Category Archives: General Microbiome

July 1, 2016

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NIH’s Lita Proctor writes about the Human Microbiome Project, oral microbiome among Cheyenne and Arapaho, Cystic Fibrosis, responses to resistant starch, the Swan Goose, sugarcane, litter decomposition.

General microbiome

Review: The National Institutes of Health Human Microbiome Project – Lita M. Proctor – Seminars in Fetal and Neonatal Medicine

Pregnancy and birth

Early-Life Events, Including Mode of Delivery and Type of Feeding, Siblings and Gender, Shape the Developing Gut Microbiota – Rocio Martin – PLOS ONE

Human oral microbiome

Oral microbiome diversity among cheyenne and arapaho individuals from Oklahoma – Andrew T. Ozga – American Journal of Physical Anthropology

Human respiratory microbiome

Pyrosequencing Unveils Cystic Fibrosis Lung Microbiome Differences Associated with a Severe Lung Function Decline – Giovanni Bacci – PLOS ONE

Human skin microbiome

The skin microbiome is different in pediatric versus adult atopic dermatitis –
Baochen Shi – Journal of Allergy and Clinical Immunology

Just colony counts: Chlorhexidine avoids skin bacteria recolonization more than triclosan – Juan H. Macias – American Journal of Infection Control

Human gut microbiome

Variable responses of human microbiomes to dietary supplementation with resistant starch – A. Venkataraman – Microbiome

Duodenal bacteria from patients with celiac disease and healthy subjects distinctly affect gluten breakdown and immunogenicity – Alberto Caminero – Gastroenterology

Predominance of Lactobacillus spp. among patients who do not acquire multidrug-resistant organisms – Rafael Araos – Clinical Infectious Diseases

Nutrition and the Microbiome: Special Edition of the Annals of the New York Academy of Sciences
Review: Nutrition and the microbiome – Karin Moelling
Review: Nutrition meets the microbiome: micronutrients and the microbiota – Hans K. Biesalski

Letter: Microbiota and Alcoholic Liver Disease – Peng Chen – Alcoholism: Clinical and Experimental Research

Animal experiments

Sex differences and hormonal effects on gut microbiota composition in mice – Elin Org – Gut Microbes

Animal microbiome

Distinctive gut microbial community structure in both the wild and farmed Swan goose (Anser cygnoides) – Wen Wang – Journal of Basic Microbiology

The gut microbiome of the sea urchin, Lytechinus variegatus from their natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles – Joseph A. Hakim – FEMS Microbiology Ecology

Analysis of microbiota on abalone (Haliotis discus hannai) in South Korea for improved product management – Min-Jung Lee – International Journal of Food Microbiology

Bacterial endosymbionts protect aphids in the field and alter parasitoid community composition – Lukas Rothacher – Ecology
Midgut fungal and bacterial microbiota of Aedes triseriatus and Aedes japonicus shift in response to La Crosse virus infection – Ephantus J. Muturi – Molecular Ecology

Plant, root, and soil microbiome

The importance of C, N and P as driver for bacterial community structure in German beech dominated forest soils – Fabian Bergkemper – Journal of Plant Nutrition and Soil Science

Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome – Rafael Soares Correa de Souza – Scientific Reports

Life in leaf litter: novel insights into community dynamics of bacteria and fungi during litter decomposition – Witoon Purahong – Molecular Ecology

Endophytic microbial diversity of the halophyte Arthrocnemum macrostachyum across plant compartments – M. del R. Mora-Ruiz – FEMS Microbiology Ecology

Conference abstract: High diversity of enzymes in plant-associated microbiomes – Christina A. Müller – New Biotechnology

Review: Plant-Mediated Systemic Interactions Between Pathogens, Parasitic Nematodes, and Herbivores Above- and Belowground – Arjen Biere – Annual Review of Phytopathology

Unearthed! The Amazing Microbiome Exposed: Editor’s Note – Stephen L. Young – Bulletin of the Ecological Society of America
Unearthed! The Amazing Microbiome Exposed: The Arising Researcher – Marnie E. Rout
Unearthed! The Amazing Microbiome Exposed: The Established Researcher – John Klironomos

Water microbiome

Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments – Benjamin J. Tully – Applied and Environmental Microbiology

Built environment microbiome

Evidence of Avian and Possum Fecal Contamination in Rainwater Tanks as Determined by Microbial Source Tracking Approaches – W. Ahmed – Applied and Environmental Microbiology

Factors Influencing Bacterial Diversity and Community Composition in Municipal Drinking Waters in the Ohio River Basin, USA – Lee F. Stanish – PLOS ONE

Microbes in space

Review: Venturing into new realms? Microorganisms in space – Christine Moissl-Eichinger – FEMS Microbiology Reviews

Techniques

Simultaneous purification of DNA and RNA from microbiota in a single colonic mucosal biopsy – Aina E. F. Moen – BMC Research Notes

Microbes in the news

The North American Beaver: Castor canadensis : A look at our local Canadian friend’s microbes – Megan McGrath – Genotek’s The Microbiome Snapshot

Human Microbiome Market : Growth, Development, and Outlook 2014 – 2020 – SB Wire

uBiome Completely Re-Imagines Microbiome Experimentation with New Launch – PR Web

Bacteria prevents mosquitoes from spreading Zika, UW-Madison study says – Wisconsin State Journal

Study sheds more light on how bacteria rapidly causes infectious diseases – News Medical

Gut bacteria spotted eating brain chemicals for the first time – Andy Coghlan – New Scientist

Large Grant to Research on Bacteria in the Nose – Statens Serum Institute

Science, publishing, and career

Great and funny read: Some things you need to know about Google Scholar – Mark Dingemans – Ideophone

June 22, 2016

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Nipple aspirate, CNS infections, fiber and food allergies, horses and honeybee bacteria, and a report from the subway citizen science project.

General human microbiome

Commentary: Lessons Learned from Probing for Impacts of Triclosan and Triclocarban on Human Microbiomes – Rolf U. Halden – mSphere

Human nipple microbiome

Characterization of the microbiome of nipple aspirate fluid of breast cancer survivors – Alfred A. Chan – Scientific Reports

Human vaginal microbiome

Impact of Probiotic SYNBIO® Administered by Vaginal Suppositories in Promoting Vaginal Health of Apparently Healthy Women – Maria Cristina Verdenelli – Current Microbiology

Human gut microbiome

Alterations of Intestinal Microbiome by Antibiotic Therapy in Hospitalized Children – Miriam R. Fernandes – Microbial Drug Resistance

Could gut microbiota serve as prognostic biomarker associated with colorectal cancer patients’ survival? A pilot study on relevant mechanism – Zhiliang Wei – Oncotarget

ASM Microbe 2016 abstract: Increased Akkermansia muciniphila and Bacteroides fragilis Group Abundance After Islamic Fasting – C. Erdogdu – ASM Microbe 2016

Press: Happy Ramadan From Your Microbiome! – Gastroenterology & Endoscopy News

Review: Inflammation and the microbiome: implications for depressive disorders – Shawn Hayley – Current Opinion in Pharmacology

Review: Role of the microbiome, probiotics, and ‘dysbiosis therapy’ in critical illness.– Wischmeyer, Paul E. – Current Opinion in Critical Care

Infection and microbiology

Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system – Steven L. Salzberg – Neurology Neuroimmunology & Neuroinflammation

Press: Diagnosing brain infections using metagenomics – Julian Harris – PHG Foundation

Animal experiments

Dietary Fiber and Bacterial SCFA Enhance Oral Tolerance and Protect against Food Allergy through Diverse Cellular Pathways – Jian Tan – Cell Reports

Press: Diet high in fiber and vitamin A key to preventing allergies to peanuts and other triggers – EurekAlert

Gut microbiota translocation to the pancreatic lymph nodes triggers NOD2 activation and contributes to T1D onset – Frederico R.C. Costa – Journal of Experimental Medicine

Cutting Edge: Commensal Microbiota Has Disparate Effects on Manifestations of Polyglandular Autoimmune Inflammation – Camilla H. F. Hansen – The Journal of Immunology

Fighting Off Wound Pathogens in Horses with Honeybee Lactic Acid Bacteria – Tobias C. Olofsson – Current Microbiology

Plant, root, and soil microbiome

Local diversity of heathland Cercozoa explored by in-depth sequencing – Christoffer Bugge Harder – the ISME Journal

Press: Immense species richness of bacterial-eating microorganisms discovered in soil – Phys.org

Characterization of cadmium-resistant bacteria and their potential for reducing accumulation of cadmium in rice grains – Xiaoyan Lin – Science of The Total Environment
Editorial special issue: Soil, plants and endophytes – Stéphane Compant – Plant and Soil

Water and extremophile microbiome

Diverse Sulfur Metabolisms from Two Subterranean Sulfidic Spring Systems – Karen Rossmassler – FEMS Microbiology Letters

Metabolic potential of microbial mats and microbialites: autotrophic capabilities described by an in silico stoichiometric approach from shared genomic resources – Daniel Cerqueda-García – Journal of Bioinformatics and Computational Biology

Waste and pollution microbiology

Microbial contamination along the main open wastewater and storm water channel of Hanoi, Vietnam, and potential health risks for urban farmers – Samuel Fuhrimann – Science of The Total Environment

Isolation of Bdellovibrio bacteriovorus from a tropical wastewater treatment plant and predation of mixed species biofilms assembled by the native community members – Shugeng Feng – Environmental Microbiology

Microbial forensics

Microbial forensics: next‐generation sequencing as catalyst – Irene Kuiper – EMBO Reports

Bioinformatics and metagenomics

MEGAN Community Edition – Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data – Daniel H. Huson – PLOS Computational Biology

Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses – François Enault – The ISME Journal

More microbiology

Rates and mechanisms of bacterial mutagenesis from maximum-depth sequencing – Justin Jee – Nature

Press: Sequencing method precise enough to reveal mechanisms by which bacteria resist antibiotics – Phys.org

Darwinolide, a New Diterpene Scaffold That Inhibits Methicillin-Resistant Staphylococcus aureus Biofilm from the Antarctic Sponge Dendrilla membranosa – Jacqueline L. von Salm – Organic Letters

Press: Antibiotics from a Sponge. Could a new compound from Antarctic sea sponges be the key to breaching MRSA’s impregnable barricades? – Michael Lucibella – Antarctic Sun

Microbes in the news

MetaSUB Citizen Science Project:
With video of researchers swabbing away: Biologists Study What Kind Of Bacteria Is On New York City Subways – CBS Local
Qiagen, CosmosID Join International Urban Microbiome Project – Genome Web

New Life Found That Lives Off Electricity. Scientists have figured out how microbes can suck energy from rocks. Such life-forms might be more widespread than anyone anticipated – Emily Singer – Quanta Magazine

High-tech program on microbiome-based research launched in Qingdao – Hu Qing – China Daily

Explained: flesh eating bacteria in the Gulf of Mexico – Dylan Baddour – Houston Chronicle

Science, publishing, and career

Your Science Conference Should Have a Code of Conduct – Brett Favaro – Frontiers in Marine Science

Science in China – A special issue looks at the country’s astonishing scientific trajectory as it seeks to secure its spot among the leaders in innovation – Nature
China by the numbers. Research capacity has grown rapidly, and now quality is on the rise – Richard Van Noorden – Nature

Global Research Council: Commit to equity for women researchers – France A. Córdova – Nature

June 15, 2016

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Microbiome evolution in vertebrates, post-antibiotic microbial competition for sugars, microbial networks in respiratory infections, bacteria in snow from Australian and Swiss Alps, Yucatan Black and Red soil microbes.

Human oral microbiome

Longitudinal assessment of sputum microbiome by sequencing of the 16S rRNA gene in non-CF bronchiectasis patients – Michael J Cox – bioRxiv

Human skin microbiome

Comprehensive pyrosequencing analysis of the bacterial microbiota of the skin of patients with seborrheic dermatitis – Akiomi Tanaka – Microbiology and Immunology

Review: Can molecular DNA-based techniques unravel the truth about diabetic foot infections? – M. Malone – Diabetes/Metabolism Research and Reviews

Human respiratory microbiome

Mycoplasma pneumoniae and Streptococcus pneumoniae caused different microbial structure and correlation network in lung microbiota – Heping Wang – Journal of Thoracic Disease

Human gut microbiome

Ecophysiological consequences of alcoholism on human gut microbiota: implications for ethanol-related pathogenesis of colon cancer – Atsuki Tsuruya – Scientific Reports

Research highlight: Intimate gut interactions: helminths and the microbiota – Nicola L Harris – Cell Research

Review: Human Gut-on-a-Chip technology: Will this revolutionize our understanding of IBD and future treatments? – Jaewon Lee – Expert Review of Gastroenterology & Hepatology

Review: Dientamoeba fragilis, the Neglected Trichomonad of the Human Bowel – Damien Stark – Clinical Microbiology Reviews

Review: Akkermansia muciniphila: a novel functional microbe with probiotic properties – C. Gómez-Gallego – Beneficial Microbes

Review: Alterations of gut microbiota in patients with irritable bowel syndrome: A systematic review and meta-analysis – Xiaojun Zhuang – Journal of Gastroenterology and Hepatology

Animal and tissue culture experiments

Host-mediated sugar oxidation promotes post-antibiotic pathogen expansion – Franziska Faber – Nature

News and Views: Microbiology: The dark side of antibiotics – Thibault G. Sana & Denise M. Monack – Nature

Genetic and transcriptional analysis of human host response to healthy gut microbiome – Allison L Richards – bioRxiv

The Microbiota Determines Susceptibility to Experimental Autoimmune Uveoretinitis – Jarmila Heissigerova – Journal of Immunology Research

Animal microbiome

Invited Review: Microbiome Evolution Along Divergent Branches of the Vertebrate Tree of Life: What’s Known and Unknown – Timothy J. Colston – Molecular Ecology

Microbial community structure of two freshwater sponges using Illumina MiSeq sequencing revealed high microbial diversity – Swapnil Gaikwad – AMB Express

Plant, root, and soil microbiome

Endophytic bacterial and fungal microbiota in sprouts, roots and stems of rice (Oryza sativa L.) – Wenfeng Wang – Microbiological Research

Yucatán in black and red: Linking edaphic analysis and pyrosequencing-based assessment of bacterial and fungal community structures in the two main kinds of soil of Yucatán State – Héctor Estrada-Medina – Microbiological Research

Water and extremophile microbiome

Global and local-scale variation in bacterial community structure of snow from the Swiss and Australian Alps – Tina Wunderlin – FEMS Microbiology Ecology

Waste, pollution, drinking water microbiology

Assessing the effects of heavy metals in ACC deaminase and IAA production on plant growth-promoting bacteria – Mendoza-Hernández José Carlos – Microbiological Research

Effect of Co-Composting Cattle Manure with Construction and Demolition Waste on the Archaeal, Bacterial, and Fungal Microbiota, and on Antimicrobial Resistance Determinants – Devin B. Holman – PLOS ONE

Anthropogenic impact on mangrove sediments triggers differential responses in the heavy metals and antibiotic resistomes of microbial communities – Lucélia Cabral – Environmental Pollution

Investigation of Archaeal and Bacterial community structure of five different small drinking water networks with special regard to the nitrifying microorganisms – Zsuzsanna Nagymáté – Microbiological Research

A survey of biofilms on wastewater aeration diffusers suggests bacterial community composition and function vary by substrate type and time – Peter A. Noble – Applied Microbiology and Biotechnology

DGGE: Synergistic effect of crude oil plus dispersant on bacterial community in a louisiana salt marsh sediment – Mohammed Al-Jawasim – FEMS Microbiology Letters

Food microbiology

Complexity and Dynamics of the Winemaking Bacterial Communities in Berries, Musts, and Wines from Apulian Grape Cultivars through Time and Space – Marinella Marzano – PLOS ONE

More microbiology

Viruses Infecting a Freshwater Filamentous Cyanobacterium (Nostoc sp.) Encode a Functional CRISPR Array and a Proteobacterial DNA Polymerase B – Caroline Chénard – mBio

Press: Virus Hacks Host Genome, Steals CRISPR to Protect Itself – GenEngNews
Virus uses ‘stolen’ CRISPR to hack its host’s immune system – Science Daily

Microbes in the news

Asgard archaea diversity in estuaries – Roy Rodriguez – REU in Subtropical Marine Ecosystems, University of Texas at Austin

Microbes in pressed grapes may predict flavor metabolites in the finished wine – American Society for Microbiology – EurekAlert

Nanoflowers can detect bacteria before they make you sick: The particles can spot even tiny amounts of E. coli – Mariella Moon – Engadget

BacteriaHysteria: Self-cleaning sheets do exist! Silvon launches bacteria-resistant bedding – Julie Pennell – Today

Science, publishing, and career

Predatory journals: Ban predators from the scientific record – Jeffrey Beall – Nature

Data sharing: A code of conduct for data on epidemics – Ilaria Capua – Nature

June 9, 2016

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Salivary microbiome in Behcet’s disease, microbial RNA in human blood, acetate implied in metabolic syndrome, effects of fire retardant on plant–microbe interactions, and a book about the marine microbiome.

Events

ASM Microbe TweetUp: Friday June 17, 11.45-12:30, in the Peer-to-Peer Exchange Zone (in the Exhibition Hall)

Focused meeting: Molecular Biology of Archaea 5, London, UK, 1-3 August 2016

Pregnancy and birth

Infant Early Gut Colonization by Lachnospiraceae: High Frequency of Ruminococcus gnavus – Valeria Sagheddu – Frontiers in Pediatrics

Review: The microbiome during pregnancy and early postnatal life – Josef Neu – Seminars in Fetal and Neonatal Medicine

Review: The human milk microbiome and factors influencing its composition and activity – Carlos Gomez-Gallego – Seminars in Fetal and Neonatal Medicine

Human blood microbiome

Total RNA Sequencing reveals microbial communities in human blood and disease specific effects – Serghei Mangul – bioRxiv

Human mouth microbiome

A Study of the Variation in the Salivary Peptide Profiles of Young Healthy Adults Acquired Using MALDI-TOF MS – Andrei Prodan – PLOS ONE

Sequencing of 16S rRNA reveals a distinct salivary microbiome signature in Behçet’s disease – Patrick Coit – Clinical Immunology

Human gut microbiome

Review: What’s bugging your teen? —The microbiota and adolescent mental health – Karen-Anne McVey Neufeld – Neuroscience & Biobehavioral Reviews

Bio-banking gut microbiome samples – Shankar Bolan – EMBO Reports

Animal experiments

Acetate mediates a microbiome–brain–β-cell axis to promote metabolic syndrome – Rachel J. Perry – Nature

Press: How altered gut microbes cause obesity – Science Daily
Fecal Transplant Shows Gut Microbes Cause Obesity – In Rats, Anyway – Science 2.0

Sex-specific Effects of Arsenic Exposure on the Trajectory and Function of the Gut Microbiome – Liang Chi – Chemical Research in Toxicology

Taxonomic assessment of rumen microbiota using total RNA and targeted amplicon sequencing approaches – Fuyong Li – Frontiers in Microbiology

Environmental filtering decreases with fish development for the assembly of gut microbiota – Qingyun Yan – Environmental Microbiology

Animal microbiome

Bacterial Community Diversity Harboured by Interacting Species – Mikaël Bili – PLOS ONE

Plant, root, and soil microbiome

Cascading effects of fire retardant on plant–microbe interactions, community composition, and invasion – Abigail Marshall – Ecological Applications

Temperature sensitivity of soil microbial communities: An application of macromolecular rate theory to microbial respiration – Charlotte J. Alster – Journal of Geophysical Research

Selection and evaluation of microorganisms for biocontrol of Verticillium dahliae in olive – A Varo – Journal of Applied Microbiology

Influence of plant genotype on the cultivable fungi associated to tomato rhizosphere and roots in different soils – Anna Poli – Fungal Biology

Arbuscular mycorrhizal fungal communities in buffelgrass pasture under intercropping and shading systems in Brazilian semiarid conditions – Karen M.S. Menezes – Agriculture, Ecosystems & Environment

Evolution of High Cellulolytic Activity in Symbiotic Streptomyces through Selection of Expanded Gene Content and Coordinated Gene Expression – Adam J. Book – PLOS Biology

Press: Chemistry lessons from bacteria may improve biofuel production – Science Daily

Review: Streptomyces as a plant’s best friend? – Tom Viaene – FEMS Microbiology Ecology

Water and extremophile microbiome

Light availability regulates the response of algae and heterotrophic bacteria to elevated nutrient levels and warming in a northern boreal peatland – Lily Y. Gu – Freshwater Biology

Metagenomic covariation along densely sampled environmental gradients in the Red Sea – Luke R Thompson – bioRxiv

Microbial community structure of Arctic seawater as revealed by pyrosequencing – Yang Li – Acta Oceanologica Sinica

A snapshot on spatial and vertical distribution of bacterial communities in the eastern Indian Ocean – Jing Wang – Acta Oceanologica Sinica

Pond Crash Forensics: Presumptive identification of pond crash agents by next generation sequencing in replicate raceway mass cultures of Nannochloropsis salina – Laura T. Carney – Algal Research

Detection of antibiotic-resistant bacteria endowed with antimicrobial activity from a freshwater lake and their phylogenetic affiliation – Zothanpuia – PeerJ

Microbial diversity in lake–river ecotone of Poyang Lake, China – Xiaolan Huang – Environmental Earth Sciences

Book: The Marine Microbiome. An Untapped Source of Biodiversity and Biotechnological Potential – Lucal J. Stal, Mariana Silvia Cretoiu – Springer

Food microbiology

Bacterial dynamics and functional analysis of microbial metagenomes during ripening of Dutch-type cheese – Davide Porcellato – International Dairy Journal

Pollution and waste microbiology

Chronic exposure to triclosan sustains microbial community shifts and alters antibiotic resistance gene levels in anaerobic digesters – Daniel Carey – Environ Sci Processes Impacts

Computational models of microbiome research, bioinformatics

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

A new way to publish metagenomics studies – Folker Meyer – BioMed Central

Techniques

RNA-stable isotope probing: from carbon flow within key microbiota to targeted transcriptomes – Tillmann Lueders – Current Opinion in Biotechnology

More microbiology

Centenary of the death of Elie Metchnikoff: A visionary and an outstanding team leader –
Jean-Marc Cavaillon – Microbes and Infection

Microbes in the news

Worcester Polytechnic Institute Students Isolate Potentially Novel Soil-Dwelling Viruses – PR Web

Yuck factor may boost hand hygiene compliance: Interview with Ashley Gregory – EurekAlert

Europe orders Italians to cut down olive trees infected with bacteria – Nick Squires – The Telegraph

It’s Not Just Restaurants—Scientists Are Fascinated With Fermented Foods Too – Jane Lear – Take Part

Science, publishing, and career

Differences in incomes of physicians in the United States by race and sex: observational study – Dan P. Ly – British Medical Journal

Press: White male doctors earn 35 percent more than black male doctors – Jennifer Adaeze Okwerekwu – STAT News

June 8, 2016

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Obesity and microbiome patterns, universality of human microbial dynamics, intestinal fungal dysbiosis, pre-eclampsia, seaweed ice-ice disease.

Pregnancy and birth

Review: A dormant microbial component in the development of pre-eclampsia – Douglas B Kell – bioRxiv

General human microbiome

Universality of human microbial dynamics – Amir Bashan – Nature

News and Views: Host-microbe interaction: Rules of the game for microbiota – Karoline Faust – Nature

Perspectives: Accounting for reciprocal host–microbiome interactions in experimental science – Thaddeus S. Stappenbeck – Nature

Human gut microbiome

Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome – Marc Sze – bioRxiv

Animal and in vitro experiments

Immunological Consequences of Intestinal Fungal Dysbiosis – Matthew L. Wheeler – Cell Host & Microbe

Editorial: The Fungal Mycobiota: Small Numbers, Large Impacts – Carol A. Kumamoto – Cell Host & Microbe

Research Highlights: Love Thy Neighbor: Sharing and Cooperativity in the Gut Microbiota – Nathan T. Porter – Cell Host & Microbe

Animal microbiome

Overfishing and nutrient pollution interact with temperature to disrupt coral reefs down to microbial scales – Jesse R. Zaneveld – Nature Communications

Restructuring of the sponge microbiome favors tolerance to ocean acidification – M. Ribes – Environmental Microbiology Reports

Plant, root, and soil microbiome

Molecular identification of new bacterial causative agent of ice-ice disease on seaweed Kappaphycus alvarezii – Marlina Achmad – PeerJ Preprint

Effect of temperature (5 °C–25 °C) on epiphytic lactic acid bacteria populations and fermentation of whole-plant corn silage – Yiqin Zhou – Journal of Applied Microbiology

Conventional methanotrophs are responsible for atmospheric methane oxidation in paddy soils – Yuanfeng Cai – Nature Communications

More microbiology

Nondegenerative Evolution in Ancient Heritable Bacterial Endosymbionts of Fungi – Stephen J. Mondo – Molecular Biology and Evolution

Historical Y. pestis Genomes Reveal the European Black Death as the Source of Ancient and Modern Plague Pandemics – Maria A. Spyrou – Cell Host & Microbe

Microbes in the news

Arlington native Alexandra Worden named American Academy of Microbiology fellow – Arlington Wicked Local

Disease Researcher Finds New Home at Valencia — in the Classroom, with Dr. Hemangi Patil – Linda Shrieves Beaty – Valencia College

From the Congress of the European Academy of Neurology in Copenhagen, Denmark: Scientists Gather to Discuss Novel Connections Between Gut Microbiome and Brain Disorders – Patricia Inacio – Multiple Sclerosis News Today

Cooperative and Combative Behaviour in the Human Gut: Probing the Microbiome, with Athena Aktipis – SciCasts

Speeding Up Drug Discovery to Fight Tuberculosis – Seattle researchers created a genetic blueprint of the cunning tuberculosis bacteria, then used it to predict and rank potential drug targets – SystemsBiology

Science, publishing, and career

What does research reproducibility mean? – Steven N. Goodman – Science Translational Medicine

Editorial: Second chances – The line between compliance and misconduct is finer than you might think – Nature

Misconduct: Lessons from researcher rehab – James M. DuBois – Nature

June 7, 2016

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Microbiomes of the lung, red coral, effect of invertebrates on water microbes, and bacteriophages are reservoirs of antibiotic resistance genes.

General microbiome

The vast unknown microbial biosphere – Carlos Pedrós-Alió – PNAS

Human respiratory microbiome

Review: The Lung Microbiome, Immunity, and the Pathogenesis of Chronic Lung Disease – David N. O’Dwyer – The Journal of Immunology

Review/Hypothesis: A Role for the Intestinal Microbiota and Virome in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)? – Navena Navaneetharaja – MDPI Journal of Clinical Medicine

Human gut microbiome

Review: The metabolic role of the gut microbiota in health and rheumatic disease: mechanisms and interventions – Shahla Abdollahi-Roodsaz – Nature Reviews Rheumatology

Animal experiments

Accelerated dysbiosis of gut microbiota during aggravation of DSS-induced colitis by a butyrate-producing bacterium – Qianpeng Zhang – Scientific Reports

Bacterial Adrenergic Sensors Regulate Virulence of Enteric Pathogens in the Gut – Cristiano G. Moreira – mBio

Animal microbiome

Spirochaetes dominate the microbial community associated with the red coral Corallium rubrum on a broad geographic scale – Jeroen A. J. M. van de Water – Scientific Reports

Plant, root, and soil microbiome

Mangrove succession enriches the sediment microbial community in South China – Quan Chen – Scientific Reports

Correlations between the composition of modular fungal communities and litter decomposition-associated ecosystem functions – Witoon Purahong – Fungal Ecology

History Leaves Its Mark on Soil Bacterial Diversity – Jennifer B. H. Martiny – mBio

Water and extremophile microbiome

Alteration of physico-chemical and microbial properties in freshwater substrates by burrowing invertebrates – Carolin Boeker – Limnologica – Ecology and Management of Inland Waters

Effects of the invasive clam Corbicula fluminea (Müller, 1774) on an estuarine microbial community – Adriana Novais – Science of The Total Environment

Delineating ecologically significant taxonomic units from global patterns of marine picocyanobacteria – Gregory K. Farrant – PNAS

Bacterial community composition and structure in an Urban River impacted by different pollutant sources – A. Mark Ibekwe – Science of The Total Environment

Population Dynamics and Community Composition of Ammonia Oxidizers in Salt Marshes after the Deepwater Horizon Oil Spill – Anne Bernhard – Frontiers in Microbiology

Review: Cannibalistic viruses in the aquatic environment: role of virophages in manipulating microbial communities – V. Marie – International Journal of Environmental Science and Technology

Built environment microbiome

Molecular investigation of bacterial communities: Data from two frequently used surfaces in the São Paulo Institute of Tropical Medicine – Tairacan Augusto Pereira da Fonseca – Data in Brief

The prevalence of foodborne pathogenic bacteria on cutting boards and their ecological correlation with background biota – Noor-Azira Abdul-Mutalib – AIMS Microbiology

Metagenomics and viruses

Metagenomic analysis reveals that bacteriophages are reservoirs of antibiotic resistance genes – Jéssica Subirats – International Journal of Antimicrobial Agents

Bioinformatics

SMART: Statistical Metabolomics Analysis—An R Tool – Yu-Jen Liang – Analytical Chemistry

Techniques

Book: Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing – Editors: Ana M. Aransay, José Luis Lavín Trueba – Springer Books

More microbiology

Coupling spatiotemporal community assembly processes to ecosystem function – Emily Graham – PeerJ Preprint

Evolution of the archaeal and mammalian information processing systems: towards an archaeal model for human disease – Zhe Lyu – Cellular and Molecular Life Sciences

Species richness influences wine ecosystem function through a dominant species – Primrose J. Boynton – Fungal Ecology

Microbes in the news
New antimicrobial material joins fight against antibiotic-resistant bacteria – Michael Irving – GizMag

Note: PNAS paper not yet out: Distinguishing Deadly Staph Bacteria from Harmless Strains – Heather Buschman – UC San Diego

Scientists craft an artificial seawater concoction. New recipe facilitates marine microbe cultivation and characterization – EurekAlert

The man who can map the chemicals all over your body: Pieter Dorrestein uses mass spectrometry to eavesdrop on the molecular conversations between microbes and their world – Paul Tullis – Nature

Stockton Kimball Awardee is Noted Bacterial Pathogenesis Researcher – University of Buffalo

MSU doctoral student Jeffrey Simkins awarded National Science Foundation fellowship to research in Australia – Montana State University – KBZK

Vaccine watches bacteria, strikes only when trouble stirs – University of Buffalo

Bacteria hairs make excellent electrical wires – Science Daily

Science, publishing, and career

My paper got published: The Prevalence of Inappropriate Image Duplication in Biomedical Research Publications – Elisabeth M. Bik, Arturo Casadevall, Ferric C. Fang – mBio

May 26, 2016

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Bioinformatics Symposium tomorrow at Stanford with free live stream, development of upper respiratory tract microbiome in infants, coral microbiome in Hawaii, calcified red algae microbiome, and metagenomics pathogen detection tool.

Events

Tomorrow, starts at 8am Pacific Time: Bioinformatics for the Microbiome, Stanford University. Will also be live streamed (and recording will be kept here for a while too) at Stanford Webcast. Due to family circumstances I won’t be able to be there, unfortunately 😦

Targeting the Microbiome – September 19-22, Boston, MA

Report from meeting earlier this week: Frontiers in Human Microbiota Symbiotic Interactions” 3rd Annual Meeting of the Bridging Biomedical Worlds Series

Jobs

Postdoc position in Pat Schloss group – Department of Microbiology & Immunology at the University of Michigan

General microbiome

Bioengineering microbial communities: Their potential to help, hinder and disgust – Diane Sivasubramaniama – Bioengineered

Pregnancy and birth

Development of Upper Respiratory Tract Microbiota in Infancy is Affected by Mode of Delivery – Astrid A.T.M. Bosch – EBioMedicine

Human respiratory microbiome

Long-Term Evolution of Burkholderia multivorans during a Chronic Cystic Fibrosis Infection Reveals Shifting Forces of Selection – Inês N. Silva – mSystems

Study shows how bacteria evolve in lungs of cystic fibrosis patients – Science Daily

Upper airway microbial colonization in patients with neuromuscular disorders – Florian Stehling – Respirology

Human gut microbiome

Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study – Toshitaka Odamaki – BMC Microbiology

Metagenomic characterization of microbial communities in situ within the deeper layers of the ileum in Crohn’s Disease – Chandra Sekhar Pedamallu – CMGH Cellular and Molecular Gastroenterology and Hepatology

Association of Systemic Sclerosis With a Unique Colonic Microbial Consortium – Elizabeth R. Volkmann – Arthritis & Rheumatology

Development of the gut microbiota and mucosal IgA responses in twins and gnotobiotic mice – Joseph D. Planer – Nature

Animal experiments

Impact of a High-Fat or High-Fiber Diet on Intestinal Microbiota and Metabolic Markers in a Pig Model – Sonja N. Heinritz – MDPI Nutrients

Immunological Consequences of Intestinal Fungal Dysbiosis – Matthew L. Wheeler – Cell Host & MIcrobe

Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease – Hiutung Chu – Science

Editorial: Microbiome: Does the brain listen to the gut? – Thomas Kuntz – eLIFE

Animal microbiome

Biogeography of planktonic and coral-associated microorganisms across the Hawaiian Archipelago – Jennifer L. Salerno – FEMS Microbiology Ecology

Codivergence of the primary bacterial endosymbiont of psyllids versus host switches and replacement of their secondary bacterial endosymbionts – Aidan A. G. Hall – Environmental Microbiology

An exploration of the fungal assemblage in each life history stage of the butterfly, Lycaeides melissa (Lycaenidae), as well as its host plant Astragalus canadensis (Fabaceae) – Joshua G. Harrison – Fungal Ecology

Comparison of the fecal microbiota in horses with Equine Metabolic Syndrome (EMS) and metabolically normal controls fed a similar all forage diet – S. Elzinga – Journal of Equine Veterinary Science

Plant, root, and soil microbiome

Characterising the microbiome of Corallina officinalis, a dominant calcified intertidal red alga – Juliet Brodie – FEMS Microbiology Ecology

Relative importance of soil properties and microbial community for soil functionality: insights from a microbial swap experiment – Manuel Delgado-Baquerizo – Functional Ecology

Effect of agricultural practices and coastal constraints on soil microbial functional properties in Mediterranean olive orchards – N. Boukhdoud – European Journal of Soil Science

Functional breadth and home-field advantage generate functional differences among soil microbial decomposers – Nicholas Fanin – Ecology

Book Chapter: Bacteria and Non-lichenized Fungi Within Biological Soil Crusts – Stefanie Maier – Biological Soil Crusts: An Organizing Principle in Drylands

Metagenomics, bioinformatics, and techniques

HoloVir: A workflow for investigating the diversity and function of viruses in invertebrate holobionts – Patrick W. Laffy – Frontiers in Microbiology

Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling – Steven Flygare – Genome Biology

Metagenomics pathogen detection tool could change how infectious diseases are diagnosed – EurekAlert

Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing – Matthew Thoendel – Journal of Microbiological Methods

BMPOS: a Flexible and User-Friendly Tool Sets for Microbiome Studies – Victor S. Pylro – Microbial Ecology

Functional foods

Reviewing Classical and Molecular Techniques Regarding Profiling of Probiotic Character of Microorganisms – Christos Stefanis – Current Research in Nutrition and Food Science

Microbes in the news

Polio-free world? Not if scientists refuse to destroy their research specimens – Helen Branswell – STAT news

The secret history of ancient toilets. By scouring the remains of early loos and sewers, archaeologists are finding clues to what life was like in the Roman world and in other civilizations – Chelsea Wald – Nature

Using Gut Bacteria To Save The Planet – John Farrell – Forbes

The Emergent Microbiome: A Revolution for the Life Sciences – Part VI, Diagnostics – Jessica L. Miles and Anthony D. Sabatelli – Lexology

May 24, 2016

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Endophytes in Miscanthus seeds, the microbes of Blood Pond Hell, microbes in indoor dust, and Dada2 sample inference from Illumina data.

General microbiome

Moonshot or mania? – Sally Adee looks behind the hype – New Scientist

Human gut microbiome

Research Highlight: Microbiota trigger inflammation – Ellen F. Carney – Nature Reviews Nephrology

Glycans affect DNA extraction and induce substantial differences in gut metagenomic studies – Emmanouil Angelakis – Scientific Reports

Microbiome of HIV-infected people – Grégory Dubourg – Microbial Pathogenesis

Review: The microbiota and immune response during Clostridium difficile infection – Erica L. Buonomo – Anaerobe

Animal experiments

Snapshot on a Pilot Metagenomic Study for the Appraisal of Gut Microbial Diversity in Mice, Cat, and Man – Coline Plé – Gastroenterology Research and Practice

Plant, root, and soil microbiome

The microbiomes and metagenomes of forest biochars – Genevieve L. Noyce – Scientific Reports

Endophytic bacteria in Miscanthus seed: implications for germination, vertical inheritance of endophytes, plant evolution and breeding – Naomi Cope-Selby – GCB Bioenergy

Impact of Faba Bean-Seed Rhizobial Inoculation on Microbial Activity in the Rhizosphere Soil during Growing Season – Anna Siczek – Int J Mol Sci

Evaluation of Strategies to Separate Root-Associated Microbial Communities: A Crucial Choice in Rhizobiome Research – Tim Richter-Heitmann – Frontiers in Microbiology

Bacterial Diversity and Community Structure in Korean Ginseng Field Soil Are Shifted by Cultivation Time – Ngoc-Lan Nguyen – PLOS ONE

Water and extremophile microbiome

Estimating planktonic diversity through spatial dominance patterns in a model ocean – Alice Soccodato – Marine Genomics

Microbial community profiling of the Chinoike Jigoku (“Blood Pond Hell”) hot spring in Beppu, Japan: isolation and characterization of Fe(III)-reducing Sulfolobus sp. strain GA1 – Yusei Masakia – Research in Microbiology

Near-Bottom Hypoxia Impacts Dynamics of Bacterioplankton Assemblage throughout Water Column of the Gulf of Finland (Baltic Sea) – Peeter Laas – PLOS ONE

Fungal communities in sediments of subtropical Chinese seas as estimated by DNA metabarcoding – Wei Li – Scientific Reports

Built environment microbiology

Characterization of the bacterial and fungal microbiome in indoor dust and outdoor air samples: a pilot study – Blake Hanson – Environmental Science: Processes & Impact

Microbiome Profiling of Drinking Water in Relation to Incidence of Inflammatory Bowel Disease – Jessica D Forbes – Canadian Journal of Microbiology

Infection microbiology

The scanning electron microscope in microbiology and diagnosis of infectious disease – Christine G. Golding – Scientific Reports

Bioinformatics

DADA2: High-resolution sample inference from Illumina amplicon data – Benjamin J Callahan – Nature Methods (OA by author)

MetaTrans: an open-source pipeline for metatranscriptomics – Xavier Martinez – Scientific Reports

An Introduction to Programming for Bioscientists: A Python-based Primer – Berk Ekmekci – Arxiv / PLOS

An Optimized Graph-Based Metagenomic Gene Classification Approach: Metagenomic Gene Analysis – Md Sarwar Kamal – Classification and Clustering in Biomedical Signal Processing

Complex heatmaps reveal patterns and correlations in multidimensional genomic data – Zuguang Gu – Bioinformatics

Unsupervised random forest: a tutorial with case studies – Nelson Lee Afanador – Journal of Chemometrics

Metagenomics

Review: The bright side of microbial dark matter: lessons learned from the uncultivated majority – Lindsey Solden – Current Opinion in Microbiology

Metabolomics

Review: Metabolomics of fecal samples: a practical consideration – Silke Matysik – Trends in Food Science & Technology

Viruses and phages

Targeted virus detection in next-generation sequencing data using an automated e-probe based approach – Marike Visser – Virology

Identification of diverse mycoviruses through metatranscriptomics characterization of the viromes of five major fungal plant pathogens – Shin-Yi Lee Marzano – Journal of Virology

Viruses and bacteria in Th2 biased allergic airway disease – Feng Lan – Allergy

More microbiology

Biofilms: Microbial Shelters Against Antibiotics – Skander Hathroubi – Microbial Drug Resistance

Microbes in the news

Building An Antibiotic To Kill Bad Microbes While Sparing Good Ones – Madeline K. Sofia – NPR

A rallying call for microbiome science national data management – A National Microbiome Data Center is essential for enabling exploration of all the environmental genomic data – EurekAlert

Could Gut Microbiome Be the Holy Grail for Diabetes Treatment? – An Expert Weighs In at International Endocrinology Congress – Business Wire

AOBiome and its Consumer Division, Mother Dirt, Founding members of the Microbiome Coalition, Helps Launch of the National Microbiome Initiative – PR Newswire

Painful pooping may stop panda sex. A gut-wrenching tummy ache can throw cold water on pandas’ love life. Amy Middleton reports. – Amy Middleton – Cosmos Magazine

May 20, 2016

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Updated microbial census, building healthy gut communities, antibiotics might worsen symptoms in transplant patients, another gut-brain connection, and FiveThirtyEight’s Gut Science week.

Events

Bioinformatics for the Microbiome Symposium at Stanford – Friday, May 27

General microbiology

Status of the Archaeal and Bacterial Census: an Update – Patrick D. Schloss – mBio

Suddenly everyone is a microbiota specialist! – Stefan A. Boers – Clinical Microbiology and Infection

Intricacies of assessing the human microbiome in epidemiologic studies – Courtney K. Robinson – Annals of Epidemiology

Pregnancy and birth

Sepsis in preterm infants causes alterations in mucosal gene expression and microbiota profiles compared to non-septic twins – María Cernada – Scientific Reports

From our lab, Editorial: Gut microbiota: How to build healthy growth-promoting gut communities – David A. Relman – Nature Reviews Gastroenterology & Hepatology

Human oral microbiome

Investigating Oral Microbiome Profiles in Children with Cleft Lip and Palate for Prognosis of Alveolar Bone Grafting – Luwei Liu – PLOS ONE

Human skin, eye, and ear microbiome (also see under Animal Experiments below)

Microbiology of Middle Ear Infections: Do You Hear What I Hear? – Donna M. Wolk – Clinical Microbiology Newsletter

Review: Impact of Microbiome on Ocular Health – Abirami Kugadas – The Ocular Surface

Human respiratory microbiome

Azithromycin therapy during RSV bronchiolitis: upper airway microbiome alterations and subsequent recurrent wheeze – Yanjiao Zhou – Journal of Allergy and Clinical Immunology

Human urinary tract microbiome

Research Highlight: Stones: Gut microbiome is unique in kidney stone disease – Rebecca Kelsey – Nature Reviews Urology

Human gut microbiome

Increased Gut Redox and Depletion of Anaerobic and Methanogenic Prokaryotes in Severe Acute Malnutrition – Matthieu Million – Scientific Reports

Topological distortion and reorganized modular structure of gut microbial co-occurrence networks in inflammatory bowel disease – Steven N. Baldassano – Scientific Reports

Hypothesis: Targeting the Ecology Within: The Role of the Gut-Brain Axis and Human Microbiota in Drug Addiction – Patrick D. Skosnik – Medical Hypotheses

Editorial: FMT — enduring strains – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Review: Gut Microbiota and Metabolic Health: The Potential Beneficial Effects of a Medium Chain Triglyceride Diet in Obese Individuals – Sabri Ahmed Rial – MDPI Nutrients

Fecal Microbiota Transplantation

Predictors of Early Failure After Fecal Microbiota Transplantation for the Therapy of Clostridium Difficile Infection: A Multicenter Study – Monika Fischer – The American Journal of Gastroenterology

Animal experiments

Ly6Chi Monocytes Provide a Link between Antibiotic-Induced Changes in Gut Microbiota and Adult Hippocampal Neurogenesis – Luisa Möhle – Cell Reports

Gut bacteria influence the birth of new brain cells in mice – Jessica Hamzelou – New Scientist

Editorial: Microbiota Alterations in Inflammatory Bowel Diseases: From Correlation to Causality – Benoit Chassaing – CMGH Cellular and Molecular Gastroenterology and Hepatology

Commentary: Canine and Human Atopic Dermatitis: Two Faces of the Same Host-Microbe Interaction – Domenico Santoro – Journal of Investigative Dermatology

Longitudinal Evaluation of the Skin Microbiome and Association with Microenvironment and Treatment in Canine Atopic Dermatitis – Charles W. Bradley – Journal of Investigative Dermatology

Plant, root, and soil microbiome

Plant community influence on soil microbial response after a wildfire in Sierra Nevada National Park (Spain) – Gema Bárcenas-Moreno – Science of The Total Environment

Insight into how organic amendments can shape the soil microbiome in long-term field experiments as revealed by network analysis – Ning Ling – Soil Biology and Biochemistry

Mycorrhiza and heavy metal resistant bacteria enhance growth, nutrient uptake and alter metabolic profile of sorghum grown in marginal soil – Faten Dhawi – Chemosphere

Built environment microbiome

Subaerial biofilms on granitic historic buildings: microbial diversity and development of phototrophic multi-species cultures – D. Vázquez-Nion

Pollution and waste microbiology

Microbial diversity and community structure in an antimony-rich tailings dump – Enzong Xiao – Applied Microbiology and Biotechnology

Food microbiology

A method to isolate bacterial communities and characterize ecosystems from food products: Validation and utilization in as a reproducible chicken meat model – Amélie Rouger – International Journal of Food Microbiology

Bioinformatics, proteomics, metabolomics

An adaptive association test for microbiome data: R package MiSPU – Chong Wu – Genome Medicine

Review: The information science of microbial ecology – Aria S Hahn – Current Opinion in Microbiology

Editorial: Proteomic interrogation of the gut microbiota: potential clinical impact – Sven-Bastiaan Haange – Expert Review of Proteomics

Microbial community metabolic modeling: A community data-driven network reconstruction – Christopher S. Henry – Journal of Cellular Physiology

More microbiology

Increased GVHD-related mortality with broad-spectrum antibiotic use after allogeneic hematopoietic stem cell transplantation in human patients and mice – Yusuke Shono – Science Translational Medicine

Some antibiotics may worsen complications in transplant patients – Science Daily

Microbes in the news

Welcome To FiveThirtyEight’s Gut Science Week – Maggie Koerth-Baker

Everybody Is Constipated, Nobody Is Constipated – Maggie Koerth-Baker

What Your Poop Says About You – Christine Laskowski

Probiotics Won’t Fix All Your Health Problems – Katherine Hobson

What Your Poop Says About You – Christine Laskowski

Is Gut Science Biased? – Anna Maria Barry-Jester

How Your Gut Affects Your Mood – Christie Aschwanden – FiveThirtyEight

Your Mouth Has Bacteria “That Could Grow on Mars,” Says a NASA Scientist – Especially if you had cheese sometime recently – Neel V. Patel – Inverse

Science, publishing, and career

Preprints for the life sciences – Jeremy M. Berg – Science

May 17, 2016

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Live blogging from the Michigan Microbial Meeting, microbiomes of Tibetan macaques and Pika, climate gases from SAR11, mycobiome of stored peanuts, and the deep biosphere.

Events

Ongoing now, with live written coverage: Michigan Meeting ““Unseen Partners: Manipulating Microbial Communities that Support Life on Earth.”

Bioinformatics for the Microbiome Symposium – Stanford Medicine – Friday May 27, 2016

Symposium: With a Little Help from My Friends: Microbial Partners in Integrative and Comparative Biology – Jan 4-8 2017, New Orleans

General microbiome

Microbiome Data Science: Understanding Our Microbial Planet – Nikos C. Kyrpides – Trends in Microbiology

Animal experiments

Antiviral effect of vitamin A on norovirus infection via modulation of the gut microbiome
Heetae Lee – Scientific Reports

A single gene of a commensal microbe affects host susceptibility to enteric infection – Mi Young Yoon – Nature Communications

Conference abstract: The Impact of Dietary Soy on Gut Microbiome – India R Gill – The FASEB Journal

Animal microbiome

Marked variation between winter and spring gut microbiota in free-ranging Tibetan Macaques (Macaca thibetana) – Binghua Sun – Scientific Reports

Pika population density is associated with composition and diversity of gut microbiota – Huan Li – Frontiers in Microbiology

Review: The bovine milk microbiota: insights and perspectives from -omics studies – Mol Biosyst

Plant, root, and soil microbiome

Soil pH, total phosphorus, climate and distance are the major factors influencing microbial activity at a regional spatial scale – Haichuan Cao – Scientific Reports

Biochar alters the soil microbiome and soil function: results of next generation amplicon sequencing across Europe – Joseph R. Jenkins – GCB Bioenergy

Biochar as a novel niche for culturing microbial communities in composting – Daquan Sun – Waste Management

Review: Omic Relief for the Biotically Stressed: Metabolomics of Plant Biotic Interactions –
Hezi Tenenboim – Trends in Plant Science

Temperature sensitivity of soil microbial communities: an application of macromolecular rate theory to microbial respiration – Charlotte J. Alster – Biogeosciences

Water and extremophile microbiome

The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol – Jing Sun – Nature Microbiology

News coverage: 
Story behind the paper: Climate gases from SAR11 – Stephen Giovannoni – Nature Microbiology Community Blog
Tiny organisms have huge effect on world’s atmosphere – Science Daily

Bacterial and archaeal communities in the deep-sea sediments of inactive hydrothermal vents in the Southwest India Ridge – Likui Zhang – Scientific Reports

Depth-dependent and seasonal variability in archaeal community structure in the subarctic and subtropical western North Pacific – Ryo Kaneko – Journal of Oceanography

Exploring the interaction patterns among taxa and environments from marine metagenomic data – Ze-Gang Wei – Quantitative Biology

Review: Analysis of Low-Biomass Microbial Communities in the Deep Biosphere – Y. Morono – Advances in Applied Microbiology

Undergraduate thesis: Oases of Microbial Life in the Highest Elevation Fumaroles on Earth – Adam Solon – University of Colorado-Boulder

Food microbiology

Variation in fungal microbiome (mycobiome) and aflatoxins during simulated storage of in-shell peanuts and peanut kernels – Fuguo Xing – Scientific Reports

Microbiology of death

Involvement of microbial mats in early fossilization by decay delay and formation of impressions and replicas of vertebrates and invertebrates – Miguel Iniesto – Scientific Reports

Pollution and waste microbiology

Correlating microbial community profiles with geochemical conditions in a watershed heavily contaminated by an antimony tailing pond – Enzong Xiao – Environmental Pollution

pH modulates arsenic toxicity in Bacillus licheniformis DAS-2 – K. Tripti – Ecotoxicology and Environmental Safety

News coverage: Bacteria discovered to remove arsenic from soil – BK Mishral – Times of India

More microbiology

Immunization with a heat-killed preparation of the environmental bacterium Mycobacterium vaccae promotes stress resilience in mice – Stefan O. Reber – PNAS

News coverage: Immunization with bacteria promotes stress resilience, coping behaviors in mice, CU-Boulder study finds – University of Colorado Boulder

Natural mutations in a Staphylococcus aureus virulence regulator attenuate cytotoxicity but permit bacteremia and abscess formation – Sudip Das – PNAS

Range expansions transition from pulled to pushed waves as growth becomes more cooperative in an experimental microbial population – Saurabh R. Gandhi – PNAS

Microbes and art

Creating art with bacteria at New England Biolabs – Jennie Oemig – Wicked Local Beverly

Microbes in the news

Interviewing the Founder of the World #1 Microbiome Investment fund: Isabelle De Cremoux – Labiotech

How Soil Microbes Fight Climate Change – They’re our microscopic allies in making dirt a major resource for storing excess carbon – Esther Ngumbi – Scientific American

Everything You Need to Know About Obama’s New Microbiome Initiative – Tiny organisms. Big budgets. – Kastalia Medrano – Inverse

Welcome To FiveThirtyEight’s Gut Science Week – Maggie Koerth-Baker – Five Thirty Eight
What Your Poop Says About You – Christine Laskowski – Five Thirty Eight

FAQ on Microbiology of Built Environments from the American Academy of Microbiology – Jonathan Eisen – MicroBEnet

At A Texas Body Farm, Studying The Decay Of Donated Corpses – Kai Kupferschmidt – World Crunch

Children with and without multiple sclerosis have differences in gut bacteria – EurekAlert

Bathroom Reader: A Brief History of the Toilet – Zack Fediay – uBiome Blog

Linfield Wine Lecture Series: Managing Expectations: The Microbiome in Agriculture – Jack Gilbert – Linfield College

Science, publishing, and career

Point of View: Avoiding a lost generation of scientists – Justin Q Taylor – eLIFE

Twitter won’t count links and photos as part of your 140 characters – Dave Gershgorn – PopSci

Bruno Lemaitre on Science and Narcissism – Leonid Schneider – For Better Science

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Illustration by Leonid Schneider