Category Archives: Science – Career – Publishing

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 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

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

July 25, 2016

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Increased accuracy in microbiome studies, the traveling microbiome, Vibrios on microplastics, and microbes in infant formula.

Human respiratory microbiome

Immune Response and Mortality Risk Relate to Distinct Lung Microbiomes in HIV-Pneumonia Patients – Meera K Shenoy – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

Biliary Microbiota, Gallstone Disease and Infection with Opisthorchis felineus – Irina V. Saltykova – PLOS Neglected Tropical Diseases

Opinion: Current Knowledge and Future Research Directions on Fecal Bacterial Patterns and Their Association with Asthma – Shantelle Claassen-Weitz – Frontiers in Microbiology

Review: Gut microbiota in autoimmunity: potential for clinical applications – Donghyun Kim – Archives of Pharmacal Research

Review: The Traveling Microbiome – Mark S. Riddle – Current Infectious Disease Reports

Plant, root, and soil microbiome

Browsing by an invasive herbivore promotes development of plant and soil communities during primary succession – Peter J. Bellingham – Journal of Ecology

Review: “Omics” Tools for Better Understanding the Plant–Endophyte Interactions –
Sanjana Kaul – Frontiers in Plant Science

Water and extremophile microbiome

Can the Bacterial Community of a High Arctic Glacier Surface Escape Viral Control? – Sara M. E. Rassne – Frontiers in Microbiology

Analysis of the bacteriorhodopsin-producing haloarchaea reveals a core community that is stable over time in the salt crystallizers of Eilat, Israel – Nikhil Ram-Mohan – Extremophiles

Dangerous hitchhikers? Evidence for potentially pathogenic Vibrio spp. on microplastic particles – Inga V. Kirstein – Marine Environmental Research

Press: Hitching a ride? Deadly bacteria cling on to discarded plastic – Science Focus

Review: Monitoring and managing microbes in aquaculture – Towards a sustainable industry – Mikkel Bentzon-Tilia – Microbial Biotechnology

Food microbiology

Pulque, a Traditional Mexican Alcoholic Fermented Beverage: Historical, Microbiological, and Technical Aspects – Adelfo Escalante – Frontiers in Microbiology

Flow Cytometric and 16S Sequencing Methodologies for Monitoring the Physiological Status of the Microbiome in Powdered Infant Formula Production – Amir H. P. Anvarian – Frontiers in Microbiology

Techniques

Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies – Daryl M Gohl – Nature Biotechnology

A Modified SDS-Based DNA Extraction Method for High Quality Environmental DNA from Seafloor Environments – Vengadesh Perumal Natarajan – Frontiers in Microbiology

More microbiology

A New Genomics-Driven Taxonomy of Bacteria and Archaea: Are We There Yet? – George M. Garrity – Journal of Clinical Microbiology

Microbes in the news

University of Alberta researchers aim to close the ‘fibre gap’ – Clare Clancy – Edmonton Journal

Oil-degrading bacteria to undergo field trials – T. Nandakumar – The Hindu

How we simulated a microscopic ‘wind farm’ – powered by bacteria – Tyler Shendruk – The Conversation

Microrobots Can Carry Out Medical Operations By Copying A Certain Bacteria – Jeanette Walsh – Stock News USA

Could parasite found in cat feces fight ovarian cancer? Scientists identify specific protein which trains the body to kill tumors – Mia De Graaf – Daily Mail

How do bacteria take up vitamins? – Research in Germany

BioFlash podcast: Why Big Pharma is hungry for bacteria – Biz Journals

Science, publishing, and career

Towards a typology of academic peer review styles – Kevin Wang – Urban Geography

Bik’s Non-Microbiology Picks

All the weird things kids have swallowed, in one hospital’s collection – Megan Thielking – STAT news

July 24, 2016

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

Pregnancy and birth

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

Human oral microbiome

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

Human gut microbiome

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

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

Animal and other experiments

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

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

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

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

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

Plant, root, and soil microbiome

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

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

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

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

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

Water microbiome

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

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

Archeological microbes

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

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

Built environment microbiome

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

More microbes

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

Metagenomics and bioinformatics

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

Microbes in the news

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

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

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

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

Science, publishing, and career

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

Women in Science: An Illustrated Who’s Who

July 20, 2016

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Jobs

Postdoc: Arbuscular mycorrhizal fungi and associated microbiota – Boyce Thompson Institute at Cornell campus (NY) (via ASM)

Pregnancy and birth

Why Don’t All Infants Have Bifidobacteria in Their Stool? – Gerald W. Tannock – Frontiers in Microbiology

Not liking this title: I did not see that coming! It is more than bugs in the bagina – Tamsin Board – Molecular Reproduction and Development

The Probiotics in Pregnancy Study (PiP Study): rationale and design of a double-blind randomised controlled trial to improve maternal health during pregnancy and prevent infant eczema and allergy – Christine Barthow – BMC Pregnancy and Childbirth

Human skin microbiome

Age-related differences in morphological characteristics of residual skin surface components collected from the surface of facial skin of healthy male volunteers – N. E. Chalyk – Skin Research and Technology

Human respiratory microbiome

Metagenome and Metatranscriptome Profiling of Moderate and Severe COPD Sputum in Taiwanese Han Males – Shih-Wei Lee – PLOS ONE

Human gut microbiome

Bacterial and Fungal Microbiota Changes Distinguish C. difficile Infection from Other Forms of Diarrhea: Results of a Prospective Inpatient Study – William Sangster – Frontiers in Microbiology

Effects of Arabinoxylan and Resistant Starch on Intestinal Microbiota and Short-Chain Fatty Acids in Subjects with Metabolic Syndrome: A Randomised Crossover Study – Stine Hald – PLOS ONE

Review: Intestinal microbiota and chronic constipation – Ying Zhao – Springer Plus

Animal experiments

Intestinal Microbiota Promotes Psoriasis-Like Skin Inflammation by Enhancing Th17 Response – Zuzana Zákostelská – PLOS ONE

Animal microbiome

Effects of 16S rDNA sampling on estimates of the number of endosymbiont lineages in sucking lice – Julie M. Allen – PeerJ

Plant, root, and soil microbiome

Patterns of natural fungal community assembly during initial decay of coniferous and broadleaf tree logs – Annemieke van der Wal – Ecosphere

Bioinformatics

CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community – Thomas Richard Connor – bioRxiv

More microbiology

Synchronized cycles of bacterial lysis for in vivo delivery – M. Omar Din – Nature

Press: Self-destructing bacteria are engineered to kill cancer cells – Sally Adee – New Scientist

Microbes in the news

Algae are melting away the Greenland ice sheet. ‘Black and Bloom’ project explores how microorganisms help to determine the pace of Arctic melting – Alexandra Witze – Nature

Science, publishing, and career

Featuring Bik’s Picks! Scientific literature: Information overload – Esther Landhuis – Nature

The unsung heroes of CRISPR. The soaring popularity of gene editing has made celebrities of the principal investigators who pioneered the field — but their graduate students and postdocs are often overlooked – Heidi Ledford – Nature

2016 Raymond and Beverly Sackler Prize in Convergence Research: QnAs with Stephen Quake – Prashant Nair – PNAS

Bik’s Picks

5 Questions: Randall Stafford advocates a plant-based diet – INterview with Randall Stafford – Stanford Medicine

July 18, 2016

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Gut bacteria in the lung in case of sepsis or ARDS, metagenomics along a depth gradient, and microbes in peanut processing plants.

Pregnancy and birth

Screening of vulvovaginal infections during pregnancy in resource constrained settings: Implications on preterm delivery – Chaitanya Tellapragada – Journal of Infection and Public Health

Human respiratory microbiome/ Animal experiments

Enrichment of the lung microbiome with gut bacteria in sepsis and the acute respiratory distress syndrome – Robert P. Dickson

Human gut microbiome

Impact of Cranberries on Gut Microbiota and Cardiometabolic Health: Proceedings of the Cranberry Health Research Conference 2015 – Jeffrey B Blumberg – Advances in Nutrition

Review: On the pathogenesis of insulin-dependent diabetes mellitus: the role of microbiota – Elena Gianchecchi – Immunologic Research

Plant, root, and soil microbiome

Arbuscular mycorrhizal fungi induced changes in rhizosphere, essential oil and mineral nutrients uptake in dill/common bean intercropping system – W. Weisany – Annals of Applied Biology

Water and extremophile microbiome

Comparative metagenomics unveils functions and genome features of microbialite-associated communities along a depth gradient – Aurélien Saghaï – Environmental Microbiology

Comparative Analysis of Microbial Communities in Iron-Dominated Flocculent Mats in Deep Sea Hydrothermal Environments – Hiroko Makita – Applied and Environmental Microbiology

Food production microbiology

Microbiological contamination in peanut confectionery processing plants – Joyce de Almeida Carminati – Journal of Applied Microbiology

Microbes in the news

First virus-hunter in space will test DNA-decoding device – STATnews

Microbe of the month: Nanopusillus acidilobi, an archaeon found in Yellowstone National Park – Jennifer Tsang – The Microbial Menagerie

Sewage in the Saluda deserves more attention, politicians, river advocates say – Sammy Fretwell – The State

Science, publishing, and career

The 7 biggest problems facing science, according to 270 scientists – Julia Belluz – Vox

5 health and medicine issues to watch for at the GOP convention – David Nather – STATnews

 

July 13, 2016

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So many great new papers that it’s hard to choose! Liver quickly clears bacteria from blood, microbiology of death, mobile genes in human microbiomes from Fiji and the USA, Splenda makes fly more hungry, feather degrading bacilli, underwater microscopy, and what is being transferred in a stool transplant.

Events and jobs

Annual Meeting of the Microbial Ecology Division – November 4, 2016, Nijmegen, The Netherlands

Senior/Tenure Track scientists for the Department of Marine Microbiology and Biochemistry – NIOZ The Netherlands

Microbiome of Death

“Biology of Death” Special Issue – Current Biology
Microbiology of death – Jessica L. Metcalf
Also read (non-microbiology but sadly beautiful): Death and the octopus – Florian Maderspacher

Also appropriate in this category is this video protocol: Removal of Exogenous Materials from the Outer Portion of Frozen Cores to Investigate the Ancient Biological Communities Harbored Inside – Robyn A. Barbato – JOVE

Pregnancy and birth

Early Life Antibiotic Exposure and Weight Development in Children – Catherine A. Mbakwa – The Journal of Pediatrics

Preview: Tummy Time: The Infant Microbiota–IgA Connection – Tyler A. Rice – Cell Host & Microbe

Review: The microbiome in early life: implications for health outcomes – Sabrina Tamburini – Nature Medicine

Special issue with abstracts from the 3rd International Congress on Pre- and Probiotics
in Journal of Pediatric Gastroenterology and Nutrition

A Prebiotic Formula Improves the Gastrointestinal Bacterial Flora in Toddlers – Ya-Ling Chen – Gastroenterology Research and Practice

Human blood “microbiome”

Editorial: Fast-Track Clearance of Bacteria from the Liver – Cristina Llorente – Cell Host & Microbe
Dual-Track Clearance of Circulating Bacteria Balances Rapid Restoration of Blood Sterility with Induction of Adaptive Immunity – Steven P. Broadley – Cell Host & Microbe
CRIg Functions as a Macrophage Pattern Recognition Receptor to Directly Bind and Capture Blood-Borne Gram-Positive Bacteria – Zhutian Zeng – Cell Host & Microbe

Human skin microbiome

What if scalp flora was involved in sensitive scalp onset? – A. Guichard – International Journal of Cosmetic Science

Human gut microbiome

Mobile genes in the human microbiome are structured from global to individual scales – I. L. Brito – Nature

Press: Microbiome ‘social network’ revealed by gene swaps
Movement of genes across and between microorganism species could influence humans’ susceptibility to disease – Peter Andrey Smith – Nature News

Fecal Transplants: What Is Being Transferred? – Diana P. Bojanova – PLOS Biology

Press: Poo transplants transfer much more than bacteria. Viruses, fungi – even sloughed colon cells – may affect how well a faecal transplant works – Belinda Smith – Cosmos

Animal experiments

Sucralose Promotes Food Intake through NPY and a Neuronal Fasting Response – Qiao-Ping Wang – Cell Metabolism

Press: Artificial sweeteners trick flies into thinking they’re starving – Lindzi Wessel – STAT News

Investigation into Host Selection of the Cecal Acetogen Population in Rabbits after Weaning – Chunlei Yang – PLOS ONE

Animal microbiome

Genome evolution in the obligate but environmentally active luminous symbionts of flashlight fish – Tory A. Hendry – Genome Biology and Evolution

Deep divergence and rapid evolutionary rates in gut-associated Acetobacteraceae of ants – Bryan P. Brown – BMC Microbiology

Feather-degrading bacilli in the plumage of wild birds: Prevalence and relation to feather wear – Cody M. Kent – The Auk Ornithological Advances

Press: Feather-munching bacteria damage wild bird plumage – EurekAlert

Multi-scale ecological filters shape the crayfish microbiome – James Skelton – PeerJ Preprint

Plant, root, and soil microbiome

Rapid response of arbuscular mycorrhizal fungal communities to short-term fertilization in an alpine grassland on the Qinghai-Tibet Plateau – Xingjia Xiang – PeerJ

High-throughput sequencing of 16S rRNA Gene Reveals Substantial Bacterial Diversity on the Municipal Dumpsite – Kilaza Samson Mwaikono – BMC Microbiology

Temporal and Spatial Variation of Soil Bacteria Richness, Composition, and Function in a Neotropical Rainforest – Stephanie N Kivlin – PLOS ONE

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

The role of arbuscular mycorrhizal fungi in plant uptake, fractions, and speciation of antimony – Yuan Wei – Applied Soil Ecology

Review: Bidirectional Interaction between Phyllospheric Microbiotas and Plant Volatile Emissions – Gerard Farré-Armengol – Trends in Plant Science

Water microbiome

Underwater microscopy for in situ studies of benthic ecosystems – Andrew D. Mullen – Nature Communications

Press: Underwater microscope provides new views of ocean-floor sea creatures in their natural setting – Jules Jaffe – The Conversation

Identifying the key taxonomic categories that characterize microbial community diversity using full-scale classification: a case study of microbial community in the sediments of Hangzhou Bay – Tianjiao Dai – FEMS Microbiology Ecology

Novel acsF gene primers revealed a diverse phototrophic bacterial population including Gemmatimonadetes in the Lake Taihu – Yili Huang – Applied and Environmental Microbiology

Allelopathic interactions involving benthic phototrophic microorganisms – Joey L. Allen – Environmental Microbiology Reports

Metagenomics and bioinformatics

Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond – Satoshi Hiraoka – Microbes and Environments

Metabolites

Research Highlight: Keeping microbial metabolites at bay – Andrea Du Toit – Nature Reviews Microbiology

Techniques

New Primers for Discovering Fungal Diversity Using Nuclear Large Ribosomal DNA – Asma Asemaninejad – PLOS ONE

Not sure what is new here, but: Multiplex amplicon sequencing for microbe identification in community-based culture collections – Jaderson Silveira Leite Armanhi – Scientific Reports

Applying CRISPR–Cas9 tools to identify and characterize transcriptional enhancers – Rui Lopes – Nature Reviews Molecular Cell Biology

Phages and viruses

Perspective: Piggyback-the-Winner in host-associated microbial communities – Cynthia B Silveira – NPJ Biofilms

Microbes in the news

Fill Your House With Microbes and Live With an Animal, Say Yale Researchers – Drake Baer

Unfortunately, no update from his DIY stool transplant with Hadza feces: The Human Microbiome as Road Kill in the Age of the Anthropocene – Jeff Leach – Human Food Project

Studies find that manipulating gut microbes may reverse the negative effect of a high fat – EurekAlert

Archaea: Breakthrough in Reconstruction of Warm Climate Phases – Marine Technology News

Alarming Antibiotic-Resistant Superbug Discovered In NYer’s Bacteria Sample – Miranda Katz – Gothamist

How bacteria can help prospectors find oil – Fram Dinshaw – The Chronicle Herald

With link to video: Tiny ‘racetracks’ show how bacteria get organized – EurekAlert

Microbes and Money

uBiome and University of Oxford Investigate the Relationship Between the Human Microbiome and Personality – PR web

Commercializing the Microbiome: No Guts, No Glory – Michael Darcy – DRG

Evelo and Epiva Merge to Become a Leading Immuno-Microbiome Platform Company – BioSpace

Merck to open new Cambridge facility for microbiome research this year – Boston Business Journal

Science, publishing, and career

How Australia fails mid-career scientists – Catherine Osborne – ABC Australia

How President Obama could really lead on open access – Michael Eisen – it is NOT junk

Where are all the award winning women scientists? – Tenure, she wrote

Bik’s Picks

Organ delivery by 1,000 drones – Michael Francisco – Nature Biotechnology