ethics and microbiome research, oversimplifying microbiome studies, viruses destroy archaea in the deep seafloor, Clostridium difficile in patients sharing hospital beds.

General microbiome

Perspective: Ethical issues in microbiome research and medicine – Rosamond Rhodes – BMC Medicine

Interview: Science communication: the dangers of oversimplifying microbiome studies – Interview with Lauren Freeman and Saray Ayala – Ben Johnson – NPJ Biofilms Community

Human gut microbiome

Preview: Making It Stick: A Compelling Case for Precision Microbiome Reconstitution – David Berry – Cell Host & Microbe

Preview: A Commensal Protozoan Strikes a Balance in the Gut – P’ng Loke – Cell Host & Microbe

Animal models

Intestinal microbiota could transfer host Gut characteristics from pigs to mice – H. Diao – BMC Microbiology

Plant, root, and soil microbiome

Review: How lichens impact on terrestrial community and ecosystem properties – Johan Asplund – Biological Reviews

Water (and coral) microbiology

Virus-mediated archaeal hecatomb in the deep seafloor – Roberto Danovaro – Science Advances

Press: Deep-Sea Viruses Destroy Archaea. Viruses are responsible for the majority of archaea deaths on the deep ocean floors, scientists show – Ruth Williams – The Scientist

Multifaceted impacts of the stony coral Porites astreoides on picoplankton abundance and community composition – Sean P. McNally – Limnology and Oceanography

Food microbiology

Ultrasound improves chemical reduction of natural contaminant microbiota and Salmonella enterica subsp. enterica on strawberries – Denes Kaic Alves do Rosário – International Journal of Food Microbiology

Techniques

Greater than X kb: a quantitative assessment of preservation conditions on genomic DNA quality, and a proposed standard for genome-quality DNA – Daniel G. Mulcahy – PeerJ

Metagenomics

Diverse Intestinal Bacteria Contain Putative Zwitterionic Capsular Polysaccharides with Anti-inflammatory Properties – C. Preston Neff – Cell Host & Microbe

Other microbiology

Division of labour in microorganisms: an evolutionary perspective – Stuart A. West – Nature Reviews Microbiology

Receipt of Antibiotics in Hospitalized Patients and Risk for Clostridium difficile Infection in Subsequent Patients Who Occupy the Same Bed – Daniel E. Freedberg – JAMA

Press: Antibiotics Encourage Spread of C.diff To Subsequent Patients Who Occupy the Same Bed and Haven’t Received Antibiotics: Interview with Daniel Freedberg – Medical Research

Microbes in the news

The Conversation Gut Series:

RI Hospital receives $500,000 CDC grant to research new approach for combating antibiotic resistance. Microbiome research will help prevent ongoing spread of multi-drug resistant bacteria – EurekAlert

Science, publishing, and career

How Are Scientists Using Social Media in the Workplace? – Kimberley Collins – PLOS ONE

5 retractions and a sack for Pfizer lead cancer researcher Min-Jean Yin – Leonid Schneider – For Better Science
Pfizer fires employee, requests five retractions – Alison McCook – Retraction Watch

Bik’s non-microbiology Picks

Genomics is failing on diversity – Alice B. Popejoy & Stephanie M. Fullerton – Nature
The Simons Genome Diversity Project: 300 genomes from 142 diverse populations – Swapan Mallick – Nature

September 23, 2016

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Microbial dysbiosis in familial Crohn’s Disease, probiotic treatment of captive Colorado Toads, microbiome forecasting in the ocean, a new r package for phylogenetic trees, and MacArthur winner Dianne Newman.

General microbiome

Classic Spotlight: 16S rRNA Redefines Microbiology – Igor B. Zhulin – Journal of Bacteriology

Human vaginal microbiome

Microbiome Composition and Function Drives Wound-Healing Impairment in the Female Genital Tract – Alexander S. Zevin – PLOS Pathogens

Human respiratory microbiome

Clinical implications of microbial biofilms in chronic rhinosinusitis and orbital cellulitis – Niranjan Nayak – BMC Ophthalmology

Human gut microbiome

Bacteriome and Mycobiome Interactions Underscore Microbial Dysbiosis in Familial Crohn’s Disease – G. Hoarau – mBio

Prebiotic Effects of Xylooligosaccharides on the Improvement of Microbiota Balance in Human Subjects – Shyh-Hsiang Lin – Gastroenterology Research and Practice

Metformin and the Gut Microbiome in Diabetes – Sridevi Devaraj – Clinical Chemistry

Classic Spotlight: Bacteroides thetaiotaomicron, Starch Utilization, and the Birth of the Microbiome Era – George A. O’Toole – Journal of Bacteriology

Review: The human microbiome and juvenile idiopathic arthritis – Anouk Verwoerd – Pediatric Rheumatology

Animal experiments

A secreted bacterial peptidoglycan hydrolase enhances tolerance to enteric pathogens – Kavita J. Rangan – Science

Animal microbiome

Probiotic treatment restores protection against lethal fungal infection lost during amphibian captivity – Jordan G. Kueneman – Proceedings of the Royal Society B

Press: Probiotic treatment protects endangered Colorado toads from lethal fungal infection – University of Colorado Boulder

Plant, root, and soil microbiome

Microbial nitrification in throughfall of a Japanese cedar associated with archaea from the tree canopy – Keiji Watanabe – Springer Plus

Spatial heterogeneity of physicochemical properties explains differences in microbial composition in arid soils from Cuatro Cienegas, Mexico – Silvia Pajares – PeerJ

Taxonomic resolution is a determinant of biodiversity effects in arbuscular mycorrhizal fungal communities – Haishui Yang – Journal of Ecology

Water microbiome

Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone – Stilianos Louca – PNAS

New model could point way to microbiome forecasting in the ocean – Science Daily

Built environment microbiome

Buzz Off! An Evaluation of Ultrasonic Acoustic Vibration for the Disruption of Marine Microorganisms on Sensor Housing Materials – Jonathan S. McQuillan – Letters in Applied Microbiology

Bioinformatics and metagenomics

MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples – Moreno Zolfo – Nucleic Acids Resarch

ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data – Guangchuang Yu – Methods in Ecology and Evolution

Techniques

This article is not about primer barcodes, but compares 16S rRNA V6 PCR/454 sequencing to V4 PCR/Illumina sequencing:
Choice of molecular barcode will affect species prevalence but not bacterial community composition – Karen Lebret – Marine Genomics

Webinar | Combating the “garbage-in-garbage-out” paradigm: The importance of library prep in next-gen sequencing workflows – Maura Costello – Science

Microbes in the news

Bacteria have sculpted the world we live in, and that’s why MacArthur winner Dianne Newman studies them – Deborah Netburn – LA Times

Book Review: “Let Them Eat Dirt: Saving Your Child from an Oversanitized World” provides suggestions for a microbially rich and healthy childhood – Anne Estes – Mostly Microbes

Professionally printed version of Gut Check:The Microbiome Game available for a limited time from MOBIO. See below for a chance to win a free copy! – Anne Estes – Mostly Microbes

New Research Collaboration Explores Microbiome of the Space Station – Astrobiology Magazine

Swarms of magnetic bacteria could be used to deliver drugs to tumors – Science Daily

How do antibiotic-resistant bacteria get into the environment? – Suzanne Young and Valerie Harwood – The Conversation

Using bacteria to clean up oil – Anmar Frangoul – CNBC

Penn: Plant-made Antimicrobial Peptide Targets Dental Plaque and Gum Tissues – Penn News

Bacteria Hysteria

Note: little science here other than a 1997 paper, but lots of promotion for a certain manufacturer of stainless steel coffee mugs. Proceed with caution:
You should be washing your coffee mug way more than you think – Melia Robinson – Business Insider

And this one quotes a study from 1994, which looked at plant-based, not plastic sponges that were deliberately inoculated with pathogens. Proceed with caution:
Loofahs Have More Bacteria Than You Think — In Fact, You Should Probably Throw Yours Out – Lily Feinn – Bustle

Science, publishing, and career

Mark Zuckerberg and Priscilla Chan announce $3 billion effort aimed at curing disease – Shayla Love – STAT News

With some of my tweets!
A future without women – no female Future Prize nominees – Carla Bleiker – Deutsche Welle

September 20, 2016

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A review of antibiotics’ effect on the human microbiome, the pig gut microbiome, microbiome of Green Design, expanding Unifrac, and GutCheck, the Microbiome Game.

General human microbiome

Review: Antibiotic use and microbiome function – Manuel Ferrer – Biochemical Pharmacology

Human respiratory microbiome

Taxa of the Nasal Microbiome Are Associated with Influenza-Specific IgA Response to Live Attenuated Influenza Vaccine – Hannah M. Salk – PLOS ONE

Changes in the bacterial microbiome of patients with chronic rhinosinusitis after endoscopic sinus surgery – Ravi Jain – International Forum of Allergy & Rhinology

Human gut microbiome

Gastric microbiota in the functional dyspepsia patients treated with probiotic yogurt – Hirohiko Nakae – BMJ Open Gastroenterology

Animal microbiome

A reference gene catalogue of the pig gut microbiome – Liang Xiao – Nature Microbiology

Press: Gut Microbial Genes Profiled in Pigs From Diverse Breeds, Locations – Genome Web

The Prevalence of Canine Oral Protozoa and Their Association with Periodontal Disease – Niran Patel – The Journal of Eukaryotic Microbiology

Functional diversity of ant-associated bacterial communities – A. A. Dymova – Biology Bulletin

Plant, root, and soil microbiome

Can inoculation with living soil standardize microbial communities in soilless potting substrates? – Petra Bukovská – Applied Soil Ecology

Effects of saline water irrigation and fertilization regimes on soil microbial metabolic activity – Li -Juan Chen – Journal of Soils and Sediments

More on the Centralia coal mine fire (see yesterday’s post): Diversity and mechanisms of arsenic resistance among soil bacteria impacted by the ongoing Centralia coal mine fire – Taylor K Dunivin – PeerJ Preprint

Water and extremophile microbiome

Metagenomics as a preliminary screen for antimicrobial bioprospecting – Soha Al-Amoudi – Gene

Built environment microbiome

The Microbiome of Green Design: Sustainable building practices may have unforeseen consequences for microbial communities and human health – Carolyn Beans – BioScience

More microbiology

Cat-Scratch Disease in the United States, 2005–2013 – Christina A. Nelson – Emerging Infectious Diseases

Press: Don’t Kiss That Kitty: Cat-Scratch Fever Is Making People Sicker – Erin Ross – NPR

Bioinformatics and proteomics

Strategies to improve usability and preserve accuracy in biological sequence databases – Johan Bengtsson-Palme – Proteomics

Expanding the UniFrac Toolbox – Ruth G. Wong – PLOS ONE

MetaStorm: A Public Resource for Customizable Metagenomics Annotation – Gustavo Arango-Argoty – PLOS ONE

Microbes in the news

Gut Check: The Microbiome Game – MoBio
Gut Check: The Microbiome Game now available for purchase – David Coil – MicroBEnet

Antibiotic Resistant Bacteria and the World’s Peril: The U.N. General Assembly is taking on a danger that threatens the health of our entire species – Laurie Garrett – Scientific American

Scientists uncover a clever ranking strategy bacteria use to fight off viruses – NewsWire Rockefeller

Oetzi Iceman Update: Bacteria Found In Mummy’s Stomach May Lead To Cancer Research – Janice Williams – International Business News

Stone Age mummy still revealing secrets, 25 years on – Simon Sturdee – Phys.org

Lake Arrowhead Microbial Genomics #LAMG16 Report: Day 1 – David Coil – MicroBEnet

September 18, 2016

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Gut fermentation bubbles might promote decompression sickness in divers, corals of the Tropical Eastern Pacific, and a new microbiome book: Let Them Eat Dirt.

General microbiome

Review: Transitioning From Descriptive to Mechanistic Understanding of the Microbiome: The Need for a Prospective Longitudinal Approach to Predicting Disease – Victoria J. Martin – The Journal of Pediatrics

Pregnancy and early life

Shifts in Lachnospira and Clostridium sp. in the 3-month stool microbiome are associated with preschool-age asthma – Leah Stiemsma – Clinical Science

Human oral microbiome

Review: The role of bacteriophages in periodontal health and disease – Graça Pinto – Future Medicine

Human urinary tract microbiome

A diverse virome in kidney transplant patients contains multiple viral subtypes with distinct polymorphisms – Asha Rani – Scientific Reports

Human vaginal microbiome

Neither vaginal nor buccal administration of 800 μg misoprostol alters mucosal and systemic immune activation or the cervicovaginal microbiome: a pilot study – Spyros A. Kalams – The European Journal of Contraception & Reproductive Health Care

Human gut microbiome

Gut fermentation seems to promote decompression sickness in humans – Sébastien de Maistre – Journal of Applied Physiology

Review: Role of gut microbiota and nutrients in amyloid formation and pathogenesis of Alzheimer disease – Francesca Pistollato – Nutrition Reviews

Review: Enteric immunity, the gut microbiome, and sepsis: Rethinking the germ theory of disease – Javier Cabrera-Perez – Experimental Biology and Medicine

Review: Probiotic supplementation can positively affect anxiety and depressive symptoms: a systematic review of randomized controlled trials – Meysam Pirbaglou – Nutrition Research

Animal experiments

Structural modulation of the gut microbiota and the relationship with body weight: compared evaluation of liraglutide and saxagliptin treatment – Lin Wang – Scientific Reports

Microbial antigen mimics activate diabetogenic CD8 T cells in NOD mice – Ningwen Tai – Journal of Experimental Medicine

Press: Yale study shows that gut microbes could trigger type 1 diabetes – Jack Woodfield – Diabetes.co.uk

Intestinal immune maturation is accompanied by temporal changes in the composition of the microbiota – G. Den Hartog – Beneficial Microbes

Animal microbiome

First deep screening of bacterial assemblages associated with corals of the Tropical Eastern Pacific – Joicye Hernández-Zulueta – FEMS Microbiology Ecology

Bioinformatics

Reference point insensitive molecular data analysis – M. Altenbuchinger – Bioinformatics

Microbes in the news
New book: Let Them Eat Dirt – B. Brett Finlay and Marie-Claire Arrieta

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 9, 2016

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Climate change and increasing Vibrio species in North Atlantic, microbiome of the aging mouth, Antarctic soil around Little Auk colony.

Events

5th Exploring Human Host-Microbiome Interactions in Health and Disease – Welcome Genome Campus, Cambridge, UK, 7-9 September 2016

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

Hot topics in microbiology: Campden BRI conference – Campden BRI, Chipping Campden, Gloucestershire, UK, October 13-14

Today & tomorrow – live webcast – Standards for Microbiome Measurements @NIST – Jonathan Eisen – MicroBEnet

General microbiome

Note: includes 16S rRNA gene studies as well, so not metagenomic sensu stricto: An overview of major metagenomic studies on human microbiomes in health and disease – Hongfei Cui – Quantitative Biology

Brazil: A Step Forward to Empower Global Microbiome Research Through Local Leadership – Victor S. Pylro – Trends in Microbiology

Human oral microbiome

Distinct interacting core taxa in co-occurrence networks enable discrimination of polymicrobial oral diseases with similar symptoms – Takahiko Shiba – Scientific Reports

Oral microbial community typing of caries and pigment in primary dentition – Yanhui Li – BMC Genomics

Review: The subgingival periodontal microbiota of the aging mouth – Magda Feres – Periodonotology 2000

Human respiratory microbiome

Review: The microbiome in chronic inflammatory airway disease: A threatened species – Robin John Green – The South African Medical Journal

Review: Lung microbiome in human immunodeficiency virus infection – Homer L. Twigg IIIa – Translational Research

Human vaginal microbiome

Evaluation of the vaginal flora in pregnant women receiving opioid maintenance therapy: a matched case-control study – Alex Farr – BMC Pregnancy Childbirth

Human gut microbiome

Microbial Factors Associated with Postoperative Crohn’s Disease Recurrence – Emily K. Wright – Journal of Crohn’s and Colitis

The mucosal microbiota in a young child with severe non-Helicobacter gastritis – Geoffrey A. Preidis – Therapeutic Advances in Gastroenterology

Profile of Gut Microbiota Associated With the Presence of Hepatocellular Cancer in Patients With Liver Cirrhosis – M. Grąt – Transplantation Proceedings

Comparison of the gut microbial community between obese and lean peoples using 16S gene sequencing in a Japanese population – Akira Andoh – Journal of Clinical Biochemistry and Nutrition

Book Chapter: The Second Brain and Possible Interactions with the Heart – Rosa Sollazzo – Psychotherapy for Ischemic Heart Disease

Infection microbiology

Comparison of methods for the identification of microorganisms isolated from blood cultures – Aydir Cecília Marinho Monteiro – Annals of Clinical Microbiology and Antimicrobials

Animal experiments

Disturbance in the Mucosa-Associated Commensal Bacteria Is Associated with the Exacerbation of Chronic Colitis by Repeated Psychological Stress; Is That the New Target of Probiotics? – Sohei Arase – PLOS ONE

Role of the Gut Microbiome in Modulating Arthritis Progression in Mice – Xiaofei Liu – Scientific Reports

Salmonella Typhimurium utilizes a T6SS-mediated antibacterial weapon to establish in the host gut – Thibault G. Sana – PNAS

Animal microbiome

Does adaptive radiation of a host lineage promote ecological diversity of its bacterial communities? A test using gut microbiota of Anolis lizards – Tiantian Ren – Molecular Ecology

The gut microbiota of the pine weevil is similar across Europe and resembles that of other conifer-feeding beetles – Aileen Berasategui – Molecular Ecology

Plant, root, and soil microbiome

The Arctic soil bacterial communities in the vicinity of a little auk colony – Sylwia Zielinska – Frontiers in Microbiology

Soil Fungal:Bacterial Ratios Are Linked to Altered Carbon Cycling – Ashish A. Malik – Frontiers in Microbiology

Ancient landscapes and the relationship with microbial nitrification – Sasha N. Jenkins – Scientific Reports

Long-term antibiotic exposure in soil is associated with changes in microbial community structure and prevalence of class 1 integrons – David W. Cleary – FEMS Microbiology Ecology

Are Epiphytic Microbial Communities in the Carposphere of Ripening Grape Clusters (Vitis vinifera L.) Different between Conventional, Organic, and Biodynamic Grapes? – Elizabeth Kecskeméti – PLOS ONE

Bacterial communities in Antarctic lichens – Chae Haeng Park – Antarctic Science

Water and extremophile microbiome

Climate influence on Vibrio and associated human diseases during the past half-century in the coastal North Atlantic – Luigi Vezzulli – PNAS

Press: We’re trashing the oceans — and they’re returning the favor by making us sick – Chris Mooney – The Washington Post
Deadly Bacteria Spread across Oceans as Water Temperatures Rise. Cholera bacteria and others arise in more places and in greater abundance – Umair Irfan – Scientific American
Warming seas linked to rise in cholera bacteria in Europe and US – Brian Owens – New Scientist

Microbial community structure in hypolentic zones of a brine lake in a desert plateau, China – Wenzhen Yuan – Environmental Earth Sciences

Microbial diversity in sediment ecosystems (evaporites domes, microbial mats and crusts) of hypersaline Laguna Tebenquiche, Salar de Atacama, Chile – Ana B. Fernandez – Frontiers in Microbiology

Bioreactor microbiome

The full-scale anaerobic digestion microbiome is represented by specific marker populations – Jo De Vrieze – Water Research

Viruses and phages

Challenges in the analysis of viral metagenomes – Rebecca Rose – Virus Evolution

Metagenomics and bioinformatics

Bipartite graph analyses reveal inter-domain LGT involving ultrasmall prokaryotes and their divergent, membrane-related proteins – Alexander L. Jaffe – Environmental Microbiology

FARAO – The Flexible All-Round Annotation Organizer – Rickard Hammarén – Bioinformatics

Identifying wrong assemblies in de novo short read primary sequence assembly contigs – Vandna Chawla – Journal of Biosciences

A Bayesian Framework for the Classification of Microbial Gene Activity States – Craig Disselkoen – Frontiers in Microbiology

Techniques

Evaluation of 16S rRNA gene primer pairs for monitoring microbial community structures showed high reproducibility within and low comparability between datasets generated with multiple archaeal and bacterial primer pairs – Martin A. Fischer – Frontiers in Microbiology

More microbiology

Editorial: New insights into microbial ecology through subtle nucleotide variation – A M. Eren – Frontiers in Microbiology

Neisseria meningitides Can Survive in Corpses for At Least Eleven Days – Antonio Osculati – Frontiers in Cellular and Infection Microbiology

Microbes in the news

List of papers about bias in microbiome techniques: The unbearable madness of microbiome – Mick Watson – Opiniomics

Book Review: Follow your gut – The Enormous Impact of Tiny Microbes – Daniel K. Morais – Frontiers in Microbiology

Brito went to Fiji to study mobile genes in human microbiome – Tom Fleischman – Cornell Chronicle

MSU graduate awarded NSF fellowship to study disease affecting world’s citrus crops – Denise Hoepfner – Montana State University

Bacteria Could Aid Search for Creatures On Other Planets – Elizabeth Howell – Astrobiology Magazine

U.Va. scientists make important discovery about dangerous bacteria strains
Researchers pinpoint mechanisms of C. difficile strains – Daisy Xu – Cavalier Daily

Did farming practices in China create an antibiotic resistant bacteria that’s spreading around the world? – Alanna Shaikh – United Nations Dispatch

Science, publishing, and career

Dog eat dog: is a troubled expedition to Kenya causing the Smithsonian to devour its young?
A star scientist stands accused of misconduct, but colleagues say he’s being railroaded
– Michael Balter – The Verge

A “Scientific Diversity” Intervention to Reduce Gender Bias in a Sample of Life Scientists – Corinne A. Moss-Racusin – CBE Life Sciences Education

Bik’s non-microbiology Picks

Innate Immunity and Asthma Risk in Amish and Hutterite Farm Children – Michelle M. Stein – New England Journal of Medicine

August 5, 2016

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Urinary tract microbiome, preterm gut microbiota and humanized mice, fungi of Crocus (Saffron plant), and bead-beating artefacts.

General microbiome

Introduction to special issue of Molecular Metabolism: Microbiota: ‘bugging’ insights into metabolic regulation – Thomas Schwarz-Romond – Molecular Metabolism

Human oral microbiome

Transcriptome Analysis of B Cell Immune Functions in Periodontitis: Mucosal Tissue Responses to the Oral Microbiome in Aging – Jeffrey L. Ebersole – Frontiers in Immunology

Human respiratory microbiome

Randomised, double-blind, placebo-controlled trial with azithromycin selects for anti-inflammatory microbial metabolites in the emphysematous lung – Leopoldo N Segal – Thorax

Review: Microbiome in the pathogenesis of cystic fibrosis and lung transplant-related disease – Sushma K. Cribbs – Translational Research

Human urinary tract microbiome

Evaluation of the Urinary Microbiota of Women With Uncomplicated Stress Urinary Incontinence – Krystal J. Thomas-White – American Journal of Obstetrics and Gynecology

Human gut microbiome

Review: Microbiota as Mediator of Cancer Progression and Therapy – Jilian L. Pope – Translational Research

Review: The human microbiome in rheumatic autoimmune diseases: A comprehensive review – Patrick Coit – Clinical Immunology

Review: Human gut microbiota plays a role in the metabolism of drugs – Lenka Jourova – Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub

Animal experiments

Preterm infant gut microbiota affects intestinal epithelial development in a humanized gnotobiotic mouse model – Yueyue Yu – American Journal of Physiology – Gastrointestinal and Liver Physiology

Symbiotic gut commensal bacteria act as host cathepsin S activity regulators – Alex Steimle – Journal of Autoimmunity

Research Highlight (but very harsh title): Gut microbiota: Microbiota and behaviour: visiting the sins of the mother – Paul Forsythe – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

A high-resolution map of the gut microbiota in Atlantic salmon (Salmo salar): A basis for comparative gut microbial research – Karina Gajardo – Scientific Reports

Plant, root, and soil microbiome

Molecular phylogeny, diversity, community structure and plant growth promoting properties of fungal endophytes associated with the corms of Saffron plant: an insight into the microbiome of Crocus sativus Linn – Zahoor Ahmed Wani – Fungal Biology

Leaf Treatments with a Protein-Based Resistance Inducer Partially Modify Phyllosphere Microbial Communities of Grapevine – Martina Cappelletti – Frontiers in Plant Science

The Resilience of Microbial Community under Drying and Rewetting Cycles of Three Forest Soils – Xue Zhou – Frontiers in Microbiology

Fungus-associated bacteriome in charge of their host behavior – Kristin Schulz-Bohm – Fungal Genetics and Biology

Microbiota Characterization of Compost Using Omics Approaches Opens New Perspectives for Phytophthora Root Rot Control – Josefa Blaya – PLOS ONE

Water and extremophile microbiome

Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris – Sonja Oberbeckmann – PLOS ONE

Microbial Community Responses to Increased Water and Organic Matter in the Arid Soils of the McMurdo Dry Valleys, Antarctica – Heather N. Buelow – Frontiers in Microbiology

Microbial community structure shifts are associated with temperature, dispersants and nutrients in crude oil-contaminated seawaters – Long Meng – Marine Pollution Bulletin

Bioinformatics and metagenomics

Rapid resistome mapping using nanopore sequencing – Eric van der Helm – bioRxiv

Metabolomics

Metabolomics evaluation of the impact of smokeless tobacco exposure on the oral bacterium Capnocytophaga sputigena – Jinchun Sun – Toxicology in Vitro

Training in metabolomics research. II. Processing and statistical analysis of metabolomics data, metabolite identification, pathway analysis, applications of metabolomics and its future – S. Barnes – Journal of Mass Spectrometry

Techniques

Bead-beating artefacts in the Bacteroidetes to Firmicutes ratio of the human stool metagenome – Heidi C. Vebø – Journal of Microbiological Methods

Pipeline for amplifying and analyzing amplicons of the V1–V3 region of the 16S rRNA gene – Heather K. Allen – BMC Research Notes

A Single-Batch Fermentation System to Simulate Human Colonic Microbiota for High-Throughput Evaluation of Prebiotics – Risa Takagi – PLOS ONE

More microbiology

Metabolic engineering of microbial competitive advantage for industrial fermentation processes – A. Joe Shaw – Science

Microbes in the news

AGA establishes NIH-funded registry to track fecal microbiota transplants – EurekAlert

Maternal microbial inheritance—benefits of breastfeeding – Md Zohorul Islam

ASM Agar Art Calendar 2016/2017

Science, publishing, and career

What Is the Key Best Practice for Collaborating with a Computational Biologist? – Cell Systems

University of Waterloo boosts salaries of female faculty after discrepancy found – Paola Loriggio – CP24

Bik’s Non-Microbiology Picks

Circadian regulation of sunflower heliotropism, floral orientation, and pollinator visits – Hagop S. Atamian – Science
How do sunflowers follow the Sun—and to what end? – Winslow R. Briggs – Science

August 2, 2016

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Microbial mercury in Antarctic sea ice, bacteria and magnetic field, and what is living in your showerhead.

Events and jobs

Microbiomes of the Built Environment – Meeting #3  (will also be web-casted) – Monday October 17, 2016, at UC Irvine, CA

Postdoctoral position in microbial physiology/environmental microbiology, self-healing concrete, Aarhus University Denmark – Science Careers

General microbiome

Philosophical Transactions of the Royal Society B themed issue: ‘From DNA barcodes to biomes’
A new way to contemplate Darwin’s tangled bank: how DNA barcodes are reconnecting biodiversity science and biomonitoring – Mehrdad Hajibabaei
Dissecting host-associated communities with DNA barcodes – Christopher C. M. Baker
Scaling up discovery of hidden diversity in fungi: impacts of barcoding approaches – Rebecca Yahr
Insect symbionts in food webs – Ailsa H. C. McLean

Pregnancy and birth

Review: The mode of delivery affects the diversity and colonization pattern of the gut microbiota during the first year of infants’ life: a systematic review – Erigene Rutayisire – BMC Gastroenterology

Human (and animal) oral microbiome

Review: Gene Sequence Analyses of the Healthy Oral Microbiome in Humans and Companion Animals: A Comparative Review – Eric M. Davis – Journal of Veterinary Dentistry

Human respiratory microbiome

Association between Staphylococcus aureus nasal carriage and disease phenotype in patients affected by systemic lupus erythematosus – Fabrizio Conti – Arthritis Research & Therapy

Human gut microbiome

Alterations in the Fecal Microbiota of Patients with HIV-1 Infection: An Observational Study in A Chinese Population – Zongxin Ling – Scientific Reports

Animal experiments

Chronic Repression of mTOR Complex 2 Induces Changes in the Gut Microbiota of Diet-induced Obese Mice – Mi-Ja Jung – Scientific Reports

Plant, root, and soil microbiome

Environmental metabarcoding reveals contrasting microbial communities at two poplar phytomanagement sites – Julie Foulon – Science of the Total Environment

Coupling among Microbial Communities, Biogeochemistry, and Mineralogy across Biogeochemical Facies – James C. Stegen – Scientific Reports

Water and extremophile microbiome

Microbial mercury methylation in Antarctic sea ice – Caitlin M. Gionfriddo – Nature Microbiology

Press: Antarctic sea ice may be a source of mercury in southern ocean fish and birds – Phys.org

Magnetic properties of iron minerals produced by natural iron- and manganese-reducing groundwater bacteria – Alexandra Abrajevitch – Geophysical Journal International

Press: Bacteria Preserve Record of Earth’s Magnetic Fields – EOS

Evidence of small-scale spatial structuring of phytoplankton alpha- and beta-diversity in the open ocean – Erik Askov Mousing – Journal of Ecology

Food microbiology

Bacterial microbiota compositions of naturally fermented milk are shaped by both geographic origin and sample type – Z. Zhong – Journal of Dairy Science

Viruses and phages

The Double-Stranded DNA Virosphere as a Modular Hierarchical Network of Gene Sharing – Jaime Iranzo – mBio

Bioinformatics and metagenomics/metabolomics

Updated version: GutCyc: a Multi-Study Collection of Human Gut Microbiome Metabolic Models – Aria S. Hahn – bioRxiv

Microbes in the news

Is your gut making you sick?. New research suggests that the range and quantity of microbes that live in our guts could have a powerful effect on a range of conditions including depression, MS and obesity – Ann Robinson – The Guardian

How purple bacteria could help save amphibians in the Rockies : A Colorado researcher is using boreal toads’ microbiomes to help them ward off a deadly fungus – Krista Langlois – High Country News

A short and weird story: Bacteria Filled Water Almost Sends ‘Naked and Afraid’ Contestant Home – Natalie D’Alacio – Yahoo News

Your Showerhead Is Crammed Full of Bacteria That Scientists Want to Study – Kate Lunau – Motherboard

If You Had Really Good Eyesight, Could You See a Single Bacterium? – Julie Taylor – uBiomeBlog

Letter: The microbiologist who didn’t wash his hands after urinating – Peter Dawson – The Guardian

Women more likely to die from bacterial blood infection – Adrian O’Dowd – OnMedica

Sham Poo Washes Out. A bacterial pill that tried to duplicate the benefits of a fecal transplant has failed a clinical trial. What does that mean for the microbiome field? – Ed Yong – The Atlantic

Science, publishing, and career

Not “Pulling up the Ladder”: Women Who Organize Conference Symposia Provide Greater Opportunities for Women to Speak at Conservation Conferences – Stephanie Sardelis – PLOS ONE

In Australia: Stella Count: Women write twice as many books as men, but receive less than half the reviews – Daisy Dumas – Daily Life

 

August 1, 2016

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Storage conditions of infant fecal microbiota, microbial pinnacles, bioaerosols in chicken production facilities.

General microbiome

Special issue of Microbial Biotechnology, including:
Biome engineering-2020 – Harald Brüssow
Microbial bioinformatics 2020 – Mark J. Pallen
Next-generation studies of microbial biofilm communities – Scott A. Rice
Plant–microbe partnerships in 2020 – Birgit Mitter

Opinion: Controlling the Microbiome: Microhabitat Adjustments for Successful Biocontrol Strategies in Soil and Human Gut – Eveline Adam – Frontiers in Microbiology

Pregnancy and birth

Latitude in sample handling and storage for infant faecal microbiota studies: the elephant in the room? – Alexander G Shaw – Microbiome

Gut Microbiota Richness and Composition and Dietary Intake of Overweight Pregnant Women Are Related to Serum Zonulin Concentration, a Marker for Intestinal Permeability – Kati Mokkala – The Journal of Nutrition

Review: Microbial Changes during Pregnancy, Birth, and Infancy – Meital Nuriel-Ohayon – Frontiers in Microbiology

Human eye microbiome

Ocular surface microbiome in meibomian gland dysfunction in Auckland, New Zealand –
Grant A. Watters – Clinical & Experimental Ophtalmology

Human gut microbiome

Microbial diversity in individuals and their household contacts following typical antibiotic courses – Shira R. Abeles – Microbiome

Microbial Factors Associated with Post-Operative Crohn’s Disease Recurrence – Emily K Wright – Journal of Crohn’s and Colitis

Efficacy of antineoplastic treatment is associated with the use of antibiotics that modulate intestinal microbiota – Natali Pflug – OncoImmunology

Review: The oesophageal microbiome: an unexplored link in obesity-associated oesophageal adenocarcinoma – Nadeem O. Kaakoush – FEMS Microbiology Ecology

Review: Normal, Regular and Standard: Scaling the Body through Fecal Microbial Transplants – Matthew J. Wolf-Meyer – Medical Anthropology Quarterly

Review: Gut Microbiota Imbalance and Base Excision Repair Dynamics in Colon Cancer – Debolina Ray – Journal of Cancer

Review: Fine-Tuning Cancer Immunotherapy: Optimizing the Gut Microbiome – Jonathan M. Pitt – Cancer Research

Review: Irritable bowel syndrome, the microbiota and the gut-brain axis – Hans Raskov – Gut Microbes

Animal microbiome

Fish: Alterations of the gut microbiome of largemouth bronze gudgeon (Coreius guichenoti) suffering from furunculosis – Tongtong Li – Scientific Reports

Plant, root, and soil microbiome

Structure of bacterial communities in soil following cover crop and organic fertilizer incorporation – Adria L. Fernandez – Applied Microbiology and Biotechnology

Correlation analysis of enzyme activities and deconstruction of ammonia-pretreated switchgrass by bacterial-fungal communities – Abhiney Jain – Bioresource Technology

Variations of rhizosphere bacterial communities in tea (Camellia sinensis L.) continuous cropping soil by high-throughput pyrosequencing approach – Y.C. Li – Journal of Applied Microbiology

High culturability of epiphytic bacteria and frequency of biosurfactant producers on leaves – Adrien Y. Burch – Applied and Environmental Microbiology

Desiccation of sediments affects assimilate transport within aquatic plants and carbon transfer to microorganisms – Isabell von Rein – Plant Biology

Review: Emergence of plant and rhizospheric microbiota as stable interactomes – Prasun Bandyopadhyay – Protoplasma

Water and extremophile microbiome

Growth of elaborate microbial pinnacles in Lake Vanda, Antarctica – D. Y. Sumner – Geobiology

Diversity and succession of autotrophic microbial community in high-elevation soils along deglaciation chronosequence – Jinbo Liu – FEMS Microbial Ecology

Air microbiome

High throughput genomic sequencing of bioaerosols in broiler chicken production facilities – Kate M. O’Brien – Microbial Biotechnology

Bioinformatics

RevEcoR: an R package for the reverse ecology analysis of microbiomes – Yang Cao – BMC Bioinformatics

Metabolomics

Review: Metabolites: messengers between the microbiota and the immune system – Maayan Levy – Genes & Development

Techniques

Phylogenetically Structured Differences in rRNA Gene Sequence Variation among Species of Arbuscular Mycorrhizal Fungi and Their Implications for Sequence Clustering – Geoffrey L. House – Applied and Environmental Microbiology

Microbes in the news
Why is microbiome so important? Gut instinct tells you – Jessica le Roux – FoodMed

Science, publishing, and career

Intentional equity – France A. Córdova – Science

Lost in Translation: From scientists to the press and to the public – The Microbial Menagerie