January 19, 2016

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Microbiota manipulation during stem cell transplants, meh-crobial diversity in digestive tract of two sheep breeds, eukaryotes within pitcher plants,  South Atlantic Ocean, and soil affected by the 2011 Japan Tsunami.

Events

ISME16, Montreal, Canada, 21 – 26 August 2016. Registration and Submissions now open. The deadline for submitting your abstract is 18 March.

ASM Career Development Grants for Postdoctoral Women – up to 4 awards of $1,500 each. Deadline for Nominations: February 1, 2016.

Fellowships by L’Oréal USA For Women In Science. Deadline Feb 5, 2016. Program awards five women postdoctoral scientists annually with grants of $60,000 each, in any specialty.

Human oral microbiome

Salivary bacterial fingerprints of established oral disease revealed by the Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS) technique – Daniel Belstrøm – Journal of Oral Microbiology

Human gut microbiome

Sleep quality and the treatment of intestinal microbiota imbalance in Chronic Fatigue Syndrome: A pilot study – Melinda L. Jackson – Sleep Science

Fecal microbiota transplantation: A ‘How-To’ guide for nurses – Sharyn Leis – Collegian Journal

Review: Microbiota Manipulation With Prebiotics and Probiotics in Patients Undergoing Stem Cell Transplantation – Tessa M. Andermann – Current Hematologic Malignancy Reports

Review: Epigenetic Regulation of Enteric Neurotransmission by Gut Bacteria – Tor C. Savidge – Frontiers in Cellular Neuroscience

Bioreactor and animal models

Microbial Metabolism Shifts Towards an Adverse Profile with Supplementary Iron in the TIM-2 In vitro Model of the Human Colon – Guus A. M. Kortman – Frontiers in Microbiology

Video: A Novel Bioreactor for High Density Cultivation of Diverse Microbial Communities – Jacob R. Price – JOVE

Atlantic Salmon (Salmo salar L.) Gastrointestinal Microbial Community Dynamics in Relation to Digesta Properties and Diet – Kamarul Zaman Zarkasi – Microbial Ecology

Animal microbiome

Microbial diversity in the digestive tract of two different breeds of sheep – J.-L. Douglas – Journal of Applied Microbiology

Dynamics of Bacterial Community Composition in the Malaria Mosquito’s Epithelia – Majoline T. Tchioffo – Frontiers in Microbiology

Microbiota Plays a Role in Oral Immune Priming in Tribolium castaneum – Momir Futo – Frontiers in Microbiology

Plant, root, and soil microbiome

Dynamics of Viral Abundance and Diversity in a Sphagnum-Dominated Peatland: Temporal Fluctuations Prevail Over Habitat – Flore Ballaud – Frontiers in Microbiology

Biogeographic barriers drive co-diversification within associated eukaryotes of the Sarracenia alata pitcher plant system – Jordan D. Satler – PeerJ

Expanding our Understanding of the Seaweed Holobiont: RNA Viruses of the Red Alga Delisea pulchra – Tim Lachnit – Frontiers in Microbiology

New Methods To Unravel Rhizosphere Processes – Eva Oburger – Trends in Plant Science

Soil microbial responses to forest floor litter manipulation and nitrogen addition in a mixed-wood forest of northern China – Xiao-Lu Sun – Scientific Reports

Unraveling the Functions of the Macroalgal Microbiome – Ravindra Pal Singh – Frontiers in Microbiology

Water and extremophile microbiome

Diversity and bioprospection of fungal community present in oligotrophic soil of continental Antarctica – Valéria M. Godinho – Extremophiles

Novel Barite Chimneys at the Loki’s Castle Vent Field Shed Light on Key Factors Shaping Microbial Communities and Functions in Hydrothermal Systems – Ida H. Steen – Frontiers in Microbiology

High Diversity of Anaerobic Alkane-Degrading Microbial Communities in Marine Seep Sediments Based on (1-methylalkyl)succinate Synthase Genes – Marion H. Stagars – Frontiers in Microbiology

Nutrient limitation of microbial phototrophs on a debris-covered glacier – J.L. Darcy – Soil Biology and Biochemistry

Large-scale distribution of microbial and viral populations in the South Atlantic Ocean – Daniele De Corte – Environmental Microbiology Reports

Selective Pressure of Temperature on Competition and Cross-Feeding within Denitrifying and Fermentative Microbial Communities – Anna Hanke – Frontiers in Microbiology

A Lipid-Accumulating Alga Maintains Growth in Outdoor, Alkaliphilic Raceway Pond with Mixed Microbial Communities – Tisza A. S. Bell – Frontiers in Microbiology

Genomic Reconstruction of an Uncultured Hydrothermal Vent Gammaproteobacterial Methanotroph (Family Methylothermaceae) Indicates Multiple Adaptations to Oxygen Limitation – Connor T. Skennerton – Frontiers in Microbiology

Genomic and metagenomic analysis of microbes in a soil environment affected by the 2011 Great East Japan Earthquake tsunami – Satoshi Hiraoka – BMC Genomics

Oil reservoir microbiome

Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs – Ping Hu – mBio

Food microbiology

Dynamic changes in microbiota and mycobiota during spontaneous ‘Vino Santo Trentino’ fermentation – Irene Stefanini – Microbial Biotechnology

Other microbiology and techniques

Perspective: Adapting Koch’s postulates – Allyson L. Byrd, Julia Segre – Science

Depletion of human DNA in spiked clinical specimens to improve the sensitivity of pathogen detection by next generation sequencing – Mohammad R. Hasan – Journal of Clinical Microbiology

Evaluation of a new device to simplify and standardize stool sample preparation for viral molecular testing with limited hands-on-time – Linda Feghoul – Journal of Clinical Microbiology

Review: Polymicrobial Biofilm Studies: from Basic Science to Biofilm Control – Hubertine ME Willems – Current Oral Health Reports

Review: Laser microdissection: A promising tool for exploring microorganisms and their interactions with hosts – Oleg V. Podgorny – Journal of Microbiological Methods

Book: Applications of Mass Spectrometry in Microbiology – Plamen Demirev, Todd R Sandrin – Springer

Metagenomics and bioinformatics

Searching more genomic sequence with less memory for fast and accurate metagenomic profiling – Shea N Gardner – bioRxiv

An evaluation of the accuracy and speed of metagenome analysis tools – Stinus Lindgreen – Scientific Reports

Motif-based text mining of microbial metagenome redundancy profiling data for disease classification – Yin Wang – BioMed Research International

Metabolic pathways

Metabolic traits of an uncultured archaeal lineage -MSBL1- from brine pools of the Red Sea – Romano Mwirichia – Scientific Reports

Microbes in the news

Looking at the Microbiota to Improve Intestinal Transplantation Results – Jeannette Y. Wick – HCP Live

Why do I have to share my body with so many bugs? – Michael Mosley – BBC

How Bitter Taste Receptors Defend the Body against Bacteria – Robert J Lee – Scientific American

White Paper: The Future of Microbiome Research: Out of the Lab and Into the Clinic – Global Engage

How chicory may help fight plague bacteria – Jason Tetro – Popular Science

Lethal bacteria in Christmas Island feral cats sparks warning (Leptospira) – Nicolas Perpitch – ABC Australia

Microbes and art

Subvisual Subway: The Art of New York City’s Bacterial World – Emily Driscoll – Science Friday

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January 18, 2016

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Skin fungi on astronauts before, during, and after a stay at the ISS, preventing obesity by stool transplants, and microbial landscapes of food production.

Human skin microbiome

Comprehensive analysis of the skin fungal microbiota of astronauts during a half-year stay at the International Space Station – Takashi Sugita – Medical Mycology

Human gut microbiome

Review: Can We Prevent Obesity-Related Metabolic Diseases by Dietary Modulation of the Gut Microbiota? – Lena K Brahe – Advances in Nutrition

Animal models

Gut microbiota lipopolysaccharide accelerates inflamm-aging in mice – Kyung-Ah Kim – BMC Microbiology

Microbiota Control of Malaria Transmission – Miguel P. Soares – Trends in Parasitology

Plant, root, and soil microbiome

Suitability of the microbial community composition and function in a semiarid mine soil for assessing phytomanagement practices based on mycorrhizal inoculation and amendment addition – J. Kohler – Journal of Environmental Management

Relevance of in vitro agar based screens to characterize the anti-fungal activities of bacterial endophyte communities – Hanan R. Shehata – BMC Microbiology

Food microbiology

A new perspective on microbial landscapes within food production – Nicholas A Bokulich – Current Opinion in Biotechnology

Metagenomics and bioinformatics

Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis –
Veronika B. Dubinkina – BMC Bioinformatics

More microbiology

A high-precision rule-based extraction system for expanding geospatial metadata in GenBank records – Tasnia Tahsin – Journal of the American Medical Informatics Association

Microbial stress priming – a meta-analysis – Diana R. Andrade-Linares – Environmental Microbiology

Microbes in the news

Corpse-eating bacteria a forensic tool – Viviane Richter – Cosmos

Olympus Voluntarily Recalls Medical Scope Accused Of Sickening Hundreds With Antibiotic-Resistant Infections – Jaleesa Baulkman – Medical Daily. See full report at Preventable Tragedies: Superbugs and How Ineffective Monitoring of
Medical Device Safety Fails Patients

Could a Poo Transplant Cure You? – Robynne Chutkan – The Huffington Post

Companies Aim to Make Drugs from Bacteria That Live in the Gut – Mike Orcutt – MIT Technology Review

Should You Eat Poop To Lose Weight? – Bruce Y. Lee – Forbes

A Judge Dismissed A Woman’s DWI Because Her Gut Makes Its Own Booze – Cat Ferguson – BuzzFeed

A Lesson in Lyme: What the Hell is a Spirochete? – Hannah Barry – The Lyme Life

Bacteria hysteria

Note: Sponsored by the Cleaning Industry Research Institute: Study Reveals High Bacteria Levels on Footwear – CIRI Science

Hotel Hygiene Exposed – Travel Math

Science, publishing, and career

Obama’s big bet on science: It’s about far more than a cancer ‘moonshot’ – Carl Zimmer – STATnews

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January 16, 2016

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Gut microbiota in acute malnutrition, social behavior and the chimpanzee pan-microbiome, arctic marine fungi, and learning ecological networks.

General microbiome

Immune-Microbiota Interactions: Dysbiosis as a Global Health Issue – Alan C. Logan – Current Allergy and Asthma Reports

Human oral microbiome

Long-term prospective cohort study on dental implants: clinical and microbiological parameters – Henri Tenenbaum – Clinical Oral Implants Research

Human reproductive tract microbiome

Alterations in the Genital Microbiota in Women With Spinal Cord Injury – Pires, Cristhiane V.G. – Obstetrics & Gynecology

Human gut microbiome

Gut Microbiota in Children Hospitalized with Oedematous and Non-Oedematous Severe Acute Malnutrition in Uganda – Kia Hee Schultz Kristensen – PLOS Neglected Tropical Diseases

Editorial: Confounding Effects of Metformin on the Human Gut Microbiome in Type 2 Diabetes – Adil Mardinoglu – Cell Metabolism

Review: Impact of high fat diets, prebiotics and probiotics on gut microbiota and immune function, with relevance to elderly populations – Yue Liu – Nutrition and Aging

Review: Transkingdom control of viral infection and immunity in the mammalian intestine – Julie K. Pfeiffer – Science

Review: Micromanagement in the gut: microenvironmental factors govern colon mucosal biofilm structure and functionality – Rosemarie De Weirdt – NPJ Biofilms and Microbiomes

Animal models

In rats: Alternating or continuous exposure to cafeteria diet leads to similar shifts in gut microbiota compared to chow diet – Nadeem O. Kaakoush – Molecular Nutrition & Food Research

In mice: Streptomycin treatment alters the intestinal microbiome, pulmonary T cell profile and airway hyperresponsiveness in a cystic fibrosis mouse model – Mark Bazett – Scientific Reports

Animal microbiome

Social behavior shapes the chimpanzee pan-microbiome – Andrew H. Moeller – Science Advances

Environmental drivers of microbial community shifts in the giant barrel sponge, Xestospongia muta, over a shallow to mesophotic depth gradient – Kathleen M. Morrow – Environmental Microbiology

Feeding cessation alters host morphology and bacterial communities in the ascidian Pseudodistoma crucigaster – Susanna López-Legentil – Frontiers in Zoology

Plant, root, and soil microbiome

Uncultivated margins are source of soil microbial diversity in an agricultural landscape –
Luciana D’Acunto – Agriculture, Ecosystems & Environment

Editorial: Deep influence of soil microbes – Karl Gruber – Nature Plants

Review: Soil microbes and community coalescence – Matthias C. Rillig – Pedobiologia

Water and extremophile microbiome

Linkages between mineralogy, fluid chemistry, and microbial communities within hydrothermal chimneys from the Endeavor Segment, Juan de Fuca Ridge – T. J. Lin – Geochemistry, Geophysiscs, Geosystems

Exploration of microbial diversity and community structure of Lonar Lake: the only hypersaline meteorite crater lake within basalt rock – Dhiraj Paul – Frontiers in Microbiology

Vertical segregation and phylogenetic characterization of ammonia-oxidizing bacteria and archaea in the sediment of a freshwater aquaculture pond – Shimin Lu – Frontiers in Microbiology

Chytrids Dominate Arctic Marine Fungal Communities – B.T. Hassett – Environmental Microbiology

Built environment microbiome

Bacterial Monitoring in the International Space Station-“Kibo” Based on rRNA Gene Sequence – Nobuyasu Yamaguchi – Transactions of the Japan Society for Aeronautical and Space Sciences

Metagenomics and bioinformatics

Safe and complete contig assembly via omnitigs – Alexandru I. Tomescu – ArXiv

More microbiology and ecology

How clonal are bacteria over time? – B. Jesse Shapiro – BioRxiv

Transcription Factors Exhibit Differential Conservation in Bacteria with Reduced Genomes – Edgardo Galán-Vásquez – PLOS ONE

Learning Ecological Networks from Next-Generation Sequencing Data – Corinne Vacher – Advances in Ecological Research

Microbes in the news

Chimps Share Microbes When Socializing – Kate Yandell – The Scientist

How Your Social Life Changes Your Microbiome – Ed Yong – The Atlantic

Social Contact Helps Beneficial Gut Bacteria Spread – Brian Handwerk – Smithsonian

Prevent severe diarrhea by controlling levels of specific gut bacteria – Bel Marra Health

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January 15, 2016

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Distinct microbiotas in 2 West Nile Virus-carrying mosquitoes, co-occurrence networks in Chinese soil, microbial communities associated with retreating glaciers.

Events

Open for international proposals: 2016 Mo Bio Microbiome Awards – Deadline May 31

Human oral microbiome

In Vitro Cultivation of ‘Unculturable’ Oral Bacteria, Facilitated by Community Culture and Media Supplementation with Siderophores – Sonia R. Vartoukian – PLOS ONE

Human gut microbiome

Synbiotics Easing Renal Failure by Improving Gut Microbiology (SYNERGY): A Randomized Trial – Megan Rossi – Clinical Journal of the American Society of Nephrology

Perspective: Effect of Synbiotic Therapy on Gut–Derived Uremic Toxins and the Intestinal Microbiome in Patients with CKD – Nosratola D. Vaziri – Clinical Journal of the American Society of Nephrology

Animal models

Editorial: Microbiome: Fibre for the future – Eric C. Martens – Nature

Animal microbiome

Culex pipiens and Culex restuans mosquitoes harbor distinct microbiota dominated by few bacterial taxa – Ephantus J. Muturi – Parasites & Vectors

Plant, root, and soil microbiome

Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China – Bin Ma – The ISME Journal

Evidence of the Generation of Isosaccharinic Acids and Their Subsequent Degradation by Local Microbial Consortia within Hyper-Alkaline Contaminated Soils, with Relevance to Intermediate Level Radioactive Waste Disposal – Simon P. Rout – PLOS ONE

Biodiversity and succession of mycobiota associated to agricultural lignocellulosic waste-based composting – Juan Antonio López-González – Bioresource Technology

Water/soil/glacier microbiome

Shifts in diversity and function of lake bacterial communities upon glacier retreat –  Hannes Peter – The ISME Journal

Potential sources of microbial colonizers in an initial soil ecosystem after retreat of an alpine glacier – Thomas Rime – The ISME Journal

Other microbiology

Automated broad range molecular detection of bacteria in clinical samples – Andries E. Budding – Journal of Clinical Microbiology

Natural environments, nature relatedness and the ecological theater: connecting satellites and sequencing to shinrin-yoku – Jeffrey M. Craig – Journal of Physiological Anthropology

Biodegradation of antibiotic ciprofloxacin: pathways, influential factors, and bacterial community structure – Xiaobin Liao – Environmental Science and Pollution Research

Techniques

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling – Rosalinda D’Amore – BMC Genomics

Microbes in the news

Gut Microbes Need Fiber, Too – Karen Zusi – The Scientist

Would You Take Poop Pills If They Made You Thin? – Susan Rinkunas – New York Magazine

Weird headline above article about Sonnenburg Nature paper: Pet owners urged NOT to wash hands after handling animals to keep friendly bacteria – Laura Mowat – Express

Another puzzling project: ‘Child scientist’ Mustafa develops technique to protect crops from bacteria – Siasat

Stinging Report On Pandemics Makes Louis Pasteur Look Like A Prophet – Jason Beaubien – NPR

After Ebola, 2 Other Tropical Diseases Pose New Threats – Kate Kelland – Scientific American

Science, publishing, and career

Opinion: The Postdoc Crisis. A lack of jobs leaves postdocs without a future in academia in the United States. Meanwhile, other challenges threaten the postdoc community abroad – Muhammed Z. Ahmed – The Scientist

Is sexual harassment less common in biology than in astronomy? – Lenny Teytelman – The Spectroscope

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January 14, 2016

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Sorry for a late post today – I had a lot of meetings. Here is what I found:

Gut microbiota shaped via fecal microRNA, the microgenderome, dysbiosis in Vitiligo skin lesions, metatranscriptomics, and an 18th century Yersinia pestis.

General microbiome

Perspective: Taking it Personally: Personalized Utilization of the Human Microbiome in Health and Disease – Niv Zmora – Cell Host & Microbe

The Human Microbiome: Opportunities for Dynamics, Systems, and Control
(based on the IFAC blog post Translate or Die) – Travis E. Gibson – Submitted to ACC 2016

Human skin microbiome

Microbial community profiling shows dysbiosis in the lesional skin of Vitiligo subjects – Parul Ganju – Scientific Reports

Human oral microbiome

Diversity and homogeneity of oral microbiota in healthy Korean pre-school children using pyrosequencing – Soo Eon Lee – Acta Odontologica Scandinavica

Short-term effects of povidone iodine and sodium fluoride therapy on plaque levels and microbiome diversity – C Reilly – Oral Diseases

Commentary: A new association for the oral metagenome – Nicholas S Jakubovics – Oral Diseases

Human vaginal microbiome

Review: Vaginal microbiota and microbiome:- Role in health and disease – Dr Amit A. Rangari – Indian Journal of Basic and Applied Medical Research;

Human gut microbiome

Support for the Microgenderome: Associations in a Human Clinical Population – Amy Wallis – Scientific Reports

Impact of increasing fruit and vegetables and flavonoid intake on the human gut microbiota – Annett Klinder – Food & Function

Colonization potential to reconstitute a microbe community in patients detected early after fecal microbe transplant for recurrent C. difficile – Ranjit Kumar – BMC Microbiology

Review: The microbiome and its implications in intestinal transplantation – Kroemer, Alexander – Current Opinion in Organ Transplantation

Animal models

Genetic and Metabolic Signals during Acute Enteric Bacterial Infection Alter the Microbiota and Drive Progression to Chronic Inflammatory Disease – Karishma Kamdar – Cell Host & Microbe

The Host Shapes the Gut Microbiota via Fecal MicroRNA – Shirong Liu – Cell Host & Microbe

Animal microbiome

The gastrointestinal tract microbiota of the Japanese quail, Coturnix japonica – Ngare Wilkinson – Applied Microbiology and Biotechnology

Plant, root, and soil microbiome

Culturable endophytic bacterial communities associated with field grown soybean – Karla Bianca de Almeida Lopes – Journal of Applied Microbiology

Historical precipitation predictably alters the shape and magnitude of microbial functional response to soil moisture – Colin Averill – Global Change Biology

Water and waste microbiome

Development of new host-specific Bacteroides qPCRs for the identification of fecal contamination sources in water – Marta Gómez-Doñate – Microbiology Open

Bacterial diversity in oil-polluted marine coastal sediments – Alejandro Acosta-González – Current Opinion in Biotechnology

Spatial and temporal variability of bacterial communities in high alpine water spring sediments – Alfonso Esposito – Research in Microbiology

Biogeochemical, Isotopic and Bacterial Distributions Trace Oceanic Abyssal Circulation – Angelo Rubino – PLOS ONE

Metagenomics, metatranscriptomics, and bioinformatics

Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus – Kirsten I Bos – BioRxiv

Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality – Yue Jiang – BMC Microbiome Journal

Viral metagenomics and blood safety – V. Sauvage – Transfusion Clinique et Biologique

Microbes in the news

Does our Microbiome Control Us or Do We Control It? – Dina Fine Maron – Scientific American

Your gut’s trick for controlling the bacteria that live in it – New Scientist

Mammals shape their microbiome to prevent disease – Science Codex

Low-Fiber Diets Cause Waves of Extinction in the Gut – Ed Yong – The Atlantic

Bad diets today can alter our great-great-grandkids’ biology – Katherine Ellen Foley – Quartz

Thoughtful and balanced comparison: mothur and QIIME – Pat Schloss – Mothur blog

Modifying the structure of wood alters plant microbiome – Science Daily

Gut Microbiome Similar in Formula- and Combination-Fed Babies – Troy Brown – MedScape

Eglin medical group first to find bacteria unseen in humans: Borrelia turicatae – Ilka Cole – US Air Force

Protecting the infant microbiome – Kathryn Kos – Examiner

Microbiology and art

Sunshine and microbiology inspire Reading artist’s work – Francesca Perryman – Get Reading

Science, publishing, and career

Re: Your Recent Email to Your Professor: Students who use emojis in their emails and write “heeeeelp!” in the subject line don’t necessarily know better.  – Paul T. Corrigan and Cameron Hunt McNabb – Inside Higher Education

ORCID: Publishers embrace scheme to end name confusion – John Bohannon – Science

Give teachers a physics test from a woman and they’ll give her worse grades – John Timmer – Ars Technica

Astronomy’s snowballing sexual harassment scandal picks up even more cases – Rachel Feltman – Washington Post

Bik’s Picks

Inside the Eye: Nature’s Most Exquisite Creation – Ed Yong – National Geographic
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January 13, 2016

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Frozen vs fresh stool transplants, the primate skin microbiome, diet-induced extinctions, bacteria in breast milk from low income Mexican-American moms, and engineered poplar tree endosphere.

Events

Tapping the Human Microbiome (Kavli Hangout) – Tuesday, Jan. 19, 1:30 pm EST, with Janet Jansson, Rob Knight, and Jeff Miller

Pregnancy and birth microbiome

Bacterial microbiome of breast milk and child saliva from low-income Mexican-American women and children – Veronica Davé – Pediatric Research

Human vaginal microbiome

Review: Biotherapeutic agents and vaginal health – F. H. Al-Ghazzewi – Journal of Applied Microbiology

Human gut microbiome

Frozen vs Fresh Fecal Microbiota Transplantation and Clinical Resolution of Diarrhea in Patients With Recurrent Clostridium difficile Infection – Christine H. Lee – JAMA

Small Intestine Bacterial Overgrowth and Environmental Enteropathy in Bangladeshi Children – Jeffrey R. Donowitz – mBio

Animal and bioreactor models

Diet-induced extinctions in the gut microbiota compound over generations – Erica D. Sonnenburg – Nature

Intestinal epithelial TLR4 signaling affects epithelial function, colonic microbiota and promotes risk for transmissible colitis – Rishu Dheer – Infection and Immunity

Modulation of the human gut microbiota by dietary fibres occurs at the species level – Wing Sun Faith Chung – BMC Biology

Animal microbiome

Diversity and evolution of the primate skin microbiome – Sarah E. Council – Proceedings of the Royal Society B

Host-associated coral reef microbes respond to the cumulative pressures of ocean warming and ocean acidification – N. S. Webster – Scientific Reports

Plant, root, and soil microbiome

Lignin engineering in field-grown poplar trees affects the endosphere bacterial microbiome – Bram Beckers – PNAS

Invariant community structure of soil bacteria in subtropical coniferous and broadleaved forests – Xiaoli Wang – Scientific Reports

Food microbiology

Seasonal and Growth-Dependent Dynamics of Bacterial Community in Radish Sprouts – Hiroshi Asakura – Journal of Food Safety

Bacterial dynamics and metabolite changes in solid-state acetic acid fermentation of Shanxi aged vinegar – Sha Li – Applied Microbiology and Biotechnology

Transcriptomics

Functional Profiling of Unfamiliar Microbial Communities Using a Validated De Novo Assembly Metatranscriptome Pipeline – Mark Davids – PLOS ONE

Metagenomics and bioinformatics

Direct next-generation sequencing of virus-human mixed samples without pretreatment is favorable to recover virus genome – Dingchen Li – Biology Direct

Microbes in the news

DNA Genotek’s microbiome collection and stabilization blog – Lisa Gamwell – The Microbiome Snapshot

Human trials will test freeze-dried poop pills as a weight-loss treatment – David Nield – Science Alert

What is Zika virus? Interview with Derek Gatherer – Microbe Post

E. coli Slinky: Revealed: the awful anchor that lets urinary tract infections take hold – Josh Barney – University of Virginia

Bik’s Picks

Estimation of a Killer Whale (Orcinus orca) Population’s Diet Using Sequencing Analysis of DNA from Feces – Michael J. Ford – PLOS ONE

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January 12, 2016

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The ecology of microbiome research (in the new journal Nature Microbiology), gut microbiome of infants, dentition status and teeth microbes, human impact on corals, metagenomics, CRISPRs, rainforest and desert soils, and tropical oceans.

General microbiome

An assessment of US microbiome research – Elizabeth Stulberg – Nature Microbiology

Microbiome: Ecology of stable gut communities – Luke McNally – Nature Microbiology

Pregnancy and birth microbiome

Association of Cesarean Delivery and Formula Supplementation With the Intestinal Microbiome of 6-Week-Old Infants – Juliette C. Madan – JAMA Pediatrics

Human oral microbiome

Supragingival Microbial Profiles of Permanent and Deciduous Teeth in Children with Mixed Dentition – Weihua Shi – PLOS ONE

Human gut microbiome

Human Gut Bacteria Are Sensitive to Melatonin and Express Endogenous Circadian Rhythmicity – Jiffin K. Paulose – PLOS ONE

A New High-Throughput Approach to Genotype Ancient Human Gastrointestinal Parasites – Nathalie M. L. Côté – PLOS ONE

Intestinal Microbiota in Patients with Spinal Cord Injury – Bilgi Gungor – PLOS ONE

Editorial: A Potential Role for Host- Microbe Dysbiosis in Enteropathy Associated with HIV Infection – Michael D. George – Primary & Acquired Immunodeficiency Research

Review: The obese gut microbiome across the epidemiologic transition – Lara R. Dugas – Emerging Themes in Epidemiology

Animal microbiome

Obligate bacterial mutualists evolving from environmental bacteria in natural insect populations – Takahiro Hosokawa – Nature Microbiology

The Microbiome of Ehrlichia-Infected and Uninfected Lone Star Ticks (Amblyomma americanum) – R. T. Trout Fryxell – PLOS ONE

Coral microbial community dynamics in response to anthropogenic impacts near a major city in the central Red Sea – Maren Ziegler – Marine Pollution Bulletin

Application of Faecalibacterium 16S rDNA genetic marker for accurate identification of duck faeces – Da Sun – Environmental Science and Pollution Research

Review: Understanding the canine intestinal microbiota and its modification by pro-, pre- and synbiotics – what is the evidence? – Silke Schmitz – Veterinary Medicine and Science

Plant, root, and soil microbiome

Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest – Julia Elidia Lima-Perim – PLOS ONE

Corky root severity, root knot nematode galling and microbial communities in soil, rhizosphere and rhizoplane in organic and conventional greenhouse compartments –
Ariena H.C. van Bruggen – Applied Soil Ecology

Metacommunity analysis of amoeboid protists in grassland soils – Anna Maria Fiore-Donno – Scientific Reports

Microbial communities of buried soils of the Tsaritsyn Defense Line (1718–1720) – T. S. Demkina – Soil Biology

Perspective: Exploring rhizospheric interactions for agricultural sustainability: The need of integrative research on multi-trophic interactions – Rama Kant Dubey – Journal of Cleaner Production

Water microbiome

Genetic Diversity Affects the Daily Transcriptional Oscillations of Marine Microbial Populations – Irina N. Shilova – PLOS ONE

Low diversity of planktonic bacteria in the tropical ocean – Mathias Milici – Scientific Reports

Out of thin air: Microbial utilization of atmospheric gaseous organics in the surface ocean – Jesus M. Arrieta – Frontiers in Microbiology

Elevated nutrients change bacterial community composition and connectivity: high throughput sequencing of young marine biofilms – Jasmin C. Lawes – Biofouling

Waste microbiology

Dynamics of bacterial populations during bench-scale bioremediation of oily seawater and desert soil bioaugmented with coastal microbial mats – Nidaa Ali – Microbial Biotechnology

Sequential Changes of Microbial Community Composition During Biological Wastewater Treatment in Single Unit Waste Stabilization System – Subhasis Sarkar – Waste and Biomass Valorization

Diversity and interactions of microbial functional genes under differing environmental conditions: insights from a membrane bioreactor and an oxidation ditch – Yu Xia – Scientific Reports

Food microbiology

Investigation of chocolate produced from four different Brazilian varieties of cocoa (Theobroma cacao L.) inoculated with Saccharomyces cerevisiae – Aline Galvão Tavares Menezesa – Food Research International

Microbial diversity and metabolite composition of Belgian red-brown acidic ales – Isabel Snauwaert – International Journal of Food Microbiology

Metagenomics, CRISPRs, viruses, and bioinformatics

Computational prediction of CRISPR cassettes in gut metagenome samples from Chinese type-2 diabetic patients and healthy controls – Tatiana C. Mangericao – BMC Systems Biology

Identification of physical interactions between genomic regions by enChIP-Seq – Toshitsugu Fujita – BioRxiv

Metaviromics of Namib Desert Salt Pans: A Novel Lineage of Haloarchaeal Salterproviruses and a Rich Source of ssDNA Viruses – Evelien M. Adriaenssens – MDPI Viruses

A novel semi-supervised algorithm for the taxonomic assignment of metagenomic reads – Vinh Van Le – BMC Bioinformatics

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations – Matthew L Bendall – The ISME Journal

Techniques in microbiology

The 6th International Conference on Analysis of Microbial Cells at the Single Cell Level, Retz, Austria, 19-22 July, 2015 – Nina Bydlinski – New Biotechnology

Microbes in the news

Microbe Cells Don’t Outnumber Your Own – Marissa Fessenden – Smithsonian

Getting to know the vagina: Microbiomes and our health – Daniel Vosberg – McGillDaily

Acidification affects the ability of bacteria to clean our oceans – Phys.org

Science, publishing, and career

Do prestigious science journals attract bad science? – Julia Belluz – Vox

Female professors are woefully outnumbered at med schools nationwide – Melissa Bailey – STAT News
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January 11, 2016

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Bacteriome of bat flies, phyllosphere of Espeletia plants, microbial eukaryotes in a fjord, and decomposing human bodies.

Human gut microbiome

Editorial: Gut microbiota cool-down burning fat! The immune hypothesis – Remy Burcelin – Trends in Endocrinology & Metabolism

Animal models

The programming effects of nutrition-induced catch-up growth on gut microbiota and metabolic diseases in adult mice – Jia Zheng – Microbiology Open

Animal microbiome

The bacteriome of bat flies (Nycteribiidae) from the Malagasy region: a community shaped by host ecology, bacterial transmission mode, and host-vector specificity – David A Wilkinson – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Microbial and Functional Diversity within the Phyllosphere of Espeletia sp. in an Andean High Mountain Ecosystem – Carlos A. Ruiz-Pérez – Applied and Environmental Microbiology

Water and extremophile microbiome

Strong seasonality of marine microbial eukaryotes in a high-Arctic fjord (Isfjorden, West Spitsbergen) – Miriam Marquardt – Applied and Environmental Microbiology

Microbiome of death

Microbial Signatures of Cadaver Gravesoil During Decomposition – Sheree J. Finley – Microbial Ecology

Bioinformatics and metagenomics

Microvirga massiliensis sp. nov., the human commensal with the largest genome – Aurélia Caputo – Microbiology Open

Microbes in the news

Newborn Gut Bacteria Differs If Infants Breastfed Or Formula-Fed, Vaginal Or Cesarean Birthed – Tara Haelle – Forbes

Good Bacteria May Inhibit Growth Of Pathogen Causing Ear Infection And Pneumonia: Examples Of Food High In Good Bacteria – Katrina Pascual – Tech Times

College Town: WPI students literally get the dirt on bacteria-fighting viruses – Bonnie Russell – Telegram

Mark Zuckerberg’s Facebook post on vaccines sparks huge response – Ashley Welch – CBS News

Gates-backed NYC startup plumbs soil bacteria for tuberculosis therapy – Meghana Keshavan – MedCityNews

Living Bacteria Are Riding Earth’s Air Currents – Jim Morrison – Smithsonian

QIAGEN completed the acquisition of MO BIO Laboratories Inc – PR Newswire

Dirty Work: The Magic of Microbes with Sandor Katz – Matthew Zuras – Munchies

Why The Microbiome Is So Vital To Your Health – Josh Axe – Conscious Life News

What have the Romans ever done for us? Parasites in Europe and the Middle East during Roman Rule – Elisabeth Bik – microBEnet

Microbes and art

Microbial muses: Michele Banks talks about her microbial art – Nature Microbiology

Science, publishing, and career

Student Evaluations of Teaching (Mostly) Do Not Measure Teaching Effectiveness – Anne Boring – Science Open
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January 9, 2016

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Microbiomes of musk deer, Tasmanian Devils, Panamanian frogs, roots of truffle-associated Douglas firs, and the Great Barrier Reef lagoon.

General human microbiome

Editorial: Getting fat from an inflamed relationship? The revenge of the holobiont
Andrew Moore – BioEssays

Perspective: Has provoking microbiota aggression driven the obesity epidemic? – Benoit Chassaing – BioEssays

Pregnancy and birth

A Comparison of Three Bioinformatics Pipelines for the Analysis of Preterm Gut Microbiota using 16S rRNA Gene Sequencing Data – Erica Plummer- OMICS Proteomics & Bioinformatics

Review: Infection and preterm birth – Hugh C.G. Nadeau – Seminars in Fetal and Neonatal Medicine

Human gut microbiome

Gut Microbiota and Metabolic Endotoxemia in Young Obese Mexican Subjects – Radilla-Vázquez R.B. – Obesity Facts

Animal models

The Impact of Dietary Energy Intake Early in Life on the Colonic Microbiota of Adult Mice – Jinyu Xu – Scientific Reports

Western diet induces a shift in microbiota composition enhancing susceptibility to Adherent-Invasive E. coli infection and intestinal inflammation – Allison Agus – Scientific Reports

Resistant Starch Alters the Microbiota-Gut Brain Axis: Implications for Dietary Modulation of Behavior – Mark Lyte – PLOS ONE

Effects of BmCPV Infection on Silkworm Bombyx mori Intestinal Bacteria – Zhenli Sun – PLOS ONE

Antibiotic-treated versus germ-free rodents for microbiota transplantation studies – Randi Lundberg – Gut Microbes

Animal microbiome

The musk chemical composition and microbiota of Chinese forest musk deer males
Diyan Li – Scientific Reports

Pasteurellaceae bacteria from the oral cavity of Tasmanian Devils (Sarcophilus Harrisii) show high MIC values towards aminoglycosides and clindamycin – Nicole Gutman – Letters in Applied Microbiology

Skin bacterial diversity of Panamanian frogs is associated with host susceptibility and presence of Batrachochytrium dendrobatidis – Eria A Rebollar – The ISME Journal

Plant, root, and soil microbiome

Prokaryotic diversity in biodeteriorated wood coming from the Bükkábrány fossil forest – Katerina Nikolouli – International Biodeterioration & Biodegradation

Molecular screening of microbial communities for candidate indicators of multiple metal impacts in marine sediments from northern Australia – Alyssa Cornall – Environmental Toxicology and Chemistry

Characterizing root-associated fungal communities and soils of Douglas-fir (Pseudotsuga menziesii) stands that naturally produce Oregon white truffles (Tuber oregonense and Tuber gibbosum) – Gian Maria Niccolò Benucci – Mycorrhiza

Field degradation of aminopyralid and clopyralid and microbial community response to application in Alaskan soils – Patrick L. Tomco – Environmental Toxicology and Chemistry

Microbial community structure and predicted bacterial metabolic functions in biochar pellets aged in soil after 34 months – Daquan Sun – Applied Soil Ecology

Water and extremophile microbiome

Deep Microbial Life in High-Quality Granitic Groundwater from Geochemically and Geographically Distinct Underground Boreholes – Kohei Ino – Environmental Microbiology Reports

Low viral predation pressure in cold hypersaline Arctic sediments and limits on lytic replication – Jesse Colangelo-Lillis – Environmental Microbiology Reports

Metagenomic analysis suggests modern freshwater microbialites harbor a core and distinct microbial community – Richard A. White III – Frontiers in Microbiology

Partitioning of fungal assemblages across different marine habitats – T.C. Jeffries – Environmental Microbiology Reports

Impact of manufactured TiO2 nanoparticles on planktonic and sessile bacterial communities – Stéphane Jomini – Environmental Pollution

Molecular Ecology of Hypersaline Microbial Mats: Current Insights and New Directions – Hon Lun Wong – MDPI Microorganisms

Microbial genetic diversity in soils along salinealkaline gradients at the coast of Laizhou Bay – Feng Zhao – Protistology

Influence of Zinc on Bacterial Populations and their Proteolytic Enzyme Activities in Freshwater Environments: A Cross-Site Comparison – Lauren Rasmussen – Canadian Journal of Microbiology

Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events – Florent E. Angly – Peer J

Food microbiology

Exploring the phenotypic space of non-Saccharomyces wine yeast biodiversity – Debra Rossouw – Food Microbiology

Infection microbiology

Oral Phage Therapy of Acute Bacterial Diarrhea With Two Coliphage Preparations: A Randomized Trial in Children From Bangladesh – Shafiqul Alam Sarker – EBioMedicine

Book Chapter: Reducing pathobiomes could slow arms race between man and microbes
S. Romano-Bertrand – Microbiology 5

Bioinformatics and metagenomics

Neptune: A Tool for Rapid Microbial Genomic Signature Discovery – Eric Marinier – BioRxiv

Metagenomic Analyses Reveal That Energy Transfer Gene Abundances Can Predict the Syntrophic Potential of Environmental Microbial Communities – Lisa Oberding – MDPI Microorganisms

Conference abstracts from the 2015 IEEE International Conference onBioinformatics and Biomedicine (BIBM):
Leveraging the k-Nearest Neighbors classification algorithm for Microbial Source Tracking using a bacterial DNA fingerprint library – Jeffrey D McGovern
A computational framework for integrative analysis of large microbial genomics data – Erliang Zeng
Computational challenges in microbiome research – Mihai Pop

Microbes in the news

New Year’s Resolutions for your Microbiome – Anne Estes – Mostly Microbes

West Hartford Children Museum Starts Scientific Discussion Series – Kristin Stoller – Hartford Courant

Balbriggan pair named Young Scientists of the Year: Maria Louise Fufezan and Diana Bura claim first place for research into soil fertility and nematodes – Dick Ahlstrom – The Irish Times

Body’s bacteria don’t outnumber human cells so much after all – Tina Hesman Saey – Science News

Are we really made up of more bacteria than human cells? – Lindsey Kratochwill – Popular Science

P&G granted patent for prebiotic agent-containing composition targeting skin microbiome – Andrew McDougall – Cosmetic Design-Europe.com

Science, publishing, and career

Nobel winner pulls out of Melb conference run by controversial Indian company (OMICS, EB) – Andrew Masterson – The Age

Cheer up, my academic colleagues! We’re so lucky to do this job – Anonymous Academic – The Guardian

Publishers to require ORCID identifiers for authors – EurekAlert

Bik’s Picks

Healthy Diet Helps 183-Year-Old Tortoise Feel Young Again – Jason Bittel – National Geographic

 

January 8, 2016

Posted on by

Breast milk microbiota profiles, what did the Romans ever do for us, it was only a matter of thyme, and going down the wrong clay.

Pregnancy and birth

Human milk microbiota profiles in relation to birthing method, gestation and infant gender – Camilla Urbaniak – Microbiome

Early Gut Colonization of Preterm Infants: Effect of Enteral Feeding Tubes – Gómez, Marta – Journal of Pediatric Gastroenterology and Nutrition

Review: Role of the Placenta in Preterm Birth: A Review – Terry K. Morgan – American Journal of Perinatology

Human oral microbiome

Long-term efficacy of microbiology-driven periodontal laser-assisted therapy – F. S. Martelli – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

Human parasites in the Roman World: health consequences of conquering an empire – Piers D. Mitchell – Parasitology

Animal models

Microbiota-induced obesity requires farnesoid X receptor – Ava Parséus – Gut

The Gut Microbiome Is Altered in a Letrozole-Induced Mouse Model of Polycystic Ovary Syndrome – Scott T. Kelley – PLOS ONE

Animal microbiome

Heterogeneous size datasets of broiler intestinal microbial communities can be analyzed without normalization – I. Aranda-Olmedo – Poultry Science

Plant, root, and soil microbiome

Assessing Bacterial Diversity in the Rhizosphere of Thymus zygis Growing in the Sierra Nevada National Park (Spain) through Culture-Dependent and Independent Approaches
Javier Pascual – PLOS ONE

Image-based modelling of nutrient movement in and around the rhizosphere – Keith R. Daly – Journal of Experimental Botany

Unearthing the Antibacterial Mechanism of Medicinal Clay: A Geochemical Approach to Combating Antibiotic Resistance – Keith D. Morrison – Scientific Reports

Water and waste microbiology

Virome-associated antibiotic-resistance genes in an experimental aquaculture facility – Stefano Colombo – FEMS Microbiology Ecology

Biodiversity patterns of plankton assemblages at the extremes of the Red Sea – J.K. Pearman – FEMS Microbiology Ecology

Food microbiology

Taxonomic analysis of the microbial community in stored sugar beets using high-throughput sequencing of different marker genes – Sebastian Liebe – FEMS Microbiology Ecology

Bioinformatics and metagenomics

Antibiotic resistance genes across a wide variety of metagenomes – David Fitzpatrick – FEMS Microbiology Ecology

Microbes in the news

You’re Probably Not Mostly Microbes – Ed Yong – The Atlantic

Scientists discover how blue and green clays kill bacteria – National Science Foundation

Heartburn pills may help grow infection-causing bacteria in gut – Lisa Rapaport – News Daily

Good Bacteria In, Bad Bacteria Out: Biofilms In Water Pipes Filter Dangerous Pathogens Out Of Drinking Water – Lizette Borreli – Medical Daily

The Next Food Fad Is Coming: Feed Your Microbiome – Andrea Hayley, Epoch Times

Enterome Announces Collaboration with Johnson & Johnson Innovation Focused on the Discovery of Novel Targets and Therapeutics for Crohn’s Disease – PR Newswire

From the gut to the eye: commensal microbes as potential triggers of autoimmune uveitis – Atlas of Science

Changes coming with QIIME 2 – Greg Caporaso – Qiime

Science, publishing, and career

DATA CHECK: For female scientists, mixed funding results at U.S. agencies – Jeffrey Mervis – Science
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