Category Archives: Human gut

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 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

August 10, 2016

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Maternal high-fat diet and infant gut microbiome.

Pregnancy and birth

The early infant gut microbiome varies in association with a maternal high-fat diet – Derrick M. Chu – Genome Medicine

Press: Maternal high-fat diet during pregnancy can affect baby’s gut microbesMaternal high-fat diet during pregnancy can affect baby’s gut microbes – Dipali Pathak – Baylor College of Medicine

Human gut microbiome

Review: Microbiota and Neurological Disorders: A Gut Feeling – Walter H Moos – BioResearch Open Access

Press: How do the bugs in your gut affect neurodegenerative and psychiatric diseases? – EurekAlert

Animal experiments

Midgut microbiota and host immunocompetence underlie Bacillus thuringiensis killing mechanism – Silvia Caccia – PNAS

Plant, root, and soil microbiome

Yeast Biodiversity in Vineyard Environments Is Increased by Human Intervention –
João Drumonde-Neves – PLOS ONE

Microbes in the news

NIH grants $1.8 million for gut microbiome research in obesity, metabolic syndrome – Healio

How The Microbes Inside Us Went From Enemies To Purported Superhealers – Carolyn Beans – NPR

The poop scientist of Japan – and his dream toilet – Sanjena Sathian – Ozy

Gut Bacteria Mind Their Own Clock, Respond to Melatonin – Clinical Oncology

New model sheds light on secondary bacterial pneumonia – EurekAlert

Science, publishing, and career

Analysis of National Institutes of Health R01 Application Critiques, Impact, and Criteria Scores: Does the Sex of the Principal Investigator Make a Difference? – Anna Kaatz – Academic Medicine

The Government is Shortchanging Our Best Lady Scientists – Madison Pauly – Mother Jones

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 8, 2016

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Sutures, preterm birth, and vaginal dysbiosis, captive Komodo Dragons, and stochastic assembly of microbial communities.

Jobs

Assistant Professor of Biology (Microbiology): background in microbiome research, molecular mechanisms of microbial pathogenesis, virulence and/or quorum sensing, or host-pathogen interactions – California State University, East Bay

Human vaginal microbiome

Relationship between vaginal microbial dysbiosis, inflammation, and pregnancy outcomes in cervical cerclage – Lindsay M. Kindinger – Science Translational Medicine

Press: Pregnancy procedure may be associated with increased risk of premature birth and neonatal loss – Science Daily
Braided Cervical Cerclage May Raise Risk for Preterm Birth – Lara C. Pullen – MedScape

Human gut microbiome

Addendum (reanalysis of published data): Partial recovery of microbiomes after antibiotic treatment – Frédéric Raymond – Gut Microbes

Review: Microbiota and chronic inflammatory arthritis: an interwoven link – Andrea Picchianti Diamanti – Journal of Translational Medicine

Review: Microbiomic and Posttranslational Modifications as Preludes to Autoimmune Diseases – Ghislain Opdenakker – Trends in Molecular Medicine

Animal microbiome

The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat – Embriette R. Hyde – mSystems

Press: What Captive Komodo Dragons Might Tell Us About Our Own Microbiomes – UC San Diego Health

Dysbiosis of the Fecal Microbiota in Cattle Infected with Mycobacterium avium subsp. paratuberculosis – Marie-Eve Fecteau – PLOS ONE

Microbiome Composition and Diversity of the Ice-Dwelling Sea Anemone, Edwardsiella andrillae – Alison E. Murray – Integrative & Comparative Biology

Microbiota from Rhabditis regina may alter nematode entomopathogenicity – Jesús Guillermo Jiménez-Cortés – Parasitology Research

Plant, root, and soil microbiome

Soil contamination with olive mill wastes negatively affects microbial communities, invertebrates and plants – Olfa Hentati – Ecotoxicology

Arbuscular mycorrhizal fungi-assisted phytoremediation of a lead-contaminated site – Jerusa Schneider – Science of the Total Environment

Ecology of microbial communities

Effects of dispersal and selection on stochastic assembly in microbial communities – Sarah Evans – The ISME Journal

Microbes in the news

Microbes have no morals – Ed Yong – Aeon

A California City Is Fending Off Zika by Releasing 40,000 Mosquitoes Every Week – Sarah Zhang – Wired

New therapy could help treat skin infections without turning them into superbugs – Chelsea Harvey – Mashable

Getting down and dirty is good for us – Tim Krohn – Mankato Free Press

UNC researchers link gut bacteria to infant brain development – Stephen Ginley – The News & Observer

Hey Bear! Can I Sample Your Microbiota? – Scott Chimileski – American Society For Microbiology

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 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 4, 2016

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Human breast tissue microbes, foliar bacteria, SAR11 genomes, and a new book about babies growing up too clean.

Human oral microbiome

Oral, Intestinal, and Skin Bacteria in Ventral Hernia Mesh Implants – Odd Langbach – Journal of Oral Microbiology

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

Paper on periodontal disease by computer scientists, but no dentists involved, and no mentioning of ethics approval or informed consent…
Metagenomic Analysis and Features Selection in Human Oral Microbiota Associated with Periodontal Disease – Wen-Pei Chen – The 33rd Workshop on Combinatorial Mathematics and Computation Theory

Human skin/breast tissue microbiology

The Microbiome of Aseptically Collected Human Breast Tissue in Benign and Malignant Disease – Tina J. Hieken – Scientific Reports

Press: Researchers identify breast microbiome/bacterial differences between healthy and cancerous tissue – Medical Xpress

Also contains animal experiments: Transplantation of human skin microbiota in models of atopic dermatitis – Ian A. Myles – JCI Insight

Human gut microbiome

Effects of scFOS on the composition of fecal microbiota and anxiety in patients with irritable bowel syndrome: a randomized, double blind, placebo controlled study – F. Azpiroz – Neurogastroenterology & Motility

Letter: Dyspepsia and the microbiome: time to focus on the small intestine – Laurie Zhong – Gut

Review: Exposure to inorganic arsenic can lead to gut microbe perturbations and hepatocellular carcinoma – Jonathan Choiniere – Acta Pharmaceutica Sinica B

Review: Modulation of type 1 and type 2 diabetes risk by the intestinal microbiome –
Alexandra Paun – Pediatric Diabetes

Animal experiments

Pterostilbene-induced changes in gut microbiota composition in relation to obesity – Usune Etxeberria – Molecular Nutrition & Food Research

The skin microbiome in allergen-induced canine atopic dermatitis – Felipe Pierezan – Veterinary Dermatology

Plant, root, and soil microbiome

Foliar bacteria and soil fertility mediate seedling performance: a new and cryptic dimension of niche differentiation – Eric A. Griffin – Ecology

DGGE: Effect of karst rocky desertification on soil fungal communities in Southwest China – P.C. Wang – Genetics and Molecular Research

Water and extremophile microbiome

SAR11 bacteria linked to ocean anoxia and nitrogen loss – Despina Tsementzi – Nature

Press: Global warming, a dead zone and surprising bacteria – Phys.org

Sulfate reduction and inorganic carbon assimilation in acidic thermal springs of the Kamchatka peninsula – E. N. Frolov – Microbiology

Book Chapter: Bacterial Diversity of the Boka Kotorska Bay – Sandra Jokanović – The Handbook of Environmental Chemistry

Bioinformatics and metagenomics

An integrated metagenomics pipeline for strain profiling reveals novel patterns of transmission and global biogeography of bacteria – Stephen Nayfach – bioRxiv

Advances in the recovery of haplotypes from the metagenome – Samuel M Nicholls – bioRxiv

Techniques

Virtual microfluidics for digital quantification and single-cell sequencing – Liyi Xu – Nature Methods

Microbial Nanoculture as an Artificial Microniche – Tagbo H. R. Niepa – Scientific Reports

Considerations for optimizing microbiome analysis using a marker gene – Jacobo de la Cuesta-Zuluaga – Frontiers in Nutrition

Microbes in the news

Dirty baby: Just how clean does your child need to be? – Bill Daley – Chicago Tribune

New book: Let Them Eat Dirt. Saving Your Child From an Oversanitized World – B. Brett Finlay and Marie-Claire Arrieta

Cloud computing used to analyze microbiological samples – Tim Sandle – Digital Journal

Bacteria Show Capacity for Rapid, Beneficial Mutations – University of Texas News

Video: Vibrio cholerae swimming in the gut of a live zebrafish – Phys.org

How the microbiome will lead a revolution in the consumerization of personalized medicine and diet – Kobi Gershoni – Tech Crunch
Science, publishing, and career

Scholarly Olympics: How the games have shaped research. A graphical guide to the impact of the Olympics on science – Ramin Skibba – Nature

‘Kudos’ promises to help scientists promote their papers to new audiences
Increasingly popular social-media tool says it can maximize reach and impact of research – Jeffrey Perkel – Nature