Category Archives: Plant Root Soil microbiome

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 22, 2016

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Human skin microbiome

Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis – Mercedes E. Gonzalez – Journal of the American Academy of Dermatology

Animal microbiome

Yeasts from the microbiota of bats: a focus on the identification and antimicrobial susceptibility of cryptic species of Candida – Raimunda S. N. Brilhante – Journal of Medical Microbiology

Plant, root, and soil microbiome

Intrinsic factors of Peltigera lichens influence the structure of the associated soil bacterial microbiota – Diego Leiva – FEMS Microbiology Ecology

Bacterial succession on decomposing leaf litter exhibits a specific occurrence pattern of cellulolytic taxa and potential decomposers of fungal mycelia – Vojtěch Tláskal – FEMS Microbiology Ecology

Local Environmental Factors Drive Divergent Grassland Soil Bacterial Communities in the Western Swiss Alps – Erika Yashiro – Applied and Environmental Microbiology

Watershed Assessment with Beach Microbial Source Tracking (MST) and Outcomes of Resulting Gull Management – Kelly D. Goodwin – Environmental Science & Technology

Microbial ecology

The importance of neutral and niche processes for bacterial community assembly differs between habitat generalists and specialists – Jingqiu Liao – FEMS Microbiology Ecology

Bioinformatics and metagenomics

A scalable assembly-free variable selection algorithm for biomarker discovery from metagenomes – Anestis Gkanogiannis – BMC Bioinformatics

Microbes in the news

The Strange Case of the Butterfly and the Male-Murdering Microbe – Ed Yong – The Atlantic

Bigelow Lab’s role in algae industry is growing – Kevin Miller – Press Herald

Science, publishing, and career

Why academics should make time for social media – Andy Miah – Times Higher Education

Introducing our special section on “The Integrity of Science” – The New Atlantis

August 20, 2016

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Microbial eukaryotes along a pollution gradient, bacteria binding to ice, and testing the neutral theory.

Jobs and events

Assistant Professor in Genomics and Ecology of Microbial Pathogens in Food Systems Department of Food Science & Technology, University of California, Davis (via Jonathan Eisen – MicroBE.net)

Human gut microbiome

Gastrointestinal microbial populations can distinguish pediatric and adolescent Acute Lymphoblastic Leukemia (ALL) at the time of disease diagnosis – Seesandra V. Rajagopala – BMC Genomics

Review: Diet and Gut Microbial Function in Metabolic and Cardiovascular Disease Risk – Katie A. Meyer – Current Diabetes Reports

Review: Other Helicobacters and gastric microbiota – Chloë De Witte – Helicobacter

Plant, root, and soil microbiome

Spatial Distribution of Eukaryotic Communities Using High-Throughput Sequencing Along a Pollution Gradient in the Arsenic-Rich Creek Sediments of Carnoulès Mine, France – A. Volant – Microbial Ecology

Water and extremophile microbiome

Putting life on ice: bacteria that bind to frozen water – Maya Bar Dolev – Journal of the Royal Society Interface

Genetic signatures of ecological diversity along an urbanization gradient – Ryan P. Kelly – PeerJ Preprint

Surveys, simulation and single-cell assays relate function and phylogeny in a lake ecosystem – Sarah P. Preheim – Nature Microbiology

Book: Microbes from Hell: archaea and hyperthermophiles – Patrick Forterre

Drinking water and water treatment microbiology

Elucidation of Taste- and Odor-Producing Bacteria and Toxigenic Cyanobacteria in a Midwestern Drinking Water Supply Reservoir by Shotgun Metagenomic Analysis – Timothy G. Otten – Applied and Environmental Microbiology

Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics – Johan Bengtsson-Palme – Science of the Total Environment

Microbial Ecology

Testing the Neutral Theory of Biodiversity with Human Microbiome Datasets – Lianwei Li – Scientific Reports

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

Microbes in the news

We need to stop sanitizing everything and let bacteria back in our lives – Joselin Linder – New York Post

Bacteria may be key to environmentally friendly extraction of minerals – Angela Kean – S&P Capital IQ

Science, publishing, and career

What lurks in ageing academics’ unvisited personal archives? – Ron Iphofen – Times Higher Education
Army report says science director creating ‘environment of fear’ at USAMRIID – Sylvia Carignan – Frederick News Post

August 19, 2016

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Gingivitis and periodontitis in Malawian cohort, gut Bifidobacteria during aging, picornaviruses in rats from 2 locations.

Jobs and events

QIIME 2 workshop Nov 4-5 (just prior to SSSA meeting) in Phoenix, AZ – Greg Caporaso – Microbe.net

Three postdoctoral researchers and one Ph.D. student: role of microbes in post-fire soil organic matter dynamics – University of Wisconsin-Madison

Human oral microbiome

Distinguishing the Signals of Gingivitis and Periodontitis in Supragingival Plaque: A Cross-Sectional Cohort Study in Malawi – Liam Shaw – Applied and Environmental Microbiology

Press: Investigators chart microbial ecology of gingivitis, periodontitis – EurekAlert

Association of metabolic syndrome and chronic periodontitis in Colombians – Adriana Jaramillo – Clinical Oral Investigations

Microbial Signatures of Oral Dysbiosis, Periodontitis and Edentulism Revealed by Gene Meter Methodology – M Colby Hunter – bioRxiv

Human gut microbiome

Review: Gut Bifidobacteria Populations in Human Health and Aging – Silvia Arboleya – Frontiers in Microbiology

Review: Correlations of host genetic and gut microbiome composition – Krystyna Dabrowska – Frontiers in Microbiology

Review: Gut Microbiota: a contributing factor to obesity – Steve M. Harakeh – Frontiers in Cellular and Infection Microbiology

Animal microbiome

High diversity of picornaviruses in rats from different continents revealed by deep sequencing – Thomas Arn Hansen – Emerging Microbes & Infections

Composition of Ileal Bacterial Community in Grazing Goats Varies across Non-rumination, Transition and Rumination Stages of Life – Jinzhen Jiao – Frontiers in Microbiology

Spatial and temporal dynamics of Pacific oyster hemolymph microbiota across multiple scales – Ana Lokmer – Frontiers in Microbiology

Plant, root, and soil microbiome

Unexpectedly high beta-diversity of root-associated fungal communities in the Bolivian Andes – Christopher J. Barnes – Frontiers in Microbiology

Fungal Assemblages in Different Habitats in an Erman’s Birch Forest – Teng Yang – Frontiers in Microbiology

Water microbiome

Chronic Polyaromatic Hydrocarbon (PAH) Contamination Is a Marginal Driver for Community Diversity and Prokaryotic Predicted Functioning in Coastal Sediments – Mathilde Jeanbille – Frontiers in Microbiology

Microbes in space

The theory and application of space microbiology: China’s experiences in space experiments and beyond – Changting Liu – Environmental Microbiology

Bioreactor microbiology

Colonic Transit Time Is a Driven Force of the Gut Microbiota Composition and Metabolism: In Vitro Evidence – William Tottey – Journal of Neurogastroenterology and Motility

Bioinformatics

Resolving microbial membership using Abundance and Variability In Taxonomy (‘AVIT ) – Anirikh Chakrabarti – Scientific Reports

Microbes in the news

Trillions of Tiny Dictators. Microbes have taken over our bodies and maybe even our minds. What, exactly, are they? – Emily Willingham – The Wall Street Journal
With a little help from my friends. The microbiome gets a worthy biography – The Economist
Eating Yogurt Is Not Enough: Rebalancing The Ecosystem Of ‘The Microbes Within Us’ – Terry Gross – NPR Fresh Air (Transcript of interview with Ed Yong)

Prebiotics Take Front and Center Stage on the 700 Club – PR NewsWire

Uncovering the female body’s secret protection against HIV – Heather Boerner – PBS Newshour

Scientific Studies Using Mice May Be Hard to Replicate Due to Gut Microbes – Paul Ratner – BigThink

Scientists Investigate How Multidrug-Resistant Pathogens are Brought into Hospitals – SciCasts

MSU team shows biofilm and mineral-producing bacteria have potential for plugging oil and gas leaks – Marshall Swearingen – Montana State University

Montana Officials Close Yellowstone River To Fight Fish-Killing ParasiteMontana Officials Close Yellowstone River To Fight Fish-Killing Parasite – Richard Gonzales – NPR

Science, publishing, and career

Peer Review Week September 2016 #RecognizeReview – Alice Meadows – The Scholarly Kitchen

With Kate Rubins, a former PhD student in our lab: NASA Astronauts Successfully Install New Space Station Docking Port – Samantha Mathewson – Space.com

August 18, 2016

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Human gut microbiome

Aberrant IgA responses to the gut microbiota during infancy precedes asthma and allergy development – Majda Dzidic – The Journal of Allergy and Clinical Immunology

Plasmid metagenomics reveals multiple antibiotic resistance gene classes among the gut microbiomes of hospitalised patients – Tossawan Jitwasinkul – Journal of Global Antimicrobial Resistance

Review: The Role of the Microbiome in Gastrointestinal Cancer – Lydia E. Wroblewski – Gastroenterology Clinics of North America

Animal experiments

The Spectrum and Regulatory Landscape of Intestinal Innate Lymphoid Cells Are Shaped by the Microbiome – Meital Gury-BenAri – Cell

Animal microbiome

The Gut Microbiomes of Two Pachysoma MacLeay Desert Dung Beetle Species (Coleoptera: Scarabaeidae: Scarabaeinae) Feeding on Different Diets – Philippa Z. N. Franzini – PLOS ONE

A different gut microbial community between larvae and adults of a wild bumblebee nest (Bombus pascuorum) – Anneleen Parmentier – Insect Science

Plant, root, and soil microbiome

Plant Growth Promotion and Suppression of Bacterial Leaf Blight in Rice by Inoculated Bacteria – Sumera Yasmin – PLOS One

Bioinformatics

NCBI prokaryotic genome annotation pipeline – Tatiana Tatusova – Nucleic Acids Research

More microbiology

Design, synthesis, and testing toward a 57-codon genome – Nili Ostrov – Science

Microbes in the news

New polio cases in Nigeria spur massive response – Leslie Roberts – Science

Science, publishing, and career

This woman may know a secret to saving the brain’s synapses – Emily Underwood – Science

 

August 17, 2016

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Beneficial bacteria in the nose suppress pathogenic bacteria,  gut microbiome and Entamoeba histolytica infection, viromes of the Earth.

Jobs

Assistant/Associate Professor in Microbiology & Immunology, University of Illinois at Chicago – Science Careers

Internship: Coral microbiome under ocean acidification – King Abdullah University of Science and Technology – Saudi Arabia

Pregnancy and birth

Microbiota in Breast Milk of Chinese Lactating Mothers – Olga Sakwinska – PLOS ONE

Human skin microbiome

Review: Factors shaping the composition of the cutaneous microbiota – K. Szabó – British Journal of Dermatology

Human respiratory microbiome

Staphylococcus aureus Shifts toward Commensalism in Response to Corynebacterium Species – Matthew M. Ramsey – Frontiers in Microbiology

Press: New findings detail how beneficial bacteria in the nose suppress pathogenic bacteria– Science Daily

Human gut microbiome

Disease Severity and Immune Activity Relate to Distinct Interkingdom Gut Microbiome States in Ethnically Distinct Ulcerative Colitis Patients – Jordan S. Mar – mBio

Stool microbiome reveals diverse bacterial ureases as confounders of oral urea breath testing for Helicobacter pylori and Mycobacterium tuberculosis in Bamako, Mali – Mamoudou Maiga – Journal of Breath Research

Review: Antibiotics as deep modulators of gut microbiota: between good and evil – Gianluca Ianiro – Gut

Review: The Intestinal Bacterial Microbiome and E. histolytica Infection – Stacey L. Burgess – Curr Trop Med Reports

Review: The microbiome and immune regulation after transplantation – Tabibian, James H. – Transplantation

Review: Experimental design considerations in microbiota/inflammation studies – Robert J Moore – Clin Transl Immunology

Animal experiments

Wolbachia Endosymbionts Modify Drosophila Ovary Protein Levels in a Context-Dependent Manner – Steen Christensen – Applied and Environmental Microbiology

Composition of the Cockroach Gut Microbiome in the Presence of Parasitic Nematodes – Cláudia S. L. Vicente – Microbes and Environments

Animal microbiome

Link of a ubiquitous human coronavirus to dromedary camels – Victor M. Corman – PNAS

Plant, root, and soil microbiome

Changes in the composition of the RNA virome mark evolutionary transitions in green plants – Arcady Mushegian – BMC Biology

Review: Identifying the role of soil microbes in plant invasions – Wayne Dawson – Journal of Ecology

Water microbiome

Uncovering Earth’s virome – David Paez-Espino – Nature

Press: Unveiled: Earth’s Viral Diversity. Environmental datasets help researchers double the number of microbial phyla known to be infected by viruses.- Joint Genome Institute
Researchers complete unprecedented study of the global virome – Katherine Lindemann – Research Gate Blog

290 Metagenome-assembled Genomes from the Mediterranean Sea: Ongoing Effort to Generate Genomes from the Tara Oceans Dataset – Benjamin J Tully – bioRxiv

The Microbiome and Mental Health: Looking Back, Moving Forward with Lessons from Allergic Diseases – Alan C. Logan

Extremophile microbiome

Yeasts from macroalgae and lichens that inhabit the South Shetland Islands, Antarctica –
Alysson Wagner Fernandes Duarte – Environmental Microbiology Reports

Bioinformatics and metagenomics

Comparison of bacterial genome assembly software for MinION data and their applicability to medical microbiology – Kim Judge – Microbial Genomics

Fast comparison of genomic and meta-genomic reads with alignment-free measures based on quality values – Matteo Comin – BMC Medical Genomics

Gifted microbes for genome mining and natural product discovery – Richard H. Baltz – Journal of Industrial Microbiology & Biotechnology

Microbial Ecology

Biodiversity at multiple trophic levels is needed for ecosystem multifunctionality – Santiago Soliveres – Nature

Extrapolating abundance curves has no predictive power for estimating microbial biodiversity – Amy Willis – PNAS

Synergistic elimination of bacteria by phage and the immune system – Chung Yin (Joey) Leung – bioRxiv

Microbes in the news

The Counterintuitive Way That Microbes Survive in Antarctica – And what it could mean for the search for life on other worlds – Ed Yong – The Atlantic

Human Cells Make Up Only Half Our Bodies. A New Book Explains Why – Jonathan Weiner – New York Times

Journalist Edmund Soon-Weng Yong awarded 2016 Byron H. Waksman Award for excellence in the public communication of Life Sciences – NewsWise

Mouse microbes may make scientific studies harder to replicate – Kelly Servick – Science Mag

Biome, Genome, Microbiome…Houdinisome? – Jason Tetro – Germ Guy

Tiny Stanford invention purifies water in minutes using the sun – CNET

The importance of quality pre-analytical factors and their impact on microbiome analysis – Lisa Gamwell – DNA Genotek’s Microbiome Collection and Stabilization Blog

Behind paywall: Brazilian Researchers Profile Microbiome of Rio Before, During, After Olympic Games – Genome Web
Rio 2016 organizers are confident everything is fine. I’m not reassured – Sally Jenkins – Washington Post

Science, publishing, and career

Stanford programs prepare underrepresented high schoolers for careers in science, engineering and medicine – Victoria Chesley – Stanford News

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 13, 2016

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Fracking, floating islands and a multivariate statistical framework.

Human respiratory microbiome

Editorial: Another piece in the ‘research mosaic’ that describes the role of the lung microbiome in COPD – Gary B Huffnagle – Thorax

Review: Toward revision of antimicrobial therapies in hematopoietic stem cell transplantation: target the pathogens, but protect the indigenous microbiota – Alexander Khoruts – Translational Research

Human urinary tract microbiome

Note: no mention of extraction controls. Does the Urinary Microbiome Play a Role in Urgency Urinary Incontinence and Its Severity? – Lisa Karstens – Frontiers in Cellular Infection Microbiology

Human gut microbiome

Review: Gut Microbiota: Modulation of Host Physiology in Obesity – Vandana Nehra – Physiology

Close encounters of the type‐six kind: injected bacterial toxins modulate gut microbial composition – Martina Sassone‐Corsi – EMBO Reports

Plant, root, and soil microbiome

Floating islands: Metagenomic approach to characterize soil microbial diversity of Phumdi at Loktak Lake – Sampada Puranik – Water Science & Technology

Hydraulic fracturing offers view of microbial life in the deep terrestrial subsurface – Paula J. Mouser – FEMS Microbiology Ecology

Isolation studies reveal a shift in the cultivable microbiome of oak affected with Acute Oak Decline – Sandra Denman – Systematic and Applied Microbiology

Arbuscular mycorrhizal fungal communities in forest plant roots are simultaneously shaped by host characteristics and canopy-mediated light availability – Kadri Koorem – Plant and Soil

Soil and plant components ecological stoichiometry in four steppe communities in the Loess Plateau of China – Quanchao Zeng – CATENA

Effect of cobalt and silver nanoparticles and ions on Lumbricus rubellus health and on microbial community of earthworm faeces and soil – Livia Vittori Antisari – Applied Soil Ecology

Bioreactor microbiology

Engineering artificial communities for enhanced FTOH degradation – Matthew Lewis – Science of the Total Environment

Metagenomics, phages and viruses, bioinformatics

Metagenomic recovery of phage genomes of uncultured freshwater actinobacteria – Rohit Ghai – The ISME Journal

MixMC: A Multivariate Statistical Framework to Gain Insight into Microbial Communities – Kim-Anh Lê Cao – PLOS ONE

Book: Algorithms in Bioinformatics. 16th International Workshop, WABI 2016, Aarhus, Denmark, August 22-24, 2016. Proceedings
Better Identification of Repeats in Metagenomic Scaffolding – Jay Ghurye –
Compact Universal k-mer Hitting Sets – Yaron Orenstein

Proteomics

Review: Environmental Microbial Community Proteomics: Status, Challenges and Perspectives – Da-Zhi Wang – Int J Mol Sci

Microbes in the news

Saving antibiotics for when they are really needed: the Dutch example – Tony Sheldon – BMJ

Could friendly bacteria be used to treat cancer? – Paul Dyson – The Conversation

August 12, 2016

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On vacation, so here is a short and late Digest for you: Metabolomics of preterm birth, mouse gut bacteria collection, bacteria associated with mosses.

Pregnancy and birth

Use of metabolomics for the identification and validation of clinical biomarkers for preterm birth: Preterm SAMBA – Jose G. Cecatti – BMC Pregnancy and Childbirth

Animal microbiome

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota – Ilias Lagkouvardos – Nature Microbiology

First public collection of bacteria from the intestine of mice. Mouse gut bacteria find a new home – Science Daily

Environment shapes the fecal microbiome of invasive carp species – Jessica J. Eichmiller – Microbiome

Plant, root, and soil microbiome

Comparative analysis of bacteria associated with different mosses by 16S rRNA and 16S rDNA sequencing – Yang Tian – Journal of Basic Microbiology

Water microbiome

A metabolomics guided exploration of marine natural product chemical space – Dimitrios J. Floros – Metabolomics

Bioreactor microbiome

Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates – Irena Maus – Biotechnology for Biofuels

Food microbiology

Vegemite Beer: yeast extract spreads as nutrient supplements to promote fermentation – Edward D. Kerr – PeerJ

Microbial Ecology and other

Compartmentalization in PVC super-phylum: evolution and impact – Sandrine Pinos – Biology Direct

Conflicts over host manipulation between different parasites and pathogens: Investigating the ecological and medical consequences – Nina Hafer – BioEssays

Microbes in the news

Soil Has a Microbiome, too. The unique mix of microbes in soil has a profound effect on which plants thrive and which ones die – Carrie Arnold – Smithsonian

Gut bacteria have own circadian clock – MedicalXpress

Not your momma’s microbe lab: a new genetic engineering machine takes microbial design to the masses – Casey Gilman – Philly.com

How brushing your teeth could prevent cancer: Twice daily scrub reduces bacteria linked to bowel tumours – Colin Fernandez – Daily Mail

Picture of the day: Metal-oxidizing bacteria from a gold mine – Science 360

Attendee Shares Experience from DDW® 2016 Active Learning Session on the Gut Microbiome – Gasto.org

Science, publishing, and career

The manterruption is real. Why Women Talk Less Than Men at Work – Alicia Adamczyk – Time / Money Magazine

Satire: First Draft of Peer-Review Rebuttal Just Says “Fuck Off” – The Allium

 

 

August 11, 2016

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Association between gut microbiome and cardiovascular disease risk, Arctic glacial surface habitats.

Human oral microbiome

Review: Discuss the role of microorganisms in the aetiology and pathogenesis of periapical disease – Vincent Aw – Australian Endodontic Journal

Human respiratory microbiome

Environmental and mucosal microbiota and their role in childhood asthma – Lena T. Birzele – Allergy

FUT2 genotype influences lung function, exacerbation frequency and airway microbiota in non-CF bronchiectasis – Steven L Taylor – Thorax

Human vaginal microbiome

Review: Vaginal Microbiota and Lubricant Use During Labor. Implications for Nursing Research, Practice, and Policy – Katie G. McElroy – SAGE Open Nursing

Human gut microbiome

Gut Microbiome Associates With Lifetime Cardiovascular Disease Risk Profile Among Bogalusa Heart Study Participants – Tanika N Kelly – Circulation Research

Association of Intestinal Microbiota with Metabolic Markers and Dietary Habits in Patients with Type 2 Diabetes – Yamaguchi Y. – Digestion

Cardiorespiratory fitness as a predictor of intestinal microbial diversity and distinct metagenomic functions – Mehrbod Estaki – Microbiome

Bacterial invasion of the pancreas revealed after analyses of the pancreatic cyst fluids – Vilvapathy Narayanan – bioRxiv

Review: Insights into human evolution from ancient and contemporary microbiome studies – Stephanie L Schnorr – Current Opinion in Genetics & Development

http://www.sciencedirect.com/science/article/pii/S0959437X1630096X

Review: An overview of the bacterial contribution to Crohn disease pathogenesis – Moftah H Alhagamhmad – Journal of Medical Microbiology

Animal experiments

Intestinal Microbial Metabolites Are Linked to Severity of Myocardial Infarction in Rats – Vy Lam – PLOS ONE

Gut Microbial Metabolites Fuel Host Antibody Responses – Myunghoo Kim – Cell Host & Microbe

Fap2 Mediates Fusobacterium nucleatum Colorectal Adenocarcinoma Enrichment by Binding to Tumor-Expressed Gal-GalNAc – Jawad Abed – Cell Host & Microbe

Editorial: When Mr. Fap Meets the Gals – Santosh K. Ghosh – Cell Host & Microbe

Plant, root, and soil microbiome

Comparative metagenomic analysis reveals mechanisms for stress response in hypoliths from extreme hyperarid deserts – Phuong Thi Le – Genome Biology and Evolution

Review: Recent advances in actinorhizal symbiosis signaling – Emilie Froussart – Plant Molecular Biology

Water and extremophile microbiome

Marine and giant viruses as indicators of a marine microbial community in a riverine system – Lisa M. Dann – Microbiology Open

Linking microbial diversity and functionality of Arctic glacial surface habitats – Stefanie Lutz – Environmental Microbiology

More microbiology

Microbiology, philosophy and education – Maureen A. O’Malley – Microbiology Letters

Local adaptation of a bacterium is as important as its presence in structuring a natural microbial community – Pedro Gómez – Nature Communications

Review: Biofilms: an emergent form of bacterial life – Hans-Curt Flemming – Nature Reviews Microbiology

 

Microbes in the news

Mental Health, Free Will, and Your Microbiome – Maria Popova – BrainPickings

A grimy, black biofilm is starting to cover the Jefferson Memorial, and it can’t be killed – Michael E. Ruane – The Washington Post
NPS ready to battle grimy biofilm coating on Jefferson Memorial – Nick Iannelli – WTOP
The Jefferson Memorialome? The Jeffersonome? The Jefferson Microbiome? A biofilm by any other name … – Jonathan Eisen – MicroBEnet

Young Inventors Work On Secret Proteins To Thwart Antibiotic-Resistant Bacteria – Joe Palca – NPR Shots

DRDO developing bacteria from Antarctica to aid setting up of bio-toilets in India – India TV News

How the world’s tiniest organisms explain our evolution, our health, and our eventual demise: Interview with Ed Yong about Leeuwenhoek and microbes – Julia Belluz

Could Earth Bacteria Survive on Mars? LSU MARSLIFE Researcher Noelle Bryan Recovers Bacteria from the Stratosphere – Paige Brown Jarreau – Vimeo

Microbiology: Mob rule – Adrian Woolfson examines four books on the microbiological universe that churns within us – Nature

The social network in your gut – Wudan Yan – New Yorker

Bik’s non-microbiology Picks

Exoskeletons and economics: indoor arthropod diversity increases in affluent neighbourhoods – Misha Leong – Biology Letters

Research Highlight: Insect mix high in rich areas – Nature

Ancient DNA: Muddy messages about American migration – Suzanne McGowan – Nature

Science, publishing, and career

NIH sets new postdoc stipend levels – Maggie Kuo – Science

Kudos for female Antarctic researchers: to inspire the roughly 60% of early-career polar scientists who are women – Jan Strugnell – Nature

Nominate influential female Antarctic researchers and those involved in supporting research, both past and present, to potentially be included in Wikibomb event