Category Archives: Bacteria Hysteria

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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December 13, 2015

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Apple juice or almond consumption, lessons from animal studies, distinguishing between live and dead methanogens.

Human gut microbiome

Comparative study of fecal microbiota in patients with type II diabetes after consumption of apple juice for 4 weeks – Gyu-Sung Cho – Food Science and Biotechnology

Diet quality improves for parents and children when almonds are incorporated into their daily diet: a randomized, crossover study – Alyssa M. Burns – Nutrition Research

Review: Diagnosis and treatment of small intestinal bacterial overgrowth – Francesca Romana Ponziania – Expert Review of Gastroenterology & Hepatology

Review: The enteric microbiome in hepatobiliary health and disease – James H. Tabibian – Liver International

Animal models

Review: The influence of the young microbiome on inflammatory diseases—Lessons from animal studies – Katja M. Bendtsen – Birth Defects Research Part C: Embryo Today: Reviews

Plant, root, and soil microbiome

Interaction between lithification and resource availability in the microbialites of Río Mesquites, Cuatro Ciénegas, México – J. R. Corman – Geobiology

The diversity and abundance of phytase genes (BPP) in bacterial communities of the maize rhizosphere – Simone Raposo Cotta – Letters in Applied Microbiology

Bring on the wheelbarrow: Transplanting soil microbiomes leads to lasting effects on willow growth, but not on the rhizosphere microbiome – Etienne Yergeau – Frontiers in Microbiology

Differential responses of soil bacterial taxa to long-term P, N, and organic manure application – Ying Wang – Journal of Soils and Sediments

Water and extremophile microbiome

Thermal and geochemical influences on microbial biogeography in the hydrothermal sediments of Guaymas Basin, Gulf of California – Luke McKay – Environmental Microbiology Reports

Oceanic fronts: transition zones for bacterioplankton community composition – Federico Baltar – Environmental Microbiology Reports

PhD thesis: Hydrothermal Habitats: Measurements of Bulk Microbial Elemental Composition, and Models of Hydrothermal Influences on the Evolution of Dwarf Planets – Marc Francois Luarent Neveu – Arizona State University

Metagenomics and bioinformatics

Network construction and structure detection with metagenomic count data – Zhenqiu Liu – BioData Mining

A simple algorithm for identifying integrons and gene cassettes in bacteria on next generation sequencing data – Guan-Jie Hua – International Journal of Data Mining and Bioinformatics (no access for me)

Techniques

Fluorescent in situ hybridization for the localization of viruses, bacteria and other microorganisms in insect and plant tissues – Adi Kliot – Methods

Propidium monoazide treatment to distinguish between live and dead methanogens in pure cultures and environmental samples – Janine Heise – Journal of Microbiological Methods

Microbes in the news

You’re Surrounded by Bacteria That Are Waiting for You to Die – Erika Engelhaupt – National Geographic

Does That Wine Smell Good? Bacteria in Your Saliva Deserve Some of the Credit
Study shows some wine aromatics aren’t released until they meet the bacteria in our mouths – Kasey Carpenter – Wine Spectator

San Jose: Hospital nurse had tuberculosis; hundreds of babies, moms need treatment or tests – Tracy Seipel – Mercury News

Based on a 2006 paper: This Weed Takes Out Other Plants by Attacking Their “Gut Bacteria” – Esther Inglis-Arkell – Gizmodo

Bacteria Hysteria

Could your child’s teddy give them a stomach bug? Wash youngsters’ favourite toys… and other tips to keep your family lurgy-free this Christmas – The Sun

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December 8, 2015

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The CF microbiome, microbes attaching to glycoproteins in sweat, gut bacteria make cockroach poop smell attractive for other cockroaches, mycobiome of South African Cabernet vines, and seasonality of Japanese cherry orchard soil fungi.

General microbiome

Perspective: Behavioral Microbiomics: A Multi-Dimensional Approach to Microbial Influence on Behavior – Adam C.-N. Wong – Frontiers in Microbiology

Research highlight: Microbiota-based nutrition plans – Cláudio Nunes-Alves – Nature Reviews Microbiology

Pregnancy and birth

Maternal risk factors for abnormal vaginal flora during pregnancy – Cecilia Tibaldi – International Journal of Gynecology & Obstetrics

Human respiratory microbiome

MiniReview: The cystic fibrosis microbiome in an ecological perspective and its impact in antibiotic therapy – Andreia P. Magalhães – Applied Microbiology and Biotechnology

Human oral microbiome

Oral Microbiota and Risk for Esophageal Squamous Cell Carcinoma in a High-Risk Area of China – Xingdong Chen – PLOS ONE

Human skin microbiome

Sweating the small stuff: Glycoproteins in human sweat and their unexplored potential for microbial adhesion – Robyn A Peterson – Glycobiology

Human gut microbiome

Gut microbiota manipulation with prebiotics in patients with non-alcoholic fatty liver disease: a randomized controlled trial protocol – BMC Gastroenterology

Review: Current roles of specific bacteria in the pathogenesis of inflammatory
bowel disease – Lucy McMullen – Microbiology

Animal and bioreactor models

Intestinal microbiota contributes to individual susceptibility to alcoholic liver disease – M Llopis – Gut

Development of a Laboratory Model of a Phototroph-Heterotroph Mixed-Species Biofilm at the Stone/Air Interface – Federica Villa – Frontiers in Microbiology

Animal microbiome

Gut bacteria mediate aggregation in the German cockroach – Ayako Wada-Katsumata – PNAS

The deep-sea glass sponge Lophophysema eversa harbors potential symbionts responsible for the nutrient conversions of carbon, nitrogen and sulfur – Ren-Mao Tian – Environmental Microbiology

Plant, root, and soil microbiome

The Anti-Phytophthora Effect of Selected Potato-Associated Pseudomonas Strains: From the Laboratory to the Field – Anouk Guyer – Frontiers in Microbiology

Defoliation reduces soil biota – and modifies stimulating effects of elevated CO2 – Marie Dam – Ecology and Evolution

Sequence-based Analysis of the Vitis vinifera L. cv Cabernet Sauvignon Grape Must Mycobiome in Three South African Vineyards Employing Distinct Agronomic Systems – Mathabatha E. Setati – Frontiers in Microbiology

Paradox of plant growth promotion potential of rhizobacteria and their actual promotion effect on growth of barley (Hordeum vulgare L.) under salt stress – Massimiliano Cardinale – Microbiological Research

Survey of Annual and Seasonal Fungal Communities in Japanese Prunus mume Orchard Soil by Next-Generation Sequencing – Yoshinao Aoki – Advances in Microbiology

Actinobacterial Diversity in the Sediments of Five Cold Springs on the Qinghai-Tibet Plateau – Jian Yang – Frontiers in Microbiology

Bacterial diversity assessment of pristine mangrove microbial community from dhulibhashani, sundarban using 16S rRNA gene tag sequencing – Pijush Basak – Genomics Data

Microbialites in the shallow-water marine environments of the Holy Cross Mountains (Poland) in the aftermath of the Frasnian–Famennian biotic crisis – Michał Rakociński – Global and Planetary Change

No tillage combined with crop rotation improves soil microbial community composition and metabolic activity – Bingjie Sun – Environmental Science and Pollution Research

Assessing the contribution of fallen autumn leaves to airborne fungi in an urban environment – Peter J. Irga – Urban Ecosystems

Water and extremophile microbiome

Weak Coherence in Abundance Patterns Between Bacterial Classes and Their Constituent OTUs Along a Regulated River – Clara Ruiz-González – Frontiers in Microbiology

Combined Culture-Based and Culture-Independent Approaches Provide Insights into Diversity of Jakobids, an Extremely Plesiomorphic Eukaryotic Lineage – Tomáš Pánek – Frontiers in Microbiology

Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics – Kuei-Han Lin – BMC Genomics

Waste treatment

Microbial community structure associated with the high loading anaerobic codigestion of olive mill and abattoir wastewaters – Hana Gannoun – Bioresource Technology

Microbial analysis of in situ biofilm formation in drinking water distribution systems: implications for monitoring and control of drinking water quality – Isabel Douterelo – Environmental Biotechnology

Food microbiology

Pyrosequencing reveals bacterial diversity in Korean traditional wheat-based nuruk – Jyotiranjan Bal – Journal of Microbiology

Metagenomics and bioinformatics

Hunting Down Frame Shifts: Ecological Analysis of Diverse Functional Gene Sequences – Michal Strejcek – Frontiers in Microbiology

GenomeTester4: a toolkit for performing basic set operations – union, intersection and complement on k-mer lists – Lauris Kaplinski – GigaScience

Microbes in the news

Cockroaches communicate via bacteria in their feces – Elizabeth Pennisi – Science Magzine

MSU professor trekking to the Amazon to study bacteria of insects that spread disease
– Anne Cantrell, MSU News Service – Bozeman Daily

Bacterial Biofilms: A Charged Environment – Kathryn Calkins – Biomedical Beat

Maintaining Wellness, Starting From Your Gut – Julie Chen – Huffington Post

Fall into Fungi – Alex Alexiev – MicroBEnet

Caps can play a part in cleaning water, not just bottling it – Jim Johnson – Plastic News

Dirty Yamuna water harbours drug-resistant bacteria – Neetu Chandra Sharma – Daily Mail India

Cooperating bacteria isolate cheaters – Phys.org

What you should know about this ‘new’ STD: interview with Raquel Dardik – Kristine Thomason – CNN

Bacteria Hysteria

Bacteria tests: What’s growing beneath your feet? – Alex Osiadacz – KLTV

Science, publication, and career

Five selfish reasons to work reproducibly – Florian Markowetz – Genome Biology

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November 18, 2015

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My sincere apologies: the website was down most of today. I am not sure what it was – the problem was on the host server site. But I’m back, with tea rhizobacteria, bacteria reporting explosives in the soil, fungi in a glacier, and a bacterial protein preventing ice cream drip.

Animal models

Editorial: Worming Their Way into the Picture: Microbiota Help Helminths Modulate Host Immunity – Lisa A. Reynolds, B. Brett Finlay – Immunity

Plant, root, and soil microbiome

Environmental changes affect the assembly of soil bacterial community primarily by mediating stochastic processes – Ximei Zhang – Global Change Biology

Hydrologic linkages drive spatial structuring of bacterial assemblages and functioning in alpine floodplains – Remo Freimann – Frontiers in Microbiology

Resistance of Undisturbed Soil Microbiomes to Ceftriaxone Indicates Extended Spectrum β-Lactamase Activity – Joao Gatica – Frontiers in Microbiology

Assessment of Culturable Tea Rhizobacteria Isolated from Tea Estates of Assam, India for Growth Promotion in Commercial Tea Cultivars – Jintu Dutta – Frontiers in Microbiology

Water / extremophile microbiome

Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea – Meng Li – Nature Communications

Fungal biodiversity in the periglacial soil of Dosdè Glacier (Valtellina, Northern Italy) – Marinella Rodolfi – Journal of Basic Microbiology

Winter severity determines functional trait composition of phytoplankton in seasonally ice-covered lakes – Deniz Özkundakci – Global Change Biology

Seasonal and spatial patterns of microbial diversity along a trophic gradient in the interconnected lakes of the Osterseen Lake District, Bavaria – Katrin Zwirglmaier – Frontiers in Microbiology

Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities – Kemal Sanli – Frontiers in Microbiology

Metagenome and Metatranscriptome Revealed a Highly Active and Intensive Sulfur Cycle in an Oil-Immersed Hydrothermal Chimney in Guaymas Basin – Ying He – Frontiers in Microbiology

Diversity and structure of soil bacterial communities in the Fildes Region (maritime Antarctica) as revealed by 454 pyrosequencing – Neng Fei Wang – Frontiers in Microbiology

In situ Detection of Microbial Life in the Deep Biosphere in Igneous Ocean Crust – Everett C. Salas – Frontiers in Microbiology

Waste and built environment microbiology

Review: Genetically engineered microorganisms for the detection of explosives’ residues – Benjamin Shemer – Frontiers in Microbiology

Self-healing of early age cracks in cement-based materials by mineralization of carbonic anhydrase microorganism – Chunxiang Qian – Frontiers in Microbiology

Infection microbiology

Multiplex Molecular Panels for Diagnosis of Gastrointestinal Infection: Performance, Result Interpretation, and Cost-Effectiveness – Matthew J. Binnicker – Journal of Clinical Microbiology

FilmArray Respiratory Panel Assay: Comparison of Nasopharyngeal Swabs and Bronchoalveolar Lavage Samples – Natalya Azadeh – Journal of Clinical Microbiology

Editorial: Variability in Antibiotic Prescribing: An Inconvenient Truth – Lauri A. Hicks and Martin J Blaser – Journal of the Pediatric Infectious Diseases Society

Variation in Antibiotic Prescribing Across a Pediatric Primary Care Network – Jeffrey S. Gerber – Journal of the Pediatric Infectious Diseases Society

Innate Immune Signaling Activated by MDR Bacteria in the Airway – Dane Parker – Physiological Reviews

Tropheryma whipplei, a Potential Commensal Detected in Individuals Undergoing Routine Colonoscopy – M. E. Grasman -Journal of Clinical Microbiology

Bioinformatics and metagenomics

HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes – Samuel C. Forster – Nucleic Acids Research

Antibiotic Selection Pressure Determination through Sequence-Based Metagenomics – Matthias Willmann – Antimicrobial Agents and Chemotherapy

Current and future resources for functional metagenomics – Kathy N. Lam – Frontiers in Microbiology

Microbial Ecology

Slow and Fast Evolving Endosymbiont Lineages: Positive Correlation between the Rates of Synonymous and Non-Synonymous Substitution – Francisco J. Silva – Frontiers in Microbiology

Microbes in the news

How the Western Diet Has Derailed Our Evolution: Burgers and fries have nearly killed our ancestral microbiome – Moises Velasquez-Manoff – Nautilus

Bacterial biofilm protein prevents ice cream drip – Elisabeth Bik – NPJ Biofilms Community
and
Ice cream designed to drip slowly – Lydia Chain – Popular Science

Bacteria Hysteria

You Don’t Know Where That’s Been: Part 2 – KGNS TV

Science, publishing, and career

Racial bias continues to haunt NIH grants – Minorities still less likely to win biomedical funding – Erika Check Hayden – Nature

Ask Me Anything on Reddit with Carl Zimmer, science journalist at The New York Times, National Geographic and STAT.

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November 17, 2015

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Detecting bacteriophage DNA in mummies, microbiome depletion reduces obesity (in mice), viruses in city rats, microbes in alkaline hotsprings and in glaciers.

Events

European Microbiome Congress 2015: 18-19 November 2015, London.

Human respiratory tract microbiome

Viral aetiology of common colds of outpatient children at primary care level and the use of antibiotics – Janete Kamikawa – Mem. Inst. Oswaldo Cruz

Human reproductive tract microbiome

A DNA tool for early detection of vaginal dysbiosis in African women – Vicky Jespers – Research in Microbiology

Human gut microbiome

Natural mummification of the human gut preserves bacteriophage DNA – Tasha M. Santiago-Rodriguez – FEMS Microbiology Letters

Review: Inhibition of methanogenic archaea by statinsas a targeted management strategy for constipation andrelated disorders – K. Gottlieb

Review: Role of the Gut Microbiome in Uremia: A Potential Therapeutic Target – Ali Ramezani – American Journal of Kidney Diseases

Opinion: The Microbiome and Cancer: Is the ‘Oncobiome’ Mirage Real? – Ryan M. Thomas – Trends in Cancer

Review: The effect of gut microbiota on drug metabolism – Mi Jeong Kang – Expert Opinion on Drug Metabolism & Toxicology

Animal and bioreactor models

Microbiota depletion promotes browning of white adipose tissue and reduces obesity –
Nicolas Suárez-Zamorano – Nature Medicine

Variable responses of human and non-human primate gut microbiomes to a Western diet –
Katherine R. Amato – Microbiome

Research Highlight: Commensal bacterium prevents wasting – Cláudio Nunes-Alves – Nature Reviews Microbiology

Impact of a probiotic, inulin, or their combination on the piglets’ microbiota at different intestinal locations – V.A. Sattler – Beneficial Microbes

Iron Modulates Butyrate Production by a Child Gut Microbiota In Vitro – Alexandra Dostal – mBio

Research Hightlight: Scaling up spatial imaging of the gut microbiota – Naomi Attar – Nature Reviews Microbiology

Metagenomic analysis of anammox communities in three different microbial aggregates – Jianhua Guo – Environmental Microbiology

Microbial community analysis of a full-scale DEMON bioreactor – Alejandro Gonzalez-Martinez – Bioprocess and Biosystems Engineering

Re-appraisal of the phylogeny and fluorescence in situ hybridization probes for the analysis of the Competibacteraceae in wastewater treatment systems – Simon J. McIlroy – Environmental Microbiology Reports

Animal microbiome

New Type of Papillomavirus and Novel Circular Single Stranded DNA Virus Discovered in Urban Rattus norvegicus Using Circular DNA Enrichment and Metagenomics – Thomas Arn Hansen – PLOS ONE

Bleaching of Baikalian sponge affects the taxonomic composition of symbiotic microorganisms – O. V. Kaluzhnaya – Russian Journal of Genetics

Experimental Infection of Snakes with Ophidiomyces ophiodiicola Causes Pathological Changes That Typify Snake Fungal Disease – Jeffrey M. Lorch – mBio

Plant, root, and soil microbiome

Glyphosate effects on soil rhizosphere-associated bacterial communities – Molli M. Newman – Science of the Total Environment

Soil microarthropods support ecosystem productivity and soil C accrual: Evidence from a litter decomposition study in the tallgrass prairie – Jennifer L. Soong – Soil Biology and Biochemistry

Microbial communities and organic matter composition in surface and subsurface sediments of the Helgoland mud area, North Sea – Oluwatobi E. Oni – Frontiers in Microbiology

Shifts in the composition and potential functions of soil microbial communities responding to a no-tillage practice and bagasse mulching on a sugarcane plantation – Toshiko Miura – Biology and Fertility of Soils

Local climatic conditions constrain soil yeast diversity patterns in Mediterranean forests, woodlands, and scrub biome – Andrey M. Yurkov – FEMS Yeast Research

Coal mining practices reduce the microbial biomass, richness and diversity of soil –
Patricia Dorr de Quadros – Applied Soil Ecology

Water microbiome

The Fate of Marine Bacterial Exopolysaccharide in Natural Marine Microbial Communities – Zilian Zhang – PLOS ONE

Comparative study on composition and abundance of major planktons and physico-chemical characteristics among two ponds and Lake Tana, Ethiopia – Wondie Zelalem Amanu – Journal of Coastal Life Medicine

Extremophile microbiome

Metagenomics of an alkaline hot spring in Galicia (Spain): microbial diversity analysis and screening for novel lipolytic enzymes – Olalla López-López – Frontiers in Microbiology

Taxonomic characterization and the bio-potential of bacteria isolated from glacier ice cores in the High Arctic – Purnima Singh – Journal of Basic Microbiology

Built environment microbiology

Microbiota formed on attached stainless steel coupons correlate with the natural biofilm of the sink surface in domestic kitchens – Birgitte Moen – Canadian Journal of Microbiology

Towards an antimicrobial ‘microglove’ – Ewoud Reilman – Scientific Reports

Infection microbiology

Research Highlight: The Origin of a Killer Revealed by Bronze Age Yersinia Genomes – Shijulal Nelson-Sathi – Cell Host & Microbe

Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago – Simon Rasmussen – Cell

Review: The Black Death: Its origin and routes of dissemination – Kristina Lenz – Scandinavian Journal of History

Review: Emerging methodologies for pathogen identification in positive blood culture testing – Grégory Dubourg – Expert Review of Molecular Diagnostics

Microbial ecology

Integrating ecological and engineering concepts of resilience in microbial communities – Hyun-Seob Song – Frontiers in Microbiology

Perspective: Rethinking “mutualism” in diverse host-symbiont communities – Alexandra A. Mushegian – BioEssays

Techniques

Evaluating DNA Extraction Methods for Community Profiling of Pig Hindgut Microbial Community – Yang Lu – PLOS ONE

Bioinformatics, viruses, and metagenomics

The State of Software in Evolutionary Biology: code quality of 15 highly cited tools – Diego Darriba – bioRxiv

Kaiju: Fast and sensitive taxonomic classification for metagenomics – Peter Menzel – bioRxiv

A novel group of diverse Polinton-like viruses discovered by metagenome analysis – Natalya Yutin – BMC Biology

Microbes in the news

Taking Antibiotics Can Change the Gut Microbiome for Up to a Year. A new study illuminates the problems antibiotic overuse could cause for individual patients – Julie Beck – The Atlantic

Health Experts Are Explaining Drug-Resistant Bacteria Poorly: Their confusing jargon is pushing people toward bad decisions – Ed Yong – The Atlantic

5 Common Myths About Antibiotic-Resistant Bacteria – Alexandra Sifferlin – Time

There’s Life in Rocks Deep Below the Sea Floor. Seriously. – Heather Goldstone – Cape and Islands

More armadillos that carry leprosy bacteria found in Southern US – Amanda Lane – Midday Daily

Blood-Gut Barrier. Scientists identify a barrier in mice between the intestine and its blood supply, and suggest how Salmonella sneaks through it – Ruth Williams – The Scientist

Microbes Play Role in Anti-Tumor Response
Gut microbiome composition can influence the effectiveness of cancer immunotherapy in mice – Anna Azvolinsky – The Scientist

How depleting the gut microbiota protects from obesity – MedicalXpress

A Complex Disorder. Factors that likely contribute to obesity include disruptions to intercellular signaling, increased inflammation, and changes to the gut microbiome – Stephen D. Hursting – The Scientist

 

Effect of feed on microbiota balance in piglets – All About Feed

Skin Must Develop Tolerance to ‘Good’ Bacteria Early In Life, Says New Study: Research Probes How Skin’s Resident Communities of Microbes Are Established – Pete Farley – University of California San Francisco

How You’re Born May Affect Your Brain Development – Stephanie Pappas – Brain Decoder

Bacteria Hysteria

Doctors say to watch out for bacteria in your makeup bag – NBC News

Proper Use Of Wipes Kills Germs, Improper Use Could Spread Them – Maria Simbra – CBS Local

Microbiology and Art

What Lives on the Subway Pole? – Jen Kirby – New York Magazine

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November 14, 2015

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A paper from our lab(s) on inbred mouse strain gut microbiota variation, bacteria reduce fungi on toads, 20 years of bacterial genome sequencing, and 100 years of phage research.

Jobs

Tenure Track Position in Microbial Metagenomics – Texas Tech University in Lubbock, TX

Human oral microbiome

In Vitro Culture of Previously Uncultured Oral Bacterial Phylotypes – Hayley Thompson – Applied and Environmental Microbiology

Oral microbiome in chinese patients with aggressive periodontitis and their family members – Yi Li – Journal of Clinical Periodontology

Human gut microbiome

Probiotic supplementation influences faecal short chain fatty acids in infants at high risk for eczema – H.K. Kim – Beneficial Microbes

Review: Establishing a causal link between gut microbes, body weight gain and glucose metabolism in humans – towards treatment with probiotics – L.K. Stenman – Beneficial Microbes

Review: An Integrated Outlook on the Metagenome and Metabolome of Intestinal Diseases – Wanping Aw – Diseases

Animal models

I’m a co-author: Variation in Taxonomic Composition of the Fecal Microbiota in an Inbred Mouse Strain across Individuals and Time – Yana Emmy Hoy – PLOS ONE

Akkermansia muciniphila inversely correlates with the onset of inflammation, altered adipose tissue metabolism and metabolic disorders during obesity in mice – Marc Schneeberger – Scientific Reports

Effect of Clostridium perfringens infection and antibiotic administration on microbiota in the small intestine of broiler chickens – Yewande O. Fasina – Poultry Science

Host genetic control of the microbiota mediates Drosophila nutritional phenotype – John M. Chaston – Applied and Environmental Microbiology

Bromochloromethane, a methane analogue, affects the gut microbiota and metabolic profiles of the rat gastrointestinal tract – Yu-Xiang Yang – Applied and Environmental Microbiology

Animal microbiome

Inhibitory bacteria reduce fungi on early life stages of endangered Colorado boreal toads (Anaxyrus boreas) – Jordan G Kueneman – The ISME Journal

Leptospira and Bats: Story of an Emerging Friendship – Muriel Dietrich – PLOS Pathogens

Intraspecific variation in microbial symbiont communities of the sun sponge, Hymeniacidon heliophila, from intertidal and subtidal habitats – Brooke L. Weigel – Applied and Environmental Microbiology

Successive shifts in the microbial community of the surface mucus layer and tissues of the coral Acropora muricata under thermal stress – Sonny T.M. Lee – FEMS Microbiology Ecology

Invasive ants carry novel viruses in their new range and form reservoirs for a honeybee pathogen – Alexandra Sébastien – Biology Letters

Plant, root, and soil microbiome

Proteomic Analysis of Microbial Community Inhabiting Asian Dust Source Region – Simranjeet Singh Sekhon – CLEAN – Soil, Air, Water

Landscape Position Influences Microbial Composition and Function via Redistribution of Soil Water across a Watershed – Zhe Du – Applied and Environmental Microbiology

Common foliar fungi of Populus trichocarpa modify Melampsora rust disease severity – Posy E. Busby – New Phytologist

Cave microbial community composition in oceanic islands: disentangling the effect of different colored mats in diversity patterns of Azorean lava caves – Cristina Riquelme – FEMS Microbiology Ecology

Mini-review: Lichens as natural sources of biotechnologically relevant bacteria – Marcelino T. Suzuki – Applied Microbiology and Biotechnology

Water / extremophile microbiome

Single Cells within the Puerto Rico Trench Suggest Hadal Adaptation of Microbial Lineages – Rosa León-Zayas – Applied and Environmental Microbiology

Cyanobacterial community composition in Arctic soil crusts at different stages of development – Ekaterina Pushkareva – FEMS Microbiology Ecology

Effects of Volcanic Pumice Inputs on Microbial Community Composition and Dissolved C/P Ratios in Lake Waters: an Experimental Approach – B. E. Modenutti – Microbial Ecology

Phages and viruses

Multiple approaches for the detection and characterization of viral and plasmid symbionts from a collection of marine fungi – L. Nerva – Virus Research

Review: A century of the phage: past, present and future – George P. C. Salmond & Peter C. Fineran – Nature Reviews Microbiology

Genome sequencing and metagenomics

Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification – Kirsten A. Ziesemer – Scientific Reports

Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes – Stephen Nayfach – PLOS Computational Biology

SONEC: Metabolic Network-Guided Binning of Metagenomic Sequence Fragments – Matthew B. Biggs – Bioinformatics

Decreases in average bacterial community rRNA operon copy number during succession – Diana R Nemergut – The ISME Journal

Review: Twenty years of bacterial genome sequencing – Nicholas J. Loman & Mark J. Pallen – Nature Reviews Microbiology

Techniques

Community-Level Physiological Profiling of Microbial Communities in Constructed Wetlands: Effects of Sample Preparation – Mark Button – Applied Biochemistry and Biotechnology

Microbes in the news

Your Gut May Be Home To An Entirely New Form Of Life – Maddie Stone – Gizmodo

Growth Rate of Gut Bacteria Related to Specific Diseases – Rachel Lutz – HCP Live

Sweaty feet, stinky cheese, and the microbiome – Matt McCarthy – STAT

Parasitic fungi and the battle against coffee rust disease – Jim Erickson – University of Michigan

Body’s Microorganisms Could Keep Humans More Healthy – Gene Marcial – Forbes

Not creepy at all! 13 creepy pictures of the microbes that are living inside of you – Julia Calderone – Tech Insider

You’ve been fighting morning breath all wrong – Lydia Ramsey – Business Insider Australia

Bacteria-Infused Material Pulls Energy Out of Poop – But don’t get too excited, because this poop battery is terribly inefficient – William Herkewitz – Popular Mechanics

This Little Bot Walks on Water and Runs on Bacteria – Maddie Stone – Gizmodo

Why do potatoes grow pink slime? Clostridium puniceum could fight MRSA – Alexandra Sarabia – PBS NewsHour

Bacteria Hysteria

Your Unwashed Bras Are Growing (Mostly Harmless) Bacteria – Beth Skwarecki – LifeHacker

November 13, 2015

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Happy Friday the 13th! Today’s post features a gut-vascular barrier implicated in celiac disease, bison microbiota, 16S rRNA genes in metagenomics data, soil communities at neighboring sites, enriching microbial DNA, and lots of gut microbiota reviews.

Human gut microbiome

(humans and animal models; celiac disease) A gut-vascular barrier controls the systemic dissemination of bacteria – Ilaria Spadoni – Science

Dietary Fiber-Induced Improvement in Glucose Metabolism Is Associated with Increased Abundance of Prevotella – Petia Kovatcheva-Datchary – Cell Metabolism

Effect of Antibiotics on Gut Microbiota, Gut Hormones and Glucose Metabolism – Kristian H. Mikkelsen – PLOS ONE

Review: The Enteric Microbiome in Hepatobiliary Health and Disease – James H. Tabibian – Liver International

Review: Microbiota and aging – Stephan C Bischoff – Current Opinion in Clinical Nutrition & Metabolic Care

Review: The impact of gut microbiota on brain and behaviour: implications for psychiatry – Timothy G Dinan – Current Opinion in Clinical Nutrition & Metabolic Care

Review: The gut microbiota keeps enteric glial cells on the move; prospective roles of the gut epithelium and immune system – Panagiotis S. Kabouridis – Gut Microbes

Review: The joint power of sex and stress to modulate brain–gut–microbiota axis and intestinal barrier homeostasis: implications for irritable bowel syndrome – M. Pigrau – Neurogastroenterology & Motility

Review: Microbiome and Health in Past and Present Human Populations – Christina Warinner – American Anthropologist

Animal and bioreactor models

 

Individual Members of the Microbiota Disproportionately Modulate Host Innate Immune Responses – Annah S. Rolig – Cell Host & Microbe

Design and Investigation of PolyFermS In Vitro Continuous Fermentation Models Inoculated with Immobilized Fecal Microbiota Mimicking the Elderly Colon – Sophie Fehlbaum – PLOS ONE

Animal microbiome

Seasonal Shifts in Diet and Gut Microbiota of the American Bison (Bison bison) – Gaddy T. Bergmann – PLOS ONE

Fecal contamination of echinoderms: first report of heavy E. coli loading of sea urchins from a natural growing area – M Bouchoucha – Letters in Applied Microbiology

Plant, root, and soil microbiome

So close, so different: geothermal flux shapes divergent soil microbial communities at neighbouring sites – A. L. Gagliano – GeoBiology

Soil microorganisms behave like macroscopic organisms: patterns in the global distribution of soil euglyphid testate amoebae – Enrique Lara – Journal of Biogeography

Arsenic uptake, arsenite efflux and plant growth in hyperaccumulator Pteris vittata: Role of arsenic-resistant bacteria – Yong-He Han – Chemosphere

Rhizosphere microbiome metagenomics of gray mangroves (Avicennia marina) in the Red Sea – Hanin Alzubaidy – Gene

Review: Current trends in Bt crops and their fate on associated microbial community dynamics: a review – Amit Kishore Singh – Protoplasma

Built environment and waste treatment

Separate treatment of hospital and urban wastewaters: A real scale comparison of effluents and their effect on microbial communities – Teofana Chonova – Science of the Total Environment

Bioinformatics and metagenomics

Introducing REAGO: Reconstructing 16S rRNA genes in metagenomic data – Cheng Yuan – Bioinformatics

Techniques
Enriching microbial DNA: Changes in 16s RNA Gene Microbial Community Profiling by Concentration of Prokaryotic DNA – Angela Glassing – Journal of Microbiological Methods

The Sequence of Sequencers: The History of Sequencing DNA – James M. Heather – Genomics

Microbes in the news

Water Quality in Green Buildings – Katherine Dahlhausen – MicroBEnet

Video: Jonathan Eisen: Microbes in Food and Agriculture: Dr. Jonathan Eisen speaking at UC Davis’s Institute for Food and Ag Literacy round table about the impact the microbiome has made and potential relevance in health, food, and agriculture.

Want a Stronger Defense System against Diseases? Add Some Worms – Sheena Faherty – Scientific American

From garden to gut: New book from UW’s David Montgomery explores an unfolding scientific revolution – Hannah Hickey – University of Washington

Video in Dutch: How many bacteria do you exchange during French Kissing? A demonstration by microbiologist Remco Kort

Bacteria and bacteriophages collude in the formation of clinically frustrating biofilms – Phys.org

Extreme bacteria live in odd corners of the ecosystem – North Country Public Radio

Bacteria Hysteria

Sponsored report: Bacteria, Fecal Matter Found in Rain Puddles on Ground

Science, publishing, and career

In the eye of the Twitterstorm: Social media is shaking up how scientists talk about gender issues – Lauren Morello – Nature
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October 30, 2015

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Cave microbiome, vaginal bacteria in cute minipigs, and “disordered” home dust microbiome, and an update on the Beard Microbiome.

Human gut microbiome

Oatmeal porridge: impact on microflora-associated characteristics in healthy subjects – Jørgen Valeur – British Journal of Nutrition

Animal models

The vaginal microbiome is stable in prepubertal and sexually mature Ellegaard Göttingen Minipigs throughout an estrous cycle – Emma Lorenzen – Veterinary Research

Biofilm-associated bacterial amyloids dampen inflammation in the gut: oral treatment with curli fibres reduces the severity of hapten-induced colitis in mice – Gertrude O Oppong – NPJ Biofilms and Microbiomes

Disease tolerance mediated by microbiome E. coli involves inflammasome and IGF-1 signaling – Alexandria M. Palaferri Schieber – Science

Cave microbiome

Microbial mediation of complex subterranean mineral structures – Nicola Tisato – Scientific Reports

Built environment microbiome

Home dust microbiota is disordered in homes of low-income asthmatic children – Christina E. Ciaccio – Journal of Asthma

Food microbiology

A Large Set of Newly Created Interspecific Saccharomyces Hybrids Increases Aromatic Diversity in Lager Beers – Stijn Mertens – Applied and Environmental Microbiology

T-RFLP: Bacterial community and proteome analysis of fresh-cut lettuce as affected by packaging – Mariasole Di Carli – FEMS Microbiology Letters

Viruses and phages

Virus Satellites Drive Viral Evolution and Ecology – Belén Frígols – PLOS Genetics

Bioinformatics and metagenomics

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning – Brian Cleary – Nature Biotechnology

Multi-view Clustering of Microbiome Samples by Robust Similarity Network Fusion and Spectral Clustering – Y. Zhang – Computational Biology and Bioinformatics, IEEE/ACM Transactions

Bacteria in the news

The strain in metagenomics: Two computational tools extract strain-level information from reams of microbial sequence data. – Tal Nawy – Nature Methods

Bacteria found to play role in cow’s milk intolerance – SunCoast news

‘Superhero’ microbiome bacteria protect against deadly symptoms during infection – Salk Institute – EurekAlert

Can changes in the brain affect your microbiome? UB researchers are investigating – Ellen Goldbaum – University at Buffalo

BacteriaHysteria

Not news at all: I-Team: Everyday items we touch are loaded with bacteria – Ryan Walsh – WWLP

Beard microbiome

This was actually funny:  Will Forte (actor from “The Last Man on Earth”) has beard swabbed for bacteria test, fails, at Jimmy Fallon show – Yahoo Video

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October 28, 2015

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A global microbiome initiative, diversity of bumblebee gut microbes and rhizophere, and the microbiome of Brazilian banknotes.

General microbiome

Microbiology: Create a global microbiome effort – Nicole Dubilier, Margaret McFall-Ngai& Liping Zhao – Nature

A unified initiative to harness Earth’s microbiomes – A. P. Alivisatos – Science

Human gut microbiome

Two healthy diets modulate gut microbial community improving insulin sensitivity in a human obese population – Carmen Haro – Journal of Clinical Endocrinology & Metabolism

Animal microbiome

Mollusk: Characterization of Bacterial Communities Associated with the Tyrian Purple Producing Gland in a Marine Gastropod – Ajit Kumar Ngangbam – PLOS ONE

Bees: Colony contact contributes to the diversity of gut bacteria in bumblebees (Bombus terrestris) – Annelies Billiet – Insect Science

Plant, root, and soil microbiome

Complementarity among plant growth promoting traits in rhizospheric bacterial communities promotes plant growth – Mangal Singh – Scientific Reports

Analysis of the community compositions of rhizosphere fungi in soybeans continuous cropping fields – Li Bai – Microbiological Research

Plant Invasions Associated with Change in Root-Zone Microbial Community Structure and Diversity – Richard R. Rodrigues – PLOS ONE

Water microbiome

Large-Scale Biomonitoring of Remote and Threatened Ecosystems via High-Throughput Sequencing – Joel F. Gibson – PLOS ONE

Food microbiome

A Novel Bacteriophage Targeting Cronobacter sakazakii is a Potential Biocontrol Agent in Foods – Ju-Hoon Lee – Applied and Environmental Microbiology

Money microbiome

Molecular Analysis of Bacterial Microbiota on Brazilian Currency Note Surfaces –
Tairacan Augusto Pereira da Fonseca – Int. J. Environ. Res. Public Health

Microbial Ecology, more microbes

Fungal communities as an experimental approach to Darwin’s naturalization hypothesis –
María Camila Morales – Research in Microbiology

Inferring Infection Patterns Based on a Connectivity Map of Host Transcriptional Responses – Lu Han – Scientific Reports

Techniques

DNA Barcoding through Quaternary LDPC Codes – Elizabeth Tapia – PLOS ONE

Metagenomics

Highly divergent ancient gene families in metagenomic samples are compatible with additional divisions of life – Philippe Lopez – Biology Direct

Microbes in the news

Hey Obama, Can We Have a Unified Microbiome Initiative? Yours, the microbiologists – Ed Yong – The Atlantic

Intestinal Worms ‘Talk’ With Gut Bacteria – Talal Al-Khatib – Discovery

Intestinal Worms May Boost Our Immune System By Communicating With Gut Bacteria – Ed Cara – Medical Daily

Collecting dust from the International Space Station: an author Q+A – Sophie Marchant – BioMedCentral Blogs

Antarctic Bacteria Prove Resilient – Glacier Hub

Bacteria-Powered Shirts Vent When You Sweat – Glenn McDonald – Discovery

New Sherwin-Williams paint kills infection-causing bacteria – Nathan Bomey – USA Today

Bacteria Hysteria

Nasty Bacteria Found In Halloween Masks – MSN
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October 15, 2015

Posted on by

Upcoming Reddit AMA with Jessica Richman, oral microbiome transplants, meta-analysis of the indoor environment, African gut microbiota, corals, lichens, and more.

Events

Ask Me Anything (AMA) with Jessica Richman from uBiome on Reddit. October 16 from 10-11am PT

Human oral microbiome

Towards microbiome transplant as a therapy for periodontitis: an exploratory study of periodontitis microbial signature contrasted by oral health, caries and edentulism – Alex E. Pozhitkov – BMC Oral Health

Human gut microbiome

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease – James D. Lewis – Cell Host & Microbe

Variation in rural African gut microbiota is strongly correlated with colonization by Entamoeba and subsistence – Elise R Morton – BioRxiv

The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids – Jingyuan Fu – Circulation Research

Animal models

Analysis of Bacterial Communities during Clostridium difficile Infection in the Mouse – Ekaterina G. Semenyuk – Infection and Immunity

Structural & Functional Consequences of Chronic Psychosocial Stress on the Microbiome & Host – Aadil Bharwani – Psychoneuroendocrinology

Animal microbiome

Pyrosequencing of the bacteria associated with Platygyra carnosus corals with skeletal growth anomalies reveals differences in bacterial community composition in apparently healthy and diseased tissues – Jenny C. Ng – Frontiers in Microbiology

Plant, root, and soil microbiome

Microbiome change by symbiotic invasion in lichens – Mats Wedin – Environmental Microbiology

Species coexistence in simple microbial communities: unravelling the phenotypic landscape of co-occurring Metschnikowia species in floral nectar – María I. Pozo – Environmental Microbiology

Fungal Biodiversity in the Alpine Tarfala Valley – Claudia Coleine – Microorganisms

Effects of long-term drainage on microbial community composition vary between peatland types – Zuzana Urbanová – Soil Biology and Biochemistry

Geological connectivity drives microbial community structure and connectivity in polar, terrestrial ecosystems – Belinda C. Ferrari – Environmental Microbiology

Soil organic matter quantity and quality shape microbial community compositions of subtropical broadleaved forests – Junjun Ding – Molecular Biology

Built environment microbiome

Microbiota of the indoor environment: a meta-analysis – Rachel I. Adams – Microbiome

Microbial ecology

Private benefits and metabolic conflicts shape the emergence of microbial interdependencies – Sylvie Estrela – Environmental Microbiology

Techniques

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples – Alma E. Parada – Environmental Microbiology

Microbes in the news

Metagenomics Digs Up Microbiome Riches: Researchers Are Consulting Metagenomic Maps and Equipping Themselves with Computational Models and Analytical Tools – GenEnNews

Differences in treatment effect on out-of-balance microbiome in Crohn’s disease – EurekAlert

Pets and Owners May Share MRSA Bacteria – Rachael Rettner – LiveScience

Cultural Riches: Researchers devise new techniques to facilitate growing bacteria collected from the environment – Anna Azvolinsky – The Scientist

This could be our best defense against the antibiotic apocalypse: Carl Zimmer on phage therapy – Lydia Ramsey – Business Insider

Bacteria Hysteria

Millions of mattresses are swarming with bacteria and mould that ‘trigger skin infections, asthma and allergies’ – Fiona Macrae – Daily Mail

Microbiology and art

These Photos Reveal How Magnificent Our World Is On The Micro Level: The award-winning images represent some of the best microphotography from around the world – Jacqueline Howard – Huffington Post

How Lining Yao adapted bacteria into living clothing and biomaterials – Matt Kamen – Wired

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