Category Archives: General Microbiome

December 16, 2015 #2

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Role of Lactobacillus in early pregnancy, skin microbiome of psoriasis patients before and after a spa treatment, retroviruses in coprolites, colonization of germ-free cockroach guts, more decomposing pigs, kitty poop, and de novo clustering methods are just better. So many papers, I had to do a second installment today.

General human microbiome

Review: Human Microbiome and Its Association With Health and Diseases – Asmaa Althani – Journal of Cellular Physiology

Review: Microbiota, Parasites and Immunity – Judith Allen – Parasite Immunology

Pregnancy and birth (and vaginal microbiome)

Role of Lactobacillus Species in the Intermediate Vaginal Flora in Early Pregnancy: A Retrospective Cohort Study – Alex Farr – PLOS ONE

Human Breast Milk miRNA, Maternal Probiotic Supplementation and Atopic Dermatitis in Offspring – Melanie Rae Simpson – PLOS ONE

Review: The Infant Microbiome: Implications for Infant Health and Neurocognitive Development – Yang, Irene – Nursing Research

Human oral microbiome

Association between Herpesviruses and Chronic Periodontitis: A Meta-Analysis Based on Case-Control Studies – Ce Zhu – PLOS ONE

Short-term Effects of Povidone Iodine and Sodium Fluoride Therapy on Plaque Levels and Microbiome Diversity – Cavan Reilly – Oral Diseases

Review: Saliva and viral infections – Paul L. A. M. Corstjens – Periodontology 2000

Review: The physiology of salivary secretion – Gordon B. Proctor – Periodontology 2000

Human skin microbiome

Skin Microbiome in Patients With Psoriasis Before and After Balneotherapy at the Thermal Care Center of La Roche-Posay – Richard Martin – Journal of Drugs in Dermatology

Importance of Lid Hygiene Before Ocular Surgery: Qualitative and Quantitative Analysis of Eyelid and Conjunctiva Microbiota – Peral, Assumpta – Eye & Contact Lens

Human gut microbiome

Coprolites: Retroviral DNA Sequences as a Means for Determining Ancient Diets – Jessica I. Rivera-Perez – PLOS ONE

Model microbiome

The deterministic assembly of complex bacterial communities in germ-free cockroach guts – Aram Mikaelyan – Applied and Environmental Microbiology

The piglet as a model for studying dietary components in infant diets: effects of galacto-oligosaccharides on intestinal functions – A. Alizadeh – British Journal of Nutrition

Lactobacillus crispatus inhibits growth of Gardnerella vaginalis and Neisseria gonorrhoeae on a porcine vaginal mucosa model – Laura M. Breshears – BMC Microbiology

Vancomycin treatment and butyrate supplementation modulate gut microbe composition and severity of neointimal hyperplasia after arterial injury – Karen J. Ho – Physiological Reports

Necrobiome: the microbiome of death

Shifts in soil biodiversity—A forensic comparison between Sus scrofa domesticus and vegetation decomposition – Ayodeji O. Olakanye – Science & Justice

Animal microbiome

A Longitudinal Study of the Feline Faecal Microbiome Identifies Changes into Early Adulthood Irrespective of Sexual Development – Oliver Deusch – PLOS ONE

Spatial Homogeneity of Bacterial Communities Associated with the Surface Mucus Layer of the Reef-Building Coral Acropora palmata – Dustin W. Kemp – PLOS ONE

Salmonella enterica Serovars Enteritidis Infection Alters the Indigenous Microbiota Diversity in Young Layer Chicks – Khin K. Z. Mon – Frontiers in Veterinary Science

Niche Limits of Symbiotic Gut Microbiota Constrain the Salinity Tolerance of Brine Shrimp – Odrade Nougué – The American Naturalist

Opinion: Blurred lines: pathogens, commensals, and the healthy gut – Paul Wigley – Frontiers in Veterinary Science

Review: The gut microbiome and its potential role in the development and function of newborn calf gastrointestinal tract – Nilusha Malmuthuge – Frontiers in Veterinary Science

Review: An introduction to the avian gut microbiota and the effects of yeast-based prebiotic-type compounds as potential feed additives – Stephanie M. Roto – Frontiers in Veterinary Science

Plant, root, and soil microbiome

Biological attributes of rehabilitated soils contaminated with heavy metals – Jessé Valentim dos Santos – Environmental Science and Pollution Research

Comparison between cultivated and total bacterial communities associated with Cucurbita pepo using cultivation-dependent techniques and 454 pyrosequencing – N. Eevers – Systematic and Applied Microbiology

Euphorbia plant latex is inhabited by diverse microbial communities – Manjula Gunawardana – American Journal of Botany

Bioreactor and waste microbiology

Systematic investigation and microbial community profile of indole degradation processes in two aerobic activated sludge systems – Qiao Ma – Scientific Reports

Pretreatment of piggery wastewater by a stable constructed microbial consortium for improving the methane production – Jian Cai – Water Science & Technology

Bioinformatics and metagenomics

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units – Sarah L. Westcott – PeerJ

Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database – Jarmo Ritari – BMC Genomics

RisaAligner software for aligning fluorescence data between Agilent 2100 Bioanalyzer chips: Application to soil microbial community analysis – Elisabeth Navarro – BioTechniques

Review: Metagenomics: Retrospect and Prospects in High Throughput Age – Satish Kumar – Biotechnology Research International

Microbes in the news

Human-gut-on-a-chip model offers hope for IBD sufferers – Kat J McAlpine – Harvard

Metagenomics Explainer, with Emory geneticist Tim Read – Lab Land, Emory Health Sciences Research blog

Your Face Is Covered in Mites, and It’s Your Parents’ Fault – Matt Simon – Wired

Science, publishing, and career

Plenty of moustaches but not enough women: cross sectional study of medical leaders – Mackenzie R Wehner – BMJ
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December 15, 2015

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Self-tracking the microbiome (quantified self), a human gut-on-a-chip model, indoor air bacteria in residences in the San Francisco Bay Area, and using probiotics on corals during oil spills.

General microbiome

Biometrics’ new identity—measuring more physical and biological traits: Research into the characteristics that are unique to an individual is addressing the need to correctly identify people in a variety of medical, social and security contexts – Andrea Rinaldi – EMBO Reports

Commentary: Self-tracking the microbiome: where do we go from here? – Carine Gimbert – Microbiome

Conference abstracts: 3th ISM World Congress on Targeting Microbiota – Journal of International Society of Microbiota Volume 1 No. 1

Pregnancy and birth

Buccal administration of human colostrum: impact on the oral microbiota of premature infants – K Sohn – Journal of Perinatology

Human mouth/ear microbiome

Pathophysiology of sinusitis of odontogenic origin – Silvio Taschieri – Journal of Investigative and Clinical Dentistry

Human gut microbiome

Different sub-type strains of Akkermansia muciniphila abundantly colonize in southern China – Xianfeng Guo – Journal of Applied Microbiology

Simultaneous fecal microbial and metabolite profiling enables accurate classification of pediatric irritable bowel syndrome – Vijay Shankar – Microbiome

Mucosal Barrier Depletion And Loss Of Bacterial Diversity Are Primary Abnormalities In Paediatric Ulcerative Colitis – Misagh Alipour – Journal of Crohn’s and Colitis

Systematic review with meta-analysis: long-term outcomes of faecal microbiota transplantation for Clostridium difficile infection – Y.-T. Li – Alimentary Pharmacology & Therapeutics

Microbiome models

Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip – Hyun Jung Kim – PNAS

Effects of antibiotics (oxytetracycline, florfenicol or tulathromycin) on neonatal calves’ faecal microbial diversity – J. Oultram – Veterinary Record

Animal microbiome

Metagenomic Assembly Reveals Hosts of Antibiotic Resistance Genes and the Shared Resistome in Pig, Chicken and Human Feces – Liping Ma – Environmental Science & Technology

The impact of rearing environment on the development of gut microbiota in tilapia larvae – Christos Giatsis – Scientific Reports

The characterization and manipulation of the bacterial microbiome of the Rocky Mountain wood tick, Dermacentor andersoni – Katie A. Clayton – Parasites & Vectors

Impact of oil spills on coral reefs can be reduced by bioremediation using probiotic microbiota – Henrique Fragoso ados Santos – Scientific Reports

Plant, root, and soil microbiome

Stronger warming effects on microbial abundances in colder regions – Ji Chen – Scientific Reports

Seasonal dynamics of the microbiome of chernozems of the long-term agrochemical experiment in Kamennaya Steppe – T. I. Chernov – Eurasian Soil Science

Water and extremophile microbiome

Metagenome-assembled genomes uncover a global brackish microbiome – Luisa W. Hugerth – Genome Biology

Similar microbial communities found on two distant seafloor basalts – Esther Singer – Frontiers in Microbiology

Microbial communities on seafloor basalts at Dorado Outcrop reflect level of alteration and highlight global lithic clades – Michael D. Lee – Frontiers in Microbiology

Bacterioplankton dynamics within a large anthropogenically impacted urban estuary – Thomas C. Jeffries – Frontiers in Microbiology

Marine microbial community structure assessed from combined metagenomic analysis and ribosomal amplicon deep-sequencing – Savvas Genitsaris – Marine Biology Research

Groundwater isolation governs chemistry and microbial community structure along hydrologic flowpaths – Sarah Ben Maamar – Frontiers in Microbiology

Review: Forged Under the Sun: Life and Art of Extremophiles from Andean Lakes – Virginia Helena Albarracín – Photochemistry and Photobiology

Food microbiology

Comparative genomics Lactobacillus reuteri from sourdough reveals adaptation of an intestinal symbiont to food fermentations – Jinshui Zheng – Scientific Reports

Built environment microbiology

Relative and contextual contribution of different sources to the composition and abundance of indoor air bacteria in residences – Marzia Miletto – Microbiome

Review: Antibiotic resistance in urban aquatic environments: can it be controlled? – Célia M. Manaia – Applied Microbiology and Biotechnology

Metagenomics, phages, and bioinformatics

Computational approaches to predict bacteriophage–host relationships – Robert A. Edwards – FEMS Microbiology Reviews

Partial least squares regression can aid in detecting differential abundance of multiple features in sets of metagenomic samples – Ondrej Libiger – Frontiers in Genetics

Techniques

A new fungal large subunit ribosomal RNA primer for high throughput sequencing surveys – Rebecca C Mueller – FEMS Microbiology Ecology

Biofilms

Classic Spotlight: Before They Were Biofilms – George A. O’Toole – Journal of Bacteriology

Microbes in the news

How Bacteria and Brown Fat Can Spur Weight Loss – Mandy Oaklander – Time

A cultural revolution in the study of the gut microbiome – Medical Xpress

Why Your Body Is Like A Rainforest… Micro-Macro Exhibition at Eden features artwork from students at local secondary schools – PirateFM

Italian olive trees are withering from this deadly bacteria – PBS Newshour

Behind the scenes: Microbial biogeography of a university campus – Ashley Ross – MicroBEnet

Irish company makes biggest breakthrough for microbiology testing in dairy industry in 100 years – Independent Ireland

Bacteria, Archaea – Some Methane In Hydraulic Fracturing Is Even More Natural Than Assumed – Science 2.0

Sweet and sticky: Bacteria use sugars to bind to human cells – Phys.org

Science, publishing, and career

The Unwritten Code of Conduct: Each day this week, my supervisor has walked into my office and made verbal demands that I remove content from my beloved blog – The Research Whisperer

A lesson on misleading graphs from the National Review – Lenny Teytelman – The Spectroscope

Women in STEM research: Better Data and Information Sharing Could Improve Oversight of Federal Grant-making and Title IX Compliance – US Government Accountability Office

Why do scientists like anonymity? Lenny Teytelman – Protocols

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December 10, 2015

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The microbiome quality control project, proton pump inhibitors, microbiome models are useful, and Cryoconites in glaciers.

General microbiome

The microbiome quality control project: baseline study design and future directions – Rashmi Sinha – Genome Biology

Human gut microbiome

Proton pump inhibitors affect the gut microbiome – Floris Imhann – Gut

Microbiome models

Your gut microbiome, deconstructed: Probing microbiome functions through simple models – Dylan Dodd, Carolina Tropini & Justin L Sonnenburg – Nature Biotechnology

Baby, It’s Cold Outside: Host-Microbiota Relationships Drive Temperature Adaptations –
Sol Gomez de la Torre Canny, John F. Rawls – Cell Host & Microbe

N-Acetyl-l-cysteine effects on multi-species oral biofilm formation and bacterial ecology –
K. Rasmussen – Letters in Applied Microbiology

Plant, root, and soil microbiome

The molecular diversity of arbuscular mycorrhizal fungi in the arsenic mining impacted sites in Hunan province of China – Yuqing Sun – Journal of Environmental Sciences

Incorporating biotic factors in species distribution modeling: are interactions with soil microbes important? – Clifton P. Bueno de Mesquita – Ecography

Water and extremophile microbiome

Temperature and trophic structure are driving microbial productivity along a biogeographical gradient – Sarah M. Gray – Ecography

Review: Cryoconite: The dark biological secret of the cryosphere – Joseph Cook – Progress in Physical Geography

Infection and transplantation microbiology

Review: The Microbiome, Systemic Immune Function, and Allotransplantation – Anoma Nellore – Clinical Microbiology Reviews

Built environment microbiology

Microbiological testing of pharmaceuticals and cosmetics in Egypt – Hend Zeitoun – BMC Microbiology

Bioinformatics and metagenomics

Influence of tree shape and evolutionary time-scale on phylogenetic diversity metrics – Florent Mazel – Ecography

Microbes in the news
Germ Warfare: Turns out that, sometimes, Mr. Microbe is your friend – Christianna McCausland – Baltimore

A gut feeling: there’s a connection between your intestines and your health – Carrie Dennett – Seattle Times

Agilent Technologies Presents Thought Leader Award to Human Microbiome Expert Jeffrey Gordon – Business Wire

Getting the Hologenome Concept Right – Seth Bordenstein – Symbionticism

A microbiologist reveals what would go wrong if all bacteria disappeared – with Jack Gilbert – Tech Insider

Microorganism Devours Its Prey in Award-Winning Video – Carl Engelking – Discover

Illumina Invests in Four Startups Through Accelerator Program – Genome Web

Phage Hunters: New biology course transforms Virginia Tech students into young scientists, research contributors – Augusta Free Press

Lab staple agar hit by seaweed shortage: Dwindling algae harvest imperils reagent essential for culturing microbes – Ewen Callaway – Nature

Lab ‘NERD’ receives $1M funding from Taiwan ministry for microbiome research – Michelle Yeomans – Cosmetics Design

uBiome Releases Predictive Engine for Over 100 Metabolic Functions Based on Microbiome Data – Virtual Strategy

Science, publishing, and career

Blog, tweet, and avoid the pitfalls – Sharon Ann Holgate – Science
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December 9, 2015

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Student activity about the microbiome that uses pasta, nutritional supplementation in Malawian infants, fungi and drywall, and microbial aerosols from soiled hospital linens.

General microbiome

Cool student activity: Modeling the Dynamic Digestive System Microbiome – Anne M. Estes – Journal of Microbiology & Biology Education

Pregnancy and birth

Persistent microbial dysbiosis in preterm premature rupture of membranes from onset until delivery – Elizabeth A. Baldwin – PeerJ

No effect of supplementation: Gut microbiota in Malawian infants in a nutritional supplementation trial – Yin Bun Cheung – Tropical Medicine & International Health

Human vaginal microbiome

Bacterial vaginosis and inflammatory response showed association with severity of cervical neoplasia in HPV-positive women – Juçara Maria de Castro-Sobrinho – Diagnostic Cytopathology

Human gut microbiome

Review: Gut Microbiota Modulation and Mucosal Immunity: Focus on Rifaximin – Loris R. Lopetuso – Mini-Reviews in Medicinal Chemistry

Animal microbiome

The effects of omeprazole therapy on bacterial colonization of the pharynx in healthy dogs – Lauren A. Sullivan – Journal of Veterinary Emergency and Critical Care

Water microbiome

Spatial Patterns in Biofilm Diversity across Hierarchical Levels of River-Floodplain Landscapes – Marc Peipoch – PLOS ONE

 

Built environment microbiome

Moisture parameters and fungal communities associated with gypsum drywall in buildings – Sandra Dedesko – Microbiome

A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses – Thomas Weinmaier – Microbiome

Microbial aerosol liberation from soiled textiles isolated during routine residuals handling in a modern health care setting – Alina Handorean – Microbiome

Phages and viruses

Better together: bacteriophage combinations significantly reduce Clostridium difficile growth in vitro and proliferation in vivo – Janet Y. Nale – Antimicrobial Agents and Chemotherapy

Infection and transplantation

A genetic modifier of the gut microbiome influences the risk of GVHD and bacteremia following HSCT – Ahmad Rayes – Biology of Blood and Marrow Transplantation

World Health Organization Estimates of the Global and Regional Disease Burden of 22 Foodborne Bacterial, Protozoal, and Viral Diseases, 2010: A Data Synthesis – Martyn D. Kirk – PLOS Medicine

Functional foods

A novel consortium of Lactobacillus rhamnosus and Streptococcus thermophilus for increased access to functional fermented foods – Remco Kort – Microbial Cell Factories

Changes in the Milk Metabolome of the Giant Panda (Ailuropoda melanoleuca) with Time after Birth – Three Phases in Early Lactation and Progressive Individual Differences – Tong Zhang – PLOS ONE

Bioinformatics and metagenomics

Small Sample Kernel Association Tests for Human Genetic and Microbiome Association Studies – Jun Chen – Genetic Epidemiology

Microbes in the news

Questions About the Science Of Beer – Matt Shipman – NC State University News

Guest Post – Stadium Seat Bacteria – PeerJ – David Coil

How microbes in your gut today hold clues to tomorrow’s medicines: For the second episode of “Science Happens,” we hung out with Pamela Silver, a scientist who wants to hack the microbiome – Carl Zimmer – STAT news

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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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December 5, 2015

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Two job openings in our lab / UCSF, parasitism in TM6, and colonization of a new island.

Jobs and Events

Two job openings in our lab / UCSF School of Dentistry (San Francisco) for our hyposalivation project: Full time study coordinator and Part time dental assistant (20 hours per week)

3rd Microbiome R&D and Business Collaboration Forum: Europe, 11–12 April 2016, London, United Kingdom

General microbiome

The Hologenome Concept: Helpful or Hollow? – Nancy A. Moran , Daniel B. Sloan – PLOS Biology

Opinion: Cross-Kingdom Similarities in Microbiome Ecology and Biocontrol of Pathogens – Gabriele Berg – Frontiers in Microbiology

Review: Molecular Players Involved in the Interaction Between Beneficial Bacteria and the Immune System – Arancha Hevia – Frontiers in Microbiology

Commentary: Towards biome-specific analysis of meta-omics data – Youssef Darzi – ISME Journal

Human gut microbiome

Insights into the Role of Erysipelotrichaceae in the Human Host – Nadeem O. Kaakoush – Frontier sin Cellular and Infection Microbiology

Review: Interaction of Intestinal Microorganisms with the Human Host in the Framework of Autoimmune Diseases – Borja Sánchez – Frontiers in Immunology

Review: Mechanisms of Microbe–Host Interaction in Crohn’s Disease: Dysbiosis vs. Pathobiont Selection – Ludovica F. Buttó – Frontiers in Immunology

Review: The role of gut microbiota and diet in experimental autoimmune encephalitis and multiple sclerosis – Tatsusada Okuno – Clinical and Experimental Neuroimmunology

Animal and bioreactor models

Identification and Phylogeny of the First T Cell Epitope Identified from a Human Gut Bacteroides Species – Maria Elisa Perez-Muñoz – PLOS ONE

Wheat bran promotes enrichment within the human colonic microbiota of butyrate-producing bacteria that release ferulic acid – Sylvia H Duncan – Environmental Microbiology

Animal microbiome

Composition of the Spruce Budworm (Choristoneura fumiferana) Midgut Microbiota as Affected by Rearing Conditions – Mathieu Landry – PLOS ONE

Plant, root, and soil microbiome

Carbon-fixation rates and associated microbial communities residing in arid and ephemerally wet Antarctic Dry Valley soils – Thomas Niederberger – Frontiers in Microbiology

Forest wildfire and grassland prescribed fire effects on soil biogeochemical processes and microbial communities: Two case studies in the semi-arid Southwest – Lisa M. Fultz – Applied Soil Ecology

Response of the soil microbial community and soil nutrient bioavailability to biomass harvesting and reserve tree retention in northern Minnesota aspen-dominated forests – Tera E. Lewandowski – Applied Soil Ecology

Disease suppression in winter wheat from novel symbiosis with forest fungi – Mary Ridout – Fungal Ecology

Comparative genomics of candidate phylum TM6 suggests that parasitism is
widespread and ancestral in this lineage – Yun Kit Yeoh – Molecular Biology and Evolution

Carbon constrains fungal endophyte assemblages along the timberline – Teng Yang – Environmental Microbiology

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

Colonization of new land by arbuscular mycorrhizal fungi – Knud Brian Nielsen – Fungal Ecology

Water and extremophile microbiome

Microbial communities reflect temporal changes in cyanobacterial composition in a shallow ephemeral freshwater lake – Jason Nicholas Woodhouse – ISME Journal

Characterization of Bacterial Communities in Deep-Sea Hydrothermal Vents from Three Oceanic Regions – Tianliang He – Marine Biotechnology

Air microbiome

PhD thesis: Microbial biodiversity of the atmosphere – Ann Maureen Klein – University of Oregon

Built environment microbiome

The biogeography of the Plastisphere: implications for policy – Linda A Amaral-Zettler – Frontiers in Ecology and the Environment

Colonization of new land by arbuscular mycorrhizal fungi – Knud Brian Nielsen – Fungal Ecology

Bioinformatics and metagenomics

COMMET: comparing and combining multiple metagenomic datasets – Nicolas Maillet – ArXiv

MetaScope – Fast and accurate identification of microbes in metagenomic sequencing data – Benjamin Buchfink – ArXiv

hc-OTU: A Fast and Accurate Method for Clustering Operational Taxonomic Unit based on Homopolymer Compaction – Seunghyun Park – ACM Transactions on Computational Biology and Bioinformatics

Functional metagenomic selection of RubisCO from uncultivated bacteria – Vanessa A. Varaljay – Environmental Microbiology

Metagenomic evidence for the presence of phototrophic Gemmatimonadetes bacteria in diverse environments – Yonghui Zeng – Environmental Microbiology Reports

Book Chapter: Metagenomics as a Tool for Enzyme Discovery: Hydrolytic Enzymes from Marine-Related Metagenomes – Ana Popovic – Prokaryotic Systems Biology

Microbes in the news

Superbug known as ‘phantom menace’ on the rise in U.S – Lena H. Sun – Washington Post

Petri dish Art: Holiday deer – Microbe World

The Blob, but smaller: Tasmania’s slime moulds – Ann Jones – ABC Australia
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December 2, 2015

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General microbiome

Microbiology: Microbiome studies need local leaders – Victor S. Pylro – Nature

Human skin microbiome

Conclusions not strongly supported by data: Chitosan Coated Textiles May Improve Atopic Dermatitis Severity by Modulating Skin Staphylococcal Profile: A Randomized Controlled Trial – Cristina Lopes – PLOS ONE

Human respiratory microbiome

Microbial, host and xenobiotic diversity in the cystic fibrosis sputum metabolome – Robert A Quinn – The ISME Journal

Perspective: In the name of ventilator-associated pneumonia prevention: lung microbiota blown away by colistin! – Saad Nseir – European Respiratory Journal

Human gut microbiome

Better link than yesterday: Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota – Kristoffer Forslund – Nature

Animal microbiome

Human Staphylococcus aureus lineages among Zoological Park residents in
Greece – E. Drougka – Open Veterinary Journal

Fecal Bacterial Composition of the Endangered Yangtze Finless Porpoises Living Under Captive and Semi-natural Conditions – Xiaoling Wan – Current Microbiology

Plant, root, and soil microbiome

Commentary: Microbiomes: Curating communities from plants – Gwyn A. Beattie – Nature

Better link than yesterday: Functional overlap of the Arabidopsis leaf and root microbiota – Yang Bai – Nature

Bioinformatics and metagenomics

A New Approach for Scalable Analysis of Microbial Communities – Ehsaneddin Asgari – ArXiv

Microbial ecology

Networks of energetic and metabolic interactions define dynamics in microbial communities – Mallory Embree

Adaptive immunity increases the pace and predictability of evolutionary change in commensal gut bacteria – João Barroso-Batista – Nature Communications

Social dynamics within decomposer communities lead to nitrogen retention and organic matter build-up in soils – Christina Kaiser – Nature Communications

Proteomics

Enhancing Metaproteomics – The value of models and defined environmental microbial systems – Florian-Alexander Herbst – Proteomics

Infection microbiology

Nature Supplement: Expanding the role of diagnostic and prognostic tools for infectious diseases in resource-poor settings – Azra C. Ghani – Nature

Microbes in the news

Bacteriophage therapy: an alternative to antibiotics? An interview with Professor Martha Clokie – April Cashin-Garbutt – News Medical

Friends for Life: How Good Bugs Keep You Healthy (Op-Ed) – Jeremy Taylor – LiveScience

Science, publishing, and career

How to build a better PhD: There are too many PhD students for too few academic jobs — but with imagination, the problem could be solved – Julie Gould – Nature

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November 30, 2015

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Red algae growing in sea otter fur, noroviruses in a Thai river, virus dispersal by hand drying, and the dark side of salad.

Jobs and events

Postdoctoral Position, Evolutionary Genomics, University of California, Davis – Gregory Lanzaro – Phylogenomics

“The Dark Side of Salad: Internalization & Movement of Human Pathogenic Bacteria in Plants,” Guest Speaker: Dr. Amanda Deering – December 2, 2015, Purdue University

General microbiome

Review: Functions of innate immune cells and commensal bacteria in gut homeostasis – Hisako Kayama – Journal of Biochemistry

Human stomach microbiome

Identification of low abundance microbiome in clinical samples using whole genome sequencing – Chao Zhang – Genome Biology

Human gut microbiome

Review: The antimicrobial effects of rifaximin on the gut microbiota – H. L. DuPont – Part of a special issue: “Understanding mechanisms of the actions of rifaximin in selected gastrointestinal diseases “- Alimentary Pharmacology & Therapeutics

Animal models

Influence of Flaxseed Oil on Fecal Microbiota, Egg Quality and Fatty Acid Composition of Egg Yolks in Laying Hens – Jun-Yeong Lee – Current Microbiology

Duodenojejunal Bypass Leads to Altered Gut Microbiota and Strengthened Epithelial Barriers in Rats – Po-Jen Yang – Obesity Surgery

Animal microbiome

Characterization of the putatively introduced red alga Acrochaetium secundatum (Acrochaetiales, Rhodophyta) growing epizoically on the pelage of southern sea otters (Enhydra lutris nereis) – Gena B. Bentall – Marine Mammal Science

The mechanism for microsporidian parasite suppression of the hindgut bacteria of the migratory locust Locusta migratoria manilensis – Shu-qian Tan – Scientific Reports

Comparative Analysis of Microbial Diversity in Termite Gut and Termite Nest Using Ion Sequencing – Arumugam Manjula – Current Microbiology

Plant, root, and soil microbiology

Seasonal dynamics of the soil microbial community: assimilation of old and young carbon sources in a long-term field experiment as revealed by natural 13C abundance – G. Börjesson – European Journal of Soil Science

Aboveground litter quality is a better predictor than belowground microbial communities when estimating carbon mineralization along a land-use gradient – Nicolas Fanin – Soil Biology and Biochemistry

Effect of rice straw application on microbial community and activity in paddy soil under different water status – Fuxia Pan – Environmental Science and Pollution Research

Determinants of the biodiversity patterns of ammonia-oxidizing archaea community in two contrasting forest stands – Jie Chen – Journal of Soils and Sediments

Water and extremophile microbiome

Assessment of bacterial species present in Pasig River and Marikina River soil using 16S rDNA phylogenetic analysis – Maria Constancia O. Carrillo – International Journal of Philippine Science and Technology

Environmental switching during biofilm development in a cold seep system and functional determinants of species sorting – Weipeng Zhang – Molecular Ecology

Molecular detection and characterization of noroviruses in river water near Thailand – K. Inoue – Letters in Applied Microbiology

Biogeochemistry and microbial diversity in the marine cavity beneath the McMurdo Ice Shelf, Antarctica – Trista J. Vick-Majors – Limnology and Oceanography

Waste microbiology

New insights into the genetic and metabolic diversity of thiocyanate-degrading microbial consortia – Mathew P. Watts – Applied Microbiology and Biotechnology

Diversity and Distribution of Arsenic-Related Genes Along a Pollution Gradient in a River Affected by Acid Mine Drainage – Angélique Desoeuvre – Microbial Ecology

Seasonal variations of microbial community in a full scale oil field produced water treatment plant – Q. Xie – Global Journal of Environmental Science and Management

Built environment microbiology

Microbial dynamics in mixed culture biofilms of bacteria surviving sanitation of conveyor belts in salmon processing plants – Solveig Langsrud – Journal of Applied Microbiology

Evaluation of the potential for virus dispersal during hand drying: a comparison of three methods – Patrick T. Kimmitt – Journal of Applied Microbiology

Metabolomics

Review: Genome-scale modelling of microbial metabolism with temporal and spatial resolution – Michael A. Henson – Biochemical Society Transactions

Bioinformatics and metagenomics

Assessing the Unseen Bacterial Diversity in Microbial Communities – Alejandro Caro-Quintero – Genome Biology Evolution

Finding New Order in Biological Functions from the Network Structure of Gene Annotations – Kimberly Glass – PLOS Computational Biology

Microbes in the news

Bacteria on the Brain: A brilliant surgeon offered an untested treatment to dying patients. Was it innovation or overreach? – Emily Eakin – The New Yorker

Legionnaires’ Disease Bacteria Found In Minneapolis Hospital Water Samples – Angela Laguipo – Tech Times

The four bugs that protect us from asthma – Elizabeth Finkel – Cosmos Magazine
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November 26, 2015

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Happy Thanksgiving, everyone! NCBI’s Pubmed nor Google Alerts did not take any holiday, so here is a post stuffed (pun intended) with new papers. For today, I got the microbiome of turkey, red wine, and coprolites. And strain-level variation in human-associated bacteria, cat periodontitis, and historical penguin activity too!

General microbiome

Nurturing the microbiome field: It is exciting to see the nucleus of a grand vision for the field, but we must make the fundamentals of the scientific method central to our mission – Pat Schloss – Science

Book: Microbial Endocrinology: Interkingdom Signaling in Infectious Disease and Health
Chapters include:

Pregnancy and birth

Preterm gut microbiota and metabolome following discharge from intensive care – Christopher J. Stewart – Scientific Reports

The role of gut microbiota in fetal methylmercury exposure: Insights from a pilot study – Toxicology Letters

Assessing the Intestinal Microbiota in the SHINE Trial – Ethan K. Gough – Clinical Infectious Diseases

Gravidas with Class III Obesity: Evaluating the Abdominal Skin Microbiota Above and Below the Panniculus – Rodney K Edwards – The Journal of Maternal-Fetal & Neonatal Medicine
Review: A Review of Antibiotic Use in Pregnancy – P. Brandon Bookstaver – Pharmacotherapy

Review: On the origin of species: Factors shaping the establishment of infant’s gut microbiota – Niels van Best – Birth Defects Research Part C: Embryo Today: Reviews

Review: Molecular characterization of the human microbiome from a reproductive perspective – Amir Mor – Fertility and Sterility

Review: Reproductive tract microbiome in assisted reproductive technologies – Jason M. Franasiak – Fertility and Sterility

Review: Gynecologic health and disease in relation to the microbiome of the female reproductive tract – Katherine A. Green – Fertility and Sterility

Human skin microbiome

Genetic associations and shared environmental effects on the skin microbiome of Korean twins – Jiyeon Si – BMC Genomics

Human respiratory microbiome

The Sputum Microbiome in Chronic Obstructive Pulmonary Disease Exacerbations
Yvonne J. Huang – Annals of the American Thoracic Society

Review: Clinical Insights into Pulmonary Exacerbations in Cystic Fibrosis from the Microbiome. What Are We Missing? – Fiona J. Whelan – Annals of the American Thoracic Society

Human oral microbiome

Microbiome of titanium and zirconia dental implants abutments – Cássio do Nascimento – Dental Materials

Human gut microbiome

Microbiota and food residues including possible evidence of pre-mammalian hair in Upper Permian coprolites from Russia – Piotr Bajdek – Lethaia

Red wine polyphenols modulate fecal microbiota and reduce markers of the metabolic syndrome in obese patients – Moreno-Indias Isabel – Food & Function

The human gut microbial ecology associated with overweight and obesity determines ellagic acid metabolism – María V. Selma – Food & Function

The severity of NAFLD is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota – Jérôme Boursier – Hepatology

Differences of microbiota in small bowel and faeces between irritable bowel syndrome patients and healthy subjects – Chen-Shuan Chung – Scandinavian Journal of Gastroenterology

Methodology, Not Concept of Fecal Microbiota Transplantation, Affects Clinical Findings – Bota Cui – Gastroenterology

The Gut-Liver Axis in Primary Sclerosing Cholangitis – Bertus Eksteen – Clinics in Liver Disease

Animal models

Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota – Marie Vétizou – Science

Antepartum Antibiotic Treatment Increases Offspring Susceptibility to Experimental Colitis: A Role of the Gut Microbiota – Peris Mumbi Munyaka – PLOS ONE

Metabolomic study on the faecal extracts of atherosclerosis mice and its application in a Traditional Chinese Medicine – Feng Tian – Journal of Chromatography B

Animal microbiome

Temporal Relationships Exist Between Cecum, Ileum, and Litter Bacterial Microbiomes in a Commercial Turkey Flock, and Subtherapeutic Penicillin Treatment Impacts Ileum Bacterial Community Establishment – Jessica L. Danzeisen – Frontiers in Veterinary Science

A Pyrosequencing Investigation of Differences in the Feline Subgingival Microbiota in Health, Gingivitis and Mild Periodontitis – Stephen Harris – PLOS ONE

Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species – Katherine R. Amato – Oecologia

Plant, root, and soil microbiome

Bacterial diversity is strongly associated with historical penguin activity in an Antarctic lake sediment profile – Renbin Zhu – Scientific Reports

Elk, sagebrush, and saprotrophs: indirect top-down control on microbial community composition and function – Anna R. Peschel – Ecology

Effect of soil salinity and nutrient levels on the community structure of the root-associated bacteria of the facultative halophyte, Tamarix ramosissima, in southwestern United States – Takeshi Taniguchi – Journal of General and Applied Microbiology

Metagenomic insights into communities, functions of endophytes, and their associates with infection by root-knot nematode, Meloidogyne incognita, in tomato roots – Bao-Yu Tia – Scientific Reports

Effect of rice straw application on microbial community and activity in paddy soil under different water status – Fuxia Pan – Environmental Science and Pollution Research

Mapping the Centimeter-Scale Spatial Variability of PAHs and Microbial Populations in the Rhizosphere of Two Plants – Amélia Bourceret – PLOS ONE

Diversity of bacterial endophytes in 3 and 15 year-old grapevines of Vitis vinifera cv. Corvina and their potential for plant growth promotion and phytopathogen control – Marco Andreolli – Microbiological Research

Review: Functions, mechanisms and regulation of endophytic and epiphytic microbial communities of plants – Charles W. Bacon – Symbiosis

Review: Culture-independent discovery of natural products from soil metagenomes – Micah Katz – Journal of Industrial Microbiology & Biotechnology

Built environment microbiology

ISS: Extracellular Lipase and Protease Production from a Model Drinking Water Bacterial Community Is Functionally Robust to Absence of Individual Members – Graham G. Willsey – PLOS ONE

Food microbiology

Bacterial Ecology of Fermented Cucumber Rising pH Spoilage as Determined by Nonculture-Based Methods – Eduardo Medina – Journal of Food Science

Microbial Ecology

Complete nitrification by Nitrospira bacteria – Holger Daims – Nature

Does Microbial Diversity Confound General Predictions? – Marie Duhamel – Trends in Plant Science

Metagenomics and bioinformatics

Population genetic analyses of metagenomes reveal extensive strain-level variation in prevalent human-associated bacteria – Stephen Nayfach – BioRxiv

Techniques

Robust and effective methodologies for cryopreservation and DNA extraction from anaerobic gut fungi – Kevin V. Solomon – Anaerobe

Collecting Fecal Samples for Microbiome Analyses in Epidemiology Studies – Rashmi Sinha – Cancer Epidemiology, Biomarkers & Prevention

Microbes in the news

Is Double-Dipping Okay? CFUs in 4 types of dips after double dipping – Digg

New Research Reveals Bacteria Associated With Feline Gum Disease for the First Time – PR Newswire

Mission space food: Sugar-growing bacteria go into orbit – Clare Wilson – New Scientist

Your Coffee Machine Is a Breeding Ground for Caffeine-Resistant Bacteria – Matthew Braga – Motherboard

Your Poop Knows Best–New Study Shows Microbiome Can Help Predict Health Responses to Certain Foods – Patrick Mustain – Scientific American

Science, publishing, and career

China pursues fraudsters in science publishing – Mara Hvistendahl – Science
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November 6, 2015

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Dog skin, kangaroo methane emissions, flea microbiome and ecology, domestication of wine yeast, and surface reflectance by roof microbes.

Events

11th International Meeting on Microbial Epidemiological Markers (IMMEM XI), March 2016, Portugal – Abstract submission deadline: November 10

General microbiome

Microbiomes in light of traits: A phylogenetic perspective – Jennifer B. H. Martiny – Science

The ecology of the microbiome: Networks, competition, and stability – Katharine Z. Coyte – Science

What makes the gut microbiome stable? – Caroline Ash – Science

Microbiome, a new dimension in cancer research – Antonio Galvao Neto – Annals of Translational Medicine

Human gut microbiome

Characterization of the salivary microbiome in patients with pancreatic cancer – Pedro J. Torres – PeerJ

Animal microbiome

What is living on your dog’s skin? Characterization of the canine cutaneous mycobiota and fungal dysbiosis in canine allergic dermatitis – C.M. Smith – FEMS Microbial Ecology

Decreasing methane yield with increasing food intake keeps daily methane emissions constant in two foregut fermenting marsupials, the western grey kangaroo and red kangaroo – Catharina Vendl – Journal of Experimental Biology

Evaluation of the bacterial microbiome of two flea species using different DNA isolation techniques provides insights into flea host ecology  – Andrea L. Lawrence – FEMS Microbiology Ecology

The functional gene composition and metabolic potential of coral-associated microbial communities – Yanying Zhang – Scientific Reports

Plant, root, and soil microbiome

Can commercial soil microbial treatments remediate plant–soil feedbacks to improve restoration seedling performance? – Lora B. Perkins – Restoration Ecology

Anthropogenic impact on diazotrophic diversity in the mangrove rhizosphere revealed by nifH pyrosequencing – Hongmei Jing – Frontiers in Microbiology

Phylogenetic diversity of culturable fungi in the Heshang Cave, central China –
Baiying Man – Frontiers in Microbiology

Review: Ongoing domestication of wine yeast: past, present and future – P.J. Chambers – Australian Journal of Grape and Wine Research

Built environment microbiology

Surface reflectance degradation by microbial communities – Meng-Dawn Cheng – Journal of Building Physics

Metagenomics and bioinformatics

The single-species metagenome: subtyping Staphylococcus aureus core genome sequences from shotgun metagenomic data – Sandeep J Joseph – BioRxiv

Metagenomics: A New Way to Illustrate the Crosstalk between Infectious Diseases and Host Microbiome – Yinfeng Zhang – International Journal of Molecular Sciences

Fizzy: feature subset selection for metagenomics – Gregory Ditzler – BMC Bioinformatics

Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities – Michael A. Peabody – BMC Bioinformatics

Microbes in the news

Our Dust, Ourselves – Emily Anthes – The New Yorker
Emily Anthes writes about Wildlife of Your Homes microbiome studies in the New Yorker – Jonathan Eisen – MicroBEnet

The Hottest New Cancer Drugs Depend on Gut Microbes – Ed Yong – The Atlantic
Gut bacteria may affect the success of cancer treatments – Sam Wong – New Scientist

This New Exhibition Is a Tour of the Human Body’s ‘Hidden Organ’ – Becky Ferreira – Motherboard

Podcast (20 min) We are a constellation of our microbiome and ourselves – Meg Tirrell and Luke Timmerman – Stat News

The strange case of the man infected with tapeworm cancer – Helen Branswell – StatNews

With a picture of human cells? 30 mind-blowing facts about the microbes that live inside of you – Julia Calderone – TechInsider
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