Category Archives: Water microbiome

November 21, 2015

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Human respiratory microbiome

Global Analysis of the Fungal Microbiome in Cystic Fibrosis Patients Reveals Loss of Function of the Transcriptional Repressor Nrg1 as a Mechanism of Pathogen Adaptation – Sang Hu Kim – PLOS Pathogens

Human gut microbiome

Review: Immune Interactions with Pathogenic and Commensal Fungi: A Two-Way Street – David M. Underhill – Immunity

Animal and other models

A Wave of Regulatory T Cells into Neonatal Skin Mediates Tolerance to Commensal Microbes – Tiffany C. Scharschmidt – Immunity

Animal microbiome

Spatial Variation of the Gut Microbiota in Broiler Chickens as Affected by Dietary Available Phosphorus and Assessed by T-RFLP Analysis and 454 Pyrosequencing – Maren Witzig – PLOS ONE

Variation in species diversity and functional traits of sponge communities near human populations in Bocas del Toro, Panama – Cole G. Easson – PeerJ

Water microbiome

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

Built environment microbiology

Fungal compositions and diversities on indoor surfaces with visible mold growths in residential buildings in the Seoul Capital Area of South Korea – C. An – Indoor Air

Characterization of Microbial Communities in Household Washing Machines – Ilka D. Nix – Tenside Surfactants Detergents

Metagenomics and Bioinformatics
DUDE-Seq: Fast Universal Denoising of Nucleotide Sequences – Byunghan Lee – ArXiv

misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads – Xiao Zhu – BMC Bioinformatics

Viruses and phages

Inferring the Clonal Structure of Viral Populations from Time Series Sequencing – Donatien F. Chedom – PLOS Computational Biology

Analysis of dsDNA and RNA viromes in methanogenic digesters reveals novel viral genetic diversity – Magdalena Calusinska – Environmental Microbiology

Microbes in the news

Entering the Natural Antibiotic Arms Race – Anne Estes – Mostly Microbes

This Synthetic Bio Company Is Hacking Microbes to Build the Smells of the Future – Britt Wray – Motherboard

U of T researchers discover mysterious fungus that defends against neighbouring bacteria – News Medical

The Secret is Out! Review of “The Secret World Inside You” at the American Museum of Natural History in New York. – Anne Estes – Mostly Microbes

Innovative microbiome technology may help fight certain infections – News Medical

Science, publication, and career

America’s science legacy – Neil deGrasse Tyson – Science

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November 19, 2015

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Fungal dysbiosis in Crohn’s disease, a vagina monologue, stool sample storage, giraffe poop, Yellowstone lake, and extraction of bacteriophages.

Pregnancy and birth

Helminth infection, fecundity, and age of first pregnancy in women – Aaron D. Blackwell – Science

A Vagina Monologue: Mom’s Stress, Bugs, and Baby’s Brain – William A. Banks – Endocrinology

Human respiratory microbiome

The sinonasal bacterial microbiome in health and disease – Vijay R. Ramakrishnan – Current Opinion in Otolaryngology & Head & Neck Surgery

Human vaginal microbiome

Cervical intraepithelial neoplasia disease progression is associated with increased vaginal microbiome diversity – A. Mitra – Scientific Reports

Human urinary tract microbiome

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

Human gut microbiome

Fungal dysbiosis in mucosa-associated microbiota of Crohn’s disease patients –
Giuseppina Liguori – Journal of Crohn’s and Colitis

Celiac Disease Genomic, Environmental, Microbiome, and Metabolomic (CDGEMM) Study Design: Approach to the Future of Personalized Prevention of Celiac Disease – Maureen M. Leonard – Nutrients

Sample storage conditions significantly influence faecal microbiome profiles – Jocelyn M Choo – Scientific Reports

Analysis of the Bacterial Diversity in Liver Abscess: Differences between
Pyogenic and Amoebic Abscesses – Miriam E. Reyna-Fabian – Am J Trop Med Hyg

Review: Gut microbiota regulates key modulators of social behavior – Arun Parashar – European Neuropsychopharmacology

Review: Metabolomic insights into the intricate gut microbial–host interaction in the development of obesity and type 2 diabetes – Magali Palau-Rodriguez – Frontiers in Microbiology

Animal models

The effect of microbial colonization on the host proteome varies by gastrointestinal location – Joshua S Lichtman – The ISME Journal

Animal microbiome

Analysis of the distal gut bacterial community by 454-pyrosequencing in captive giraffes (Giraffa camelopardalis) – Ousama AlZahal – Zoo Biology

Panamanian frog species host unique skin bacterial communities – Lisa K. Belden – Frontiers in Microbiology

Climate change stressors destabilize the microbiome of the Caribbean barrel sponge, Xestospongia muta – Michael P. Lesser – Journal of Experimental Marine Biology and Ecology

Plant, root, and soil microbiome

Bacteria in a wood fungal disease: characterization of bacterial communities in wood tissues of esca-foliar symptomatic and asymptomatic grapevines – Emilie Bruez – Frontiers in Microbiology

Water and extremophile microbiome

Shifts in the pelagic ammonia-oxidizing microbial communities along the eutrophic estuary of Yong River in Ningbo City, China – Qiufang Zhang – Frontiers in Microbiology

Distribution of cold adaptation proteins in microbial mats in Lake Joyce, Antarctica: Analysis of metagenomic data by using two bioinformatics tools – Hyunmin Koo – Journal of Microbiological Methods

Geomicrobiology of sublacustrine thermal vents in Yellowstone Lake: geochemical controls on microbial community structure and function – William P. Inskeep – Frontiers in Microbiology

Genome reconstructions indicate the partitioning of ecological functions inside a phytoplankton bloom in the Amundsen Sea, Antarctica – Tom O. Delmont – Frontiers in Microbiology

Book Chapter: Microbiological Monitoring of Lake Baikal – Valentina V. Parfenova – Novel Methods for Monitoring and Managing Land and Water Resources in Siberia

Waste microbiology

Effects of long-term radionuclide and heavy metal contamination on the activity of microbial communities, inhabiting uranium mining impacted soils – Silvena Boteva – Environmental Science and Pollution Research

Seasonal Changes in Bacterial Communities Cause Foaming in a Wastewater Treatment Plant – Ping Wang – Microbial Ecology

Temporal–spatial variation of bacterial diversity in estuary sediments in the south of Zhejiang Province, China – Xiao-Ming Lu – Applied Microbiology and Biotechnology

Viruses, metagenomics and bioinformatics

Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut – Josué L. Castro-Mejía – Microbiome

Comparison of Illumina de novo assembled and Sanger sequenced viral genomes: A case study for RNA viruses recovered from the plant pathogenic fungus Sclerotinia sclerotiorum – Mahmoud E. Khalifa – Virus Research

ve-SEQ: Robust, unbiased enrichment for streamlined detection and whole-genome sequencing of HCV and other highly diverse pathogens – David Bonsall – F1000 Research

More microbiology

Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study – Yi-Yun Liu – The Lancet Infectious Diseases

Microbes in the news

Seafloor communities create electricity. In the digital age, we’re all connected by electricity — and some microbes are too – Meghan Bartels – ScienceLine

Microbe cheerleader: interview with Richard Roberts – Gijsbert Werner – Nature
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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 11, 2015

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Red-pigmented haloarchaea in flamingo feathers, cyanobacteria of the Western Himalaya, and read-filtering of HT amplicon reads.

Human respiratory microbiome

Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention – Leah Cuthbertson – ISME Journal

Human reproductive tract microbiome

Genital tract colonization with Ureaplasma spp. and its association with abnormal vaginal flora – Ellen Vancutsem – Journal of Medical Microbiology

Impact of Bacterial Vaginosis on Perineal Tears during Delivery: A Prospective Cohort Study – Vincent Letouzey – PLOS ONE

Human gut microbiome

Carriage of enterobacteria producing extended spectrum beta-lactamases and composition of the gut microbiota in an Amerindian community – María José Gosalbes – Antimicrobial Agents and Chemotherapy

Animal microbiome (and archaea)

Occurrence of viable, red-pigmented haloarchaea in the plumage of captive flamingoes – Kyung June Yim – Scientific Reports

DGGE: Effect of chemical stress and ultraviolet radiation in the bacterial communities of zebrafish embryos – Jacinta M.M. Oliveira – Environmental Pollution

Plant, root, and soil microbiome

Some Like it High! Phylogenetic Diversity of High-Elevation Cyanobacterial Community from Biological Soil Crusts of Western Himalaya – Kateřina Čapková – Microbial Ecology

Phytostabilization of moderate copper contaminated soils using co-inoculation of Vicia faba with plant growth promoting bacteria – Imen Challougui Fatnassi – Journal of Basic Microbiology

Effects of Common Mycorrhizal Network on Plant Carbohydrates and Soil Properties in Trifoliate Orange–White Clover Association – Ze-Zhi Zhang – PLOS ONE

Distributions and compositions of old and emerging flame retardants in the rhizosphere and non-rhizosphere soil in an e-waste contaminated area of South China – Shaorui Wang – Environmental Pollution

Water microbiome

High Bacterial Diversity and Phylogenetic Novelty in Dark Euxinic Freshwaters Analyzed by 16S Tag Community Profiling – Tomàs Llorens-Marès – Microbial Ecology

Bioinformatics

Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences – Vinita Deshpande – Mycologia

A novel conceptual approach to read-filtering in high-throughput amplicon sequencing studies – Fernando Puente-Sánchez – Nucleic Acids Research

Microbes in the news

One course of antibiotics disrupts gut microbiome for a year – Medical News Today

Science, publishing, and career

Public Data Archiving in Ecology and Evolution: How Well Are We Doing? – Dominique G. Roche – PLOS Biology
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November 10, 2015

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Oral and gut microbiomes respond differently to antibiotics, looking two gifted horses in the mouth, BMIs and Bifidos, Drosophila mating, gut microbes and tumorigenesis, microbial food webs in clay rocks, and don’t forget that Bonferroni correction.

Pregnancy and birth (Probiotics too!)

Endometrial microbiome at the time of embryo transfer: next-generation sequencing of the 16S ribosomal subunit – J. M. Franasiak – Journal of Assisted Reproduction and Genetics

Association of Early Exposure of Probiotics and Islet Autoimmunity in the TEDDY Study – Ulla Uusitalo – JAMA Pediatrics

Human oral microbiome

Same Exposure but Two Radically Different Responses to Antibiotics: Resilience of the Salivary Microbiome versus Long-Term Microbial Shifts in Feces – Egija Zaura – mBio

Crossover clinical trial of different methods of removing a denture adhesive and the influence on the oral microbiota – Élen Massaro Nunes – The Journal of Prosthetic Dentistry

Human gut microbiome

Correlation between body mass index and fecal microbiota from children – A. Ignacio – Clinical Microbiology and Infection

Review: Clostridium difficile infection and intestinal microbiota interactions – C. Rodriguez – Microbial Pathogenesis

Animal and bioreactor models

A Statistical Error in: “Analysis of Caecal Microbiota in Rats Fed with Genetically Modified Rice by Real-Time Quantitative PCR” – Alexander Panchin – Journal of Food Science

In mice: Manipulation of the Gut Microbiota Reveals Role in Colon Tumorigenesis -Joseph P. Zackular – mSphere

The impacts of Wolbachia and the microbiome on mate choice in Drosophila melanogaster – Devin Arbuthnott – Journal of Evolutionary Biology

Chemostat culture systems support diverse bacteriophage communities from human feces – Tasha M. Santiago-Rodriguez – Microbiome

Symbiotic Human Gut Bacteria with Variable Metabolic Priorities for Host Mucosal Glycans – Nicholas A. Pudlo – mBio

Temporal dynamics of the metabolically active rumen bacteria colonising fresh perennial ryegrass – Sharon A. Huws – FEMS Microbiology Ecology

Animal microbiome

In-depth snapshot of the equine subgingival microbiome – Wenling Gao – Microbial Pathogenesis

Occurrence and distribution of Malassezia species on skin and external ear canal of horses – Hojjatollah Shokr – Mycoses

Review: The functionality of the gastrointestinal microbiome in non-human animals – Irene Hanning – Microbiome

Plant, root, and soil microbiome

The effect of altitudinal gradient on soil microbial community activity and structure in moso bamboo plantations – Ed-Haun Chang – Applied Soil Ecology

The Mineralosphere Concept: Mineralogical Control of the Distribution and Function of Mineral-associated Bacterial Communities – Stephane Uroz – Trends in Microbiology

Soil and Rhizosphere Associated Fungi in Grey Mangroves (Avicennia marina) from the Red Sea – A Metagenomic Approach – Marta Filipa Simões – Genomics, Proteomics & Bioinformatics

Deciphering Community Structure of Methanotrophs Dwelling in Rice Rhizospheres of an Indian Rice Field Using Cultivation and Cultivation-Independent Approaches – Pranitha S. Pandit – Environmental Microbiology

Effects of Sulfamethazine and Zinc on the Functional Diversity of Microbial Communities during Composting – Manli Duan – Environmental Microbiology

Evidence for duplication in title words: Prokaryotes in subsoil – evidence for spatial separation of oligotrophs and copiotrophs by co-occurrence networks – Michael Schloter – Frontiers in Microbiology

A minimalistic microbial food web in an excavated deep subsurface clay rock -Alexandre Bagnoud – FEMS Microbial Ecology

Water microbiome

Chemical dispersants can suppress the activity of natural oil-degrading microorganisms – Sara Kleindienst – PNAS

Extremophile microbiome

Distribution and diversity of microbial communities in meromictic soda Lake Doroninskoe (Transbaikalia, Russia) during winter – Evgeniya Matyugina – Chinese Journal of Oceanology and Limnology

Built environment microbiome

Differences in intertidal microbial assemblages on urban structures and natural rocky reef – Elisa L. Tan – Frontiers in Microbiology

Waste microbiology

Diverse Bacterial Groups Contribute to the Alkane Degradation Potential of Chronically Polluted Subantarctic Coastal Sediments – Lilian M. Guibert – Environmental Microbiology

Cultivating Microbial Dark Matter in Benzene-Degrading Methanogenic Consortia –
Fei Luo – Environmental Microbiology

Metagenomics and bioinformatics

DESM: portal for microbial knowledge exploration systems – Adil Salhi – Nucleic Acids Research

Techniques

Coupling dye-integrated polymeric membranes with smartphone detection to classify bacteria – Lígia Bueno – RSC Advances

Microbes in the news

9 Fascinating Facts About The Microbiome, The Trillions Of Microbes Hidden Inside Us — Jessica Leber – Fast Co.Exist

NTU scientists use dead bacteria to kill colorectal cancer – EurekAlert

Science, publishing, and career

(A)Historical Science: why scientists should care more about the history of science – Arturo Casadevall and Ferric C. Fang – Infection and Immunity

November 9, 2015

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Bronchial microbiome in COPD patients, tilapia pond systems, bacteria and fungi at the root tips of Pinus, and microbiome of an extreme Australian river.

Human respiratory microbiome

Influence of biofim on the bronchial microbiome in COPD patients colonized or infected by pseudomonas aeruginosa – Marian Garcia-Nuñez – European Respiratory Journal

Human gut microbiome

Review: Gut Microbiota and Host Reaction in Liver Diseases – Hiroshi Fukui – Microorganisms

Animal models

Repeated dose (28-day) administration of silver nanoparticles of varied size and coating does not significantly alter the indigenous murine gut microbiome – Laura A. Wilding – Nanotoxicology

Animal microbiome

Bacteria associated with Amblyomma cajennense tick eggs – Erik Machado-Ferreira – Genetics and Molecular Biology

Characterization of microbial communities in intensive GIFT tilapia (Oreochromis niloticus) pond systems during the peak period of breeding – Limin Fan – Aquaculture Research

Plant, root, and soil microbiome

Novel mycoviruses discovered from metatranscriptomics survey of soybean phyllosphere phytobiomes – Shin-Yi Lee Marzano – Virus Research

The local environment determines the assembly of root endophytic fungi at a continental scale – Kyriaki Glynou – Environmental Microbiology

Effects of vegetation and seasonality on bacterial communities in Amazonian dark earth and adjacent soils – Amanda Barbosa Lima – African Journal of Microbiology Research

Response of soil microbiota to nine-year application of swine manure and urea – Diana Morales – Ciencia Rural

Analysis of single root-tip microbiomes suggests that distinctive bacterial communities are selected by Pinus sylvestris roots colonized by different ectomycorrhizal fungi – Srisailam Marupakula – Environmental Microbiology

The structure of microbial community in aggregates of a typical chernozem aggregates under contrasting variants of its agricultural use – E. A. Ivanova – Soil Biology

Water management impacts on arsenic behavior and rhizosphere bacterial communities and activities in a rice agro-ecosystem – Suvendu Das – Science of The Total Environment

Functional selections of soil metagenomes identify tolerance genes against lignocellulose-derived inhibitors – Kevin J. Forsberg – Applied and Environmental Microbiology

Characterization of the core microbiota of the drainage and surrounding soil of a Brazilian copper mine – Letícia Bianca Pereira – Genetics and Molecular Biology
http://www.scielo.br/scielo.php?pid=S1415-47572015005050025&script=sci_arttext
Water / Extremophile microbiome

Extremophile microbiomes in acidic and hypersaline river sediments of Western Australia – Shipeng Lu – Environmental Microbiology Reports

Food microbiology

Impact of nisin-activated packaging on microbiota of beef burgers during storage – Ilario Ferrocino – Applied and Environmental Microbiology

Techniques

PacBio Sequencing and Its Applications – Anthony Rhoads – Genomics, Proteomics & Bioinformatics

Preservation of Uncultivated Microbial Cells for Single Cell Genomics and Cultivation in Future – Om Prakash – Single Cell Biology

Microbes in the news

Kangaroo farts won’t save the world – Their gut microbes really aren’t that special – Arielle Duhaime-Ross

Based on the data shown here, the title seems a stretch: 2015 American College of Rheumatology Annual Meeting: Microbiome Seems to Have a Role in Triggering Lupus – HCP Live

Bacteria looks to be promising in cheatgrass battle – Larry Meyer – The Argus Observer
http://www.argusobserver.com/news/bacteria-looks-to-be-promising-in-cheatgrass-

Veterinarians Warn Pet Owners About Bacteria After Flooding: increased chance of leptospirosis – TWC news
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November 7, 2015

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Human oral microbiome

Dental demineralization, radiation caries and oral microbiota in patients with head and neck cancer – Leonardo Victor Galvão-Moreira – Oral Oncology

Review: Bacterial interactions in pathogenic subgingival plaque – Hong Min Ng – Microbial Pathogenesis

Human gut microbiome

Gut Microbiota Community and Its Assembly Associated with Age and Diet in Chinese Centenarians – Fang Wang – Journal of Microbiology and Biotechnology

Gut colonization with methanobrevibacter smithii is associated with childhood weight development – Catherine A. Mbakwa – Obesity

Review: Regulation of energy balance by a gut–brain axis and involvement of the gut microbiota – Paige V. Bauer – Cellular and Molecular Life Sciences

Animal and other models

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

Mice: The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline – Jérôme Lluch – PLOS ONE

Sheep: Lung Microbiota Changes Associated with Chronic Pseudomonas aeruginosa Lung Infection and the Impact of Intravenous Colistimethate Sodium – David Collie – PLOS ONE

Human cells: The effect of short-chain fatty acids on human monocyte-derived dendritic cells – Claudia Nastasi – Scientific Reports

Review: Effect of dietary components on the gut microbiota of aquatic animals. A never-ending story? – E. Ringø – Aquaculture Nutrition

Animal microbiome

Evaluation of DNA extraction kits and phylogenetic diversity of the porcine gastrointestinal tract based on Illumina sequencing of two hypervariable regions –
Katharina Burbach – Microbiology Open

Insects: Host and Symbiont Jointly Control Gut Microbiota during Complete Metamorphosis – Paul R. Johnston – PLOS Pathogens

Plant, root, and soil microbiome

Microbial immigration across the Mediterranean via airborne dust – Riccardo Rosselli – Scientific Reports

The herbaceous landlord: integrating the effects of symbiont consortia within a single host – Roo Vandegrift – PeerJ

Review: The plant microbiome explored: implications for experimental botany – Gabriele Berg- Journal of Experimental Botany

The influence of hydrogeological disturbance and mining on coal seam microbial communities – M. J. Raudsepp – Geobiology

Soil DNA pyrosequencing and fruitbody surveys reveal contrasting diversity for various fungal ecological guilds in chestnut orchards – Paula Baptista – Environmental Microbiology Reports

Water microbiome

Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes – Guillem Salazar – Molecular Ecology

Metagenomics and bioinformatics

Global Profiling of Carbohydrate Active Enzymes in Human Gut Microbiome – Tanudeep Bhattacharya – PLOS ONE

Kernel-Penalized Regression for Analysis of Microbiome Data – Timothy W. Randolph – ArXiv

Infection and microbial detection

Development of a rapid and simplified protocol for direct bacterial identification from positive blood cultures by using matrix assisted laser desorption ionization time-of- flight mass spectrometry – Aleksandra Jakovljev – BMC Microbiology

Copper surfaces are associated with significantly lower concentrations of bacteria on selected surfaces within a pediatric intensive care unit – Michael G. Schmidt – American Journal of Infection Control

Microbial ecology

An equilibrium theory signature in the island biogeography of human parasites and pathogens – Kévin Jean – Global Ecology and Biogeography

Microbes in the news

‘The Secret World Inside You’ Explores the Microbial Human – William Grimes – The New York Times
I Contain Multitudes: Microbiomes at the American Museum of Natural History –
Sean Hutchinson – Inverse
Exploring the Inner Universe. A new American Museum of Natural History exhibit introduces visitors to the microbes within their bodies – Ashley P. Taylor – The Scientist

Sexed-up beer – Nature Biotechnology

Microbes aid cancer drugs – Mitch Leslie – Science

Gut microbiota regulates antioxidant metabolism – EurekAlert

Kitchen utensils can spread bacteria between foods, UGA study finds – Sydney Devine – University of Georgia
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November 5, 2015

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Context and the human microbiome, review about respiratory tract, gut microbiome in UC patients, arsenic effects on mouse microbiome, and microbiome of a river-to-ocean transition.

Jobs

3 PhD fellowship in Evolutionary and Ecological Metagenomics – Natural History Museum of Denmark

General microbiome

Review: Context and the human microbiome – Daniel McDonald, Amanda Birmingham and Rob Knight – Microbiome

Pregnancy and birth

Breastfeeding and the risk of dental caries: a systematic review and meta-analysis – R Tham – Acta Paediatrica

Breastfeeding and asthma and allergies: a systematic review and meta-analysis – CJ Lodge – Acta Paediatrica

Human respiratory microbiome

Review: The Microbiome and the Respiratory Tract – Robert P. Dickson – Annual Review of Physiology

Human gut microbiome

Characterization of Intestinal Microbiota in Ulcerative Colitis Patients with and without Primary Sclerosing Cholangitis – David Kevan – Journal of Crohn’s and Colitis

Extensive Modulation of the Fecal Metagenome in Children With Crohn’s Disease During Exclusive Enteral Nutrition – Christopher Quince – American Journal of Gastroenterology

Disruptions of the intestinal microbiome in necrotizing enterocolitis, short bowel syndrome, and Hirschsprung’s associated enterocolitis – Holger Till – Frontiers in Microbiology

eBook chapter: Human GI Tract Microbiota in Health and Disease: A Focus on Inflammatory Bowel Diseases – Clarissa Santos Rocha – Innovative Immunology

Review: Factors determining colorectal cancer: the role of the intestinal microbiota – Esther Nistal – Frontiers in Oncology

Animal models

In cattle: Characterising the bacterial microbiota across the gastrointestinal tracts of dairy cattle: membership and potential function – Shengyong Mao – Scientific Reports

In cattle: Manipulating rumen microbiome and fermentation through interventions during early life: a review – David R. Yáñez-Ruiz – Frontiers in Microbiology

 

In mice: Administration of defined microbiota is protective in a murine Salmonella infection model – Sarah-Lynn E. Martz – Scientific Reports

In mice: Arsenic induces structural and compositional colonic microbiome change and promotes host nitrogen and amino acid metabolism – Rishu Dheer – Toxicology and Applied Pharmacology

Drosophila: Glucose modulates Drosophila longevity and immunity independent of the microbiota – Anthony Galenza – BioRxiv

In rats: The microbiota-gut-brain axis as a potential therapeutic approach for HIV-1+ cocaine abuse – Steven B. Harrod – Drug and Alcohol Dependence

In mice: Alteration of the intestinal microbiota by short-time antibiosis protects mice from CNS-specific autoimmunity – C. Gödel – Journal of the Neurological Sciences

 

Plant, root, and soil microbiome

Water management impacts on arsenic behavior and rhizosphere bacterial communities and activities in a rice agro-ecosystem – Suvendu Das – Science of the Total Environment

Caffeine fostering of mycoparasitic fungi against phytopathogens – Akifumi Sugiyama – Plant Signaling & Behavior

Key Edaphic Properties Largely Explain Temporal and Geographic Variation in Soil Microbial Communities across Four Biomes – Kathryn M. Docherty – PLOS ONE

Fungal association and utilization of phosphate by plants: success, limitations, and future prospects – Atul K. Johri – Frontiers in Microbiology

Thesis: Manipulating the soil microbiome to increase plant health and productivity – Chaparro, Jacqueline Michelle – Colorado State University

Water and extremophile microbiome

Bacterial responses to environmental change on the Tibetan Plateau over the past half century – Yongqin Liu – Environmental Microbiology

Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient – Caroline S. Fortunato – PLOS ONE

First Insights into the Viral Communities of the Deep-sea Anoxic Brines of the Red Sea –
André Antunes – Genomics, Proteomics & Bioinformatics

Salt resistance genes revealed by functional metagenomics from brines and moderate-salinity rhizosphere within a hypersaline environment – Salvador Mirete – Frontiers in Microbiology

Research topic and call for papers: Microbiology of the rapidly changing polar environments – Frontiers in Microbiology

Food microbiology

The diversity and evolution of microbiota in traditional Turkish Divle Cave cheese during ripening – Sebnem Ozturkoglu Budak – International Dairy Journal

More microbes

Ion channels enable electrical communication in bacterial communities – Arthur Prindle – Nature

Bioinformatics

De novo clustering methods out-perform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units – Sarah L Westcott, Patrick Schloss – PeerJ Preprint

Unpublished manuscript: Improving De Novo Metatranscriptome Assembly via Machine Learning Algorithms – Hussein Mohsen – not published

Microbes in the news

eBook: Welcome to the Microbiome: Getting to Know the Trillions of Bacteria and Other Microbes In, On, and Around You – Rob DeSalle, Susan L. Perkins – eBook

Fighting Cancer With Microbes, Flagship Bets on a $35M Startup– Luke Timmerman – Forbes

Toxin Taints Crabs and Kills Sea Mammals, Scientists Warn – Jonah Bromwich – The New York Times
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