Category Archives: Metagenomics & Bioinformatics

December 9, 2014

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Human oral microbiome

* Characterization and comparison of bacterial communities in benign vocal fold lesions – Alissa S Hanshew – Microbiome

Bacterial invasion and persistence: critical events in the pathogenesis of periodontitis? – S. Ji – Journal of Periodontal Research

Human skin microbiome

This took two years to publish, but here it is: Meeting report for the 1st skin microbiota workshop, Boulder, CO October 15-16 2012 – Jack A Gilbert – Standards in Genomic Sciences

Human respiratory microbiome

Assessment of Airway Microbiota and Inflammation in Cystic Fibrosis Using Multiple Sampling Methods – Edith T. Zemanick – Annals of the American Thoracic Society

Human gut microbiome

* Stability of Gut Enterotypes in Korean Monozygotic Twins and Their Association with Biomarkers and Diet – Mi Young Lim – Scientific Reports

* Microbiota organization is a distinct feature of proximal colorectal cancers – Christine M. Dejea – PNAS USA

Review: Crosstalk between intestinal microbiota, adipose tissue and skeletal muscle as an early event in systemic low-grade inflammation and the development of obesity and diabetes – Christian Bleau – Diabetes/Metabolism Research and Reviews

Pathophysiological responses from human gut microbiome – Anindya Roy Chowdhury, Utpal Bakshi – World Journal of Translational Medicine

Animal models of microbiome research

Microbiome-metabolome analysis reveals unhealthy alterations in the composition and metabolism of ruminal microbiota with increasing dietary grain in a goat model – Sheng-yong Mao – Environmental Microbiology

Animal microbiome

Carpoglyphus lactis (Acari: Astigmata) from various dried fruits differed in associated microorganisms – Jan Hubert – Journal of Applied Microbiology

Bacterial dynamics within the mucus, tissue and skeleton of the coral Porites lutea during different seasons – Jie Li – Scientific Reports

 

Investigation of biotechnological potential of sponge-associated bacteria collected in Brazilian coast – O.C.S. Santos – Letters in Applied Microbiology

Plant microbiome

* Removal of floral microbiota reduces floral terpene emissions – Josep Peñuelas – Scientific Reports

Contrasting diversity of epibiotic bacteria and surrounding bacterioplankton of a common submerged macrophyte, Potamogeton crispus, in freshwater lakes – Dan He – FEMS Microbiology Ecology

Review: Sphagnum physiology in the context of changing climate: emergent influences of genomics, modelling and host–microbiome interactions on understanding ecosystem function – David J. Weston – Plant, Cell & Environment

Book: Principles of Plant-Microbe Interactions – Springer

Soil and sediment microbiome

Anthropogenic land use shapes the composition and phylogenetic structure of soil arbuscular mycorrhizal fungal communities – Mari Moora – FEMS Microbiology Ecology

Halophyte plant colonization as a driver of the composition of bacterial communities in salt marshes chronically exposed to oil hydrocarbons – Vanessa Oliveira – FEMS Microbiology Ecology

Changes in microbial communities in coastal sediments along natural CO2 gradients at a volcanic vent in Papua New Guinea – Felix F. Raulf – Environmental Microbiology

Nitrogen Cycling Processes and Microbial Community Composition in Bed Sediments in the Yukon River at Pilot Station – Deborah A. Repert – Journal of Geophysical Research: Biogeosciences

Soil bacterial and fungal communities respond differently to various isothiocyanates added for biofumigation – Ping Hu – Frontiers in Microbiology

Primary succession of soil enzyme activity and heterotrophic microbial communities along the chronosequence of Tianshan Mountains No. 1 Glacier, China – Jun Zeng – Antonie van Leeuwenhoek

Water microbiome

Off-site impacts of agricultural composting: role of terrestrially derived organic matter in structuring aquatic microbial communities and their metabolic potential – Thomas Pommier – FEMS Microbiology Ecology

Microbiome of the built environment

* Diversity of Bacterial Communities of Fitness Center Surfaces in a U.S. Metropolitan Area – Nabanita Mukherjee – International Journal of Environmental Research and Public Health

Food microbiology

Potentially probiotic acetic acid bacteria isolation and identification from traditional dairies microbiota – Babak Haghshenas – International Journal of Food Science & Technology

Metagenomics

Microbial community pattern detection in human body habitats via ensemble clustering framework – Peng Yang – BMC Systems Biology

Proteomics and metabolomics

Insights on the human microbiome and its xenobiotic metabolism: what is known about its effects on human physiology? – Tewes Tralau – Expert Opinion on Drug Metabolism & Toxicology

Proteomic tools to decipher microbial community structure and functioning – Florence Arsène-Ploetze – Environmental Science and Pollution Research

Systems-based approaches to unravel multi-species microbial community functioning – Florence Abram – Computational and Structural Biotechnology Journal

Amplification and other techniques

* Multi-template polymerase chain reaction – Elena Kalle – Biomolecular Detection and Quantification

Microfluidic static droplet array for analyzing microbial communication on a population gradient – Heon-Ho Jeong – Lab Chip

More microbiology papers

* Gain-of-function experiments: time for a real debate – W. Paul Duprex (with David Relman) – Nature Reviews Microbiology

Ciprofloxacin mechanism: Emergence of antibiotic resistance from multinucleated bacterial filaments – Julia Bos – PNAS USA

Microbes in the news

The fragrance of flowers depends on the fungi and bacteria that coated – Beta Wired

The Human Microbiome: Getting Personal – Katy Califf – ASM Microbe

Science, publishing, career

Scientists Are Not That Smart – Chad Orzel – New York Magazine

io9 Science Survey: Tell Us About Working With Rodents in the Lab – Annalee Newitz – io9

Best Way for Professors to Get Good Student Evaluations? Be Male – Amanda Marcotte – Slate

Bik’s Picks

Unfortunately sold out, but really cute: DNA Molecule Plush – ThinkGeek

The birth of a dinosaur footprint: Subsurface 3D motion reconstruction and discrete element simulation reveal track ontogeny (with movies) – Peter L. Falkingham – PNAS USA

Billionaire’s New Science Institute Plans “Google Maps” View of Cells – Joshn Fischman – Scientific American

Expanded DNA alphabet wins Science award – Bradley J. Fikes – UT San Diego

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Microbiome Digest, December 5, 2014

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Human oral microbiome

* Noma Affected Children from Niger Have Distinct Oral Microbial Communities Based on High-Throughput Sequencing of 16S rRNA Gene Fragments – Katrine L. Whiteson – PLOS Neglected Tropical Diseases

* Ancient DNA analysis of dental calculus – Laura S. Weyrich – Journal of Human Evolution

Human gut microbiome

* Gut microbiota are related to Parkinson’s disease and clinical phenotype – Filip Scheperjans – Movement Disorders

The role of the microbiome in immune cell development – Nita H. Salzman – Annals of Allergy, Asthma & Immunology

Ezakiella peruensis gen. nov., sp. nov. isolated from human fecal sample from a coastal traditional community in Peru – Nisha B. Patel – Anaerobe

Microbiome and Immunology

Microbial Programming of Systemic Innate Immunity and Resistance to Infection – Thomas B. Clarke – PLOS Pathogens

Animal models of microbiome research

* (see also Metabolomics) Diet and Feeding Pattern Affect the Diurnal Dynamics of the Gut Microbiome – Amir Zarrinpar – Cell Metabolism

Effects of cyclophosphamide on immune system and gut microbiota in mice – Xiaofei Xu, Xuewu Zhang – Microbiological Research

Gut microbiota and environment in patients with major burns – A preliminary report – Kentaro Shimizu – Burns

Animal microbiome

* The Feline Oral Microbiome: A Provisional 16S rRNA gene based Taxonomy with Full-length Reference Sequences – Floyd E. Dewhirst – Veterinary Microbiology

Diversity and health status specific fluctuations of intrauterine microbial communities in postpartum dairy cows – K. Wagener – Veerinary Microbiology

* Evidence of Polyethylene Biodegradation by Bacterial Strains from the Guts of Plastic-Eating Waxworms – Jun Yang – Environmental Science & Technology

Metabolomics

* Diet and Feeding Pattern Affect the Diurnal Dynamics of the Gut Microbiome – Amir Zarrinpar – Cell Metabolism

A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis – Marnix H. Medema – PLOS Computational Biology

The Evolution of Fungal Metabolic Pathways – Jennifer H. Wisecaver – PLOS Genetics

The microbial degradation of onion flavonol glucosides and their roasting products by the human gut bacteria Eubacterium ramulus and Flavonifractor plautii – Katrin Ulbrich – Food Research International

Desulfovibrio desulfuricans isolates from the gut of a single individual: Structural and biological lipid a characterization – Wei Zhang-Sun – FEBS Letters

Metagenomics

Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies – James F. Denton – PLOS Computational Biology

Microbes in the news

A Worm’s Gut Could Help Dispose of Plastic Trash: Microbes found in the guts of waxworms like to feast on polyethylene – Rachel Nuwer – Smithsonian Magazine

Friendly bacteria are protective against malaria – MedicalXpress

Self-healing Concrete Vanishes Potholes Using Bacteria. Here’s How it Works – Jan Dizon – TechTimes

Wireless Implant Eliminates Bacteria, Then Dissolves – WND

Science, publishing and career

* Ten Simple Rules for Finishing Your PhD – Jacopo Marino – PLOS Computational Biology

Bik’s Picks

Amid Bugs, Hail, Floods and Bacteria, Italian Olives Take a Beating – Elisabetta Povoledo – New York Times

See it, touch it, feel it: Researchers use ultrasound to make invisible 3-D haptic shape that can be seen and felt – Science Daily

Satire: Breaking: James Watson Faked Winning A Nobel Prize – The Allium

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Microbiome digest, December 4, 2014

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Human (gut and other) microbiome

* Temporal variability is a personalized feature of the human microbiome – Gilberto E Flores – Genome Biology

The rest of the story: the microbiome and gastrointestinal infections – Jhansi L Leslie, Vincent B Young – Current Opinion in Microbiology

* Gut Microbiota Elicits a Protective Immune Response against Malaria Transmission – Bahtiyar Yilmaz – Cell

Pregnancy and birth

The infant airway microbiome in health and disease impacts later asthma development –
Shu Mei Teo – BioRxiv

Animal models of microbiome research

Dietary Yeasts Reduce Inflammation in Central Nerve System via Microflora – Kazushiro Takata – Annals of Clinical and Translational Neurology

Effects of dietary supplementation of modified zinc oxide on growth performance, nutrient digestibility, blood profiles, fecal microbial shedding and fecal score in weanling pigs –

Jin Ho Cho – Animal Science Journal

Bioinformatics

ITScan: a web-based analysis tool for Internal Transcribed Spacer (ITS) sequences – Milene Ferro – BMC Research Notes

Next generation sequencing reads comparison with an alignment-free distance – Emanuel Weitschek – BMC Research Notes

Microbes in the news

Go Ahead, Use the Restroom – Nicholas Bakalar – New York Times

Trusting your gut, and the importance of your microbiome: Words on Wellness – Daniel Neides – Cleveland.com

Microbiome component fights malaria – Bradley J. Fikes – UT San Diego

Gut Microbes May Play a Role in AS – Diana Swift – MedPageToday

Science, publishing, and career

Getting Credit for Data – Eric Martens and Jennifer Lin – PLOS Blogs

What do young scientists want? – Beryl Lieff Benderly – Science Careers

Why Don’t More Minority Students Seek Careers In STEM Fields? – David Orenstein – RedOrbit

Bik’s Picks

Revealed: 100 safety breaches at UK labs handling potentially deadly diseases – Ian Sample – The Guardian

Why DNA pioneer James Watson just sold his Nobel Prize for $4.1 million – Susannah Locke – Vox.com

The Corrupting Power of Cancer – Lauren Richardson – PLOS Blogs

Is The Food Babe A Fearmonger? Scientists Are Speaking Out – Maria Godoy – NPR The Salt

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Microbiome Digest, December 1, 2014

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Microbiome of pregnancy and birth

Increased periodontal inflammation in women with preterm premature rupture of membranes – Pascale F. M. Stadelmann- Clinical Oral Investigations

Human respiratory microbiome

Host–microorganism interactions in lung diseases – Benjamin J. Marsland & Eva S. Gollwitzer – Nature Reviews Immunology

Animal and reactor models of microbiome research

Effects of nitrate addition to a diet on fermentation and microbial populations in the rumen of goats, with special reference to Selenomonas ruminantium having the ability to reduce nitrate and nitrite – Narito Asanuma – Animal Science Journal

Modulation of the faecal microbiome of healthy adult dogs by inclusion of potato fibre in the diet – Matthew R. Panasevich – British Journal of Nutrition

To pool or not to pool? Impact of the use of individual and pooled fecal samples for in vitro fermentation studies – Aguirre M – Journal of Microbiology Methods (Pubmed link, link to article broken as of today)

Soil and sediment microbiome

Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in Alaska – Jie Deng – Molecular Ecology

Production of gaseous hydrocarbons by microbial communities of Lake Baikal bottom sediments – O. N. Pavlova – Microbiology

Viruses and phages

Editorial on “Virus Ecology and Disturbances: Impact of Environmental Disruption on the Viruses of Microorganisms” – Heather K. Allen and Stephen T. Abedon – Frontiers in Microbiology

Transcriptomics, Proteomics

Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage – Emilie E. L. Muller – Nature Communications

Bioinformatics

A review of software for analyzing molecular sequences – Haema Nilakanta – BMC Research Notes

Other papers

Animal Phylogeny and Its Evolutionary Implications – Casey W Dunn – Annual Review of Ecology, Evolution, and Systematics

Microbes in the news

Without genes pilfered from bacteria, ticks would drop dead of the Lyme disease they carry – Darryl Fears – Washington Post

Bik’s Picks

Ancient dental plaque: A ‘whey’ into our milk drinking past? – Science Daily

Does Intermittent Fasting Have Benefits? Science Suggests Yes – Charles Q. Choi – LiveScience

10 times science ruled in 2014 – Jacqui Devaney – Mashable

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Microbiome digest, November 28, 2014

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Human gut microbiome

Effects of Surgical and Dietary Weight Loss Therapy for Obesity on Gut Microbiota Composition and Nutrient Absorption – Antje Damms-Machado – BioMed Research International

Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota – Andrew J. Stewardson – Clinical Microbiology and Infection

Potential of fecal microbiota for early-stage detection of colorectal cancer – Georg Zeller – Molecular Systems Biology

Does the microbiota play a role in the pathogenesis of autoimmune diseases? – Mairi H McLean – Gut

The gut microbiota and inflammatory bowel disease – Katsuyoshi Matsuoka and Takanori Kanai – Seminars in Immunopathology

Metagenomic analysis of the gastric microbiota cultivable from a patient 

with gastritis concomitant with Barrett’s esophagus – Andrés Julián Gutiérrez-Escobar – Rev Gastroenterol Peru

Gut microbiota in patients with type 2 diabetes mellitus – Kristine H Allin – European Journal of Endocrinology

Gut brain axis: diet microbiota interactions and implications for modulation of anxiety and depression – Ruth Ann Luna, Jane A Foster

Behçet’s syndrome patients exhibit specific microbiome signature – Clarissa Consolandi – Autoimmunity Reviews

Animal microbiome

Complete genome sequence and comparative genome analysis of Klebsiella oxytoca HKOPL1 isolated from giant panda feces – Jingwei Jiang – BMC Research Notes

Few highly abundant operational taxonomic units dominate within rumen methanogenic archaeal species in New Zealand sheep and cattle – Henning Seedorf – Applied and Environmental Microbiology

Chironomid Microbiome – Malka Halpern, Yigal Senderovich – Microbial Ecology

Plant microbiome

Understanding and engineering beneficial plant–microbe interactions: plant growth promotion in energy crops – Kerrie Farrar – Plant Biotechnology Journal

Soil and sludge microbiome

Global diversity and geography of soil fungi – Leho Tedersoo – Science

Effects of the Biocontrol Agent Aspergillus flavipes on the Soil Microflora and Soil Enzymes in the Rooting Zone of Pepper Plants Infected with Phytophthora capsici – Hui Wang – Journal of Phytopathology

Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide – Suzanne M. Prober – Ecology Letters

Soil chemical properties affect the reaction of forest soil bacteria to drought and rewetting stress – Marcin Chodak – Annals of Microbiology

Cyanobacteria and algae of buried soils and their modern analogues – A. D. Temraleeva – Paleontological Journal

Diversity and efficiency of anthracene-degrading bacteria isolated from a denitrifying activated sludge system treating municipal wastewater – Spyridon Ntougias – International Biodeterioration & Biodegradation

Water microbiome

Profile of bacterial communities in South African mine-water samples using Illumina next-generation sequencing platform – Jitendra Keshri – Applied Microbiology and Biotechnology

Temporal and Vertical Distribution of Bacterioplankton at the Gray’s Reef National Marine Sanctuary – Xinxin Lu – Applied and Environmental Microbiology

Identification of Microorganisms in Hydrocarbon-Contaminated Aquifer Samples by Fluorescence In Situ Hybridization (CARD-FISH) – Schattenhofer Martha – Springer Protocols Handbooks

Food microbiology

Influence of pig rennet on proteolysis, organic acids content and microbiota of Pecorino di Farindola, a traditional Italian ewe’s raw milk cheese – Tofalo Rosanna – Food Chemistry

Bioinformatics

Alternative for USEARCH: VSEARCH: Open and free 64-bit multithreaded tool for processing metagenomic sequences, including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling – Github

svaseq: removing batch effects and other unwanted noise from sequencing data – Jeffrey T. Leek – Nucleic Acids Research

Phages and viruses

Automated classification of tailed bacteriophages according to their neck organization – Anne Lopes – BMC Genomics

Metabolomics

Metabolic fate of neutral human milk oligosaccharides in exclusively breast-fed infants –
Viktoria Dotz – Molecular Nutrition & Food Research
http://onlinelibrary.wiley.com/doi/10.1002/mnfr.201400160/abstract

Transcriptomics

Transcriptome analysis reveals novel regulatory mechanisms in a genome-reduced bacterium – Pavel V. Mazin – Nucleic Acids Research

More microbiology

In vivo treatment of Helicobacter pylori infection with liposomal linolenic acid reduces colonization and ameliorates inflammation – Soracha Thamphiwatana – PNAS USA

Microbes in the news

How bacteria in your gut could be making you fat, allergic, or anxious – Susannah Locke – Vox

Interview with Dan Knights: UMN professor solves problems from ‘gut bugs’ to Rubik’s Cube – Richard Chin – Twin Cities

Artificial Sweeteners May Have Despicable Impacts on Gut Microbes – Sheena Faherty – Scientific American

The Human Microbiome, An Issue of Clinics in Laboratory Medicine – Google eBook

Science and art

It’s a microbial world – protozoa pancakes

Bik’s Picks

Detection of fraudulent addition of bovine whey in Ricotta cheese by iso-electric focusing
– Fabio Fuselli – Journal of Science of Food and Agriculture

DNA survives critical entry into Earth’s atmosphere – Science Daily

Bill Nye: ‘Science is true, whether or not you believe it’ – Brad Wheeler – The Globe and Mail

The Best Gifts of 2014 for Science Geeks – Smithsonian.com

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Microbiome digest, November 24, 2014

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General microbiome

Microbial sequencing to improve individual and population health – Sharon J Peacock and George M Weinstock – Genome Medicine

Human oral microbiome

Shifts in Campylobacter species abundance may reflect general microbial community shifts in periodontitis progression – Karsten Henne – Journal of Oral Microbiology

Human respiratory microbiome

Analysis of the bacterial community in chronic obstructive pulmonary disease sputum samples by denaturing gradient Gel electrophoresis and real-time PCR – Dachang Wu – BMC Pulmonary Medicine

Human gut microbiome

Microbiome and cancer – Naoko Ohtani – Seminars in Immunopathology

The Gut Microbiome and the Brain – Leo Galland – Journal of Medicinal Food

The ELDERMET biobank: Isolation and characterization of the intestinal microbiota from elderly Irish subjects – Lakshminarayanan, Bhuvaneswari

Animal models of microbiome

Hydrogen sulphide protects against NSAID-enteropathy through modulation of bile and the microbiota – Rory W Blackler – British Journal of Pharmacology

Plant microbiome

Towards a holistic understanding of the beneficial interactions across the Populus microbiome – Stéphane Hacquard – New Phytologist

Soil microbiome

Soil Fungal Communities Respond to Grassland Plant Community Richness and Soil Edaphics – Nicholas LeBlanc – Microbial Ecology

Impact of plant species evenness, dominant species identity and spatial arrangement on the structure and functioning of soil microbial communities in a model grassland – L. Massaccesi – Oecologia

Contrasting assembly processes in a bacterial metacommunity along a desiccation gradient – Angel Valverde – Frontiers in Microbiology

 

Water microbiome

Metatranscriptome of marine bacterioplankton during winter time in the North Sea assessed by total RNA sequencing – Anna Kopf – Marine Genomics

Integrated metagenomic and metaproteomic analyses of marine biofilm communities – Dagmar H. Leary – Biofouling: The Journal of Bioadhesion and Biofilm Research

 

Spatial Diversity of Bacterioplankton Communities in Surface Water of Northern South China Sea – Jialin Li – PLOS ONE

* High Genetic Diversity and Novelty in Eukaryotic Plankton Assemblages Inhabiting Saline Lakes in the Qaidam Basin – Jiali Wang – PLOS ONE

Effects of ocean acidification on the biogenic composition of the sea-surface microlayer: Results from a mesocosm study – Luisa Galgani – Journal of Geophysical Research: Oceans

Other (Food, biotechnology)

Microbial Dynamics and Control in Shale Gas Production – Jason Gaspar – Environmental Science & Technology Letters

Dynamics and diversity of microbial community succession in traditional fermentation of Shanxi aged vinegar – Zhiqiang Nie – Food Microbiology

Resilience of Aggregated Microbial Communities Subjected to Drought—Small-Scale Studies – Amélie Barthès – Microbial Ecology

Microbial diversity in sugarcane ethanol production in a Brazilian distillery using a culture-independent method – Ohana Yonara Assis Costa – Journal of Industrial Microbiology & Biotechnology

 

Metagenomics and viromes

Evaluation of viral genome assembly and diversity estimation in deep metagenomes – Daniel Aguirre de Cárcer – BMC Genomics

Niche-dependent genetic diversity in Antarctic metaviromes – Olivier Zablocki – Bacteriophage

Metabolomics

The cross-talk between opportunistic fungi and the mammalian host via microbiota’s metabolism – Luigina Romani – Seminars in Immunopathology

The metabolomics of airway diseases, including COPD, asthma and cystic fibrosis – B. Fatemeh Nobakht M. Gh. – Biomarkers

 

Metabolomics as a tool for diagnosis and monitoring in coeliac disease – Danielle Ryan – Metabolomics

 

Transcriptomics

Single-cell transcriptomics for microbial eukaryotes – Martin Kolisko – Current Biology

Bioinformatic tools

The R package otu2ot for implementing the entropy decomposition of nucleotide variation in sequence data – Alban Ramette and Pier Luigi Buttigieg – Frontiers in Microbiology

Techniques

Introduction to Genetic, Genomic, and System Analyses for Communities – Jack A. Gilbert, Nicole M. Scott – Springer Protocols Handbooks 2014

Microbes in the news

It’s all around us: Three scientists on how the microbiome shapes our world – Plus: Why you shouldn’t give probiotics to your dog – Brooke Borel

Professor’s new book aims to advance microbiome research – Brian McNeill – Phys.org

Book: Metagenomics for Microbiology, 1st Edition – Izard and Rivera – Elsevier

Symbiota Maps Plant Microbiome to Boost Crop Yields – Martin LaMonica – Xconomy

* History Lessons from Bacteria – Cindy Lu – Cell

 

Revolutionizing the interaction between plants and bacteria – Phys.org

Life’s extremists may be an untapped source of antibacterial drugs – David Salisbury – VanderBilt.edu

 

Science, publishing, career

Point of view: How postdocs benefit from building a union – Benjamin Cain

Bik’s Picks

The XKCD guid to the universe’s most bizarre physics – Randall Munroe – Wired.com

Physicists Solve Mystery of Scotch Whisky Rings – Rachel Nuwer – Scientific American

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Microbiome digest, November 21, 2014

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Microbiome general

Rare biosphere exploration using high-throughput sequencing: research progress and perspectives – Aibin Zhan, Hugh J. MacIsaac – Conservation Genetics

Human oral microbiome

Polymicrobial synergy and dysbiosis in inflammatory disease – Richard J. Lamonta, George Hajishengallis – Trends in Molecular Medicine

Human skin microbiome

* Dialogue between skin microbiota and immunity – Yasmine Belkaid, Julia A. Segre – Science

Human respiratory microbiome

Asthma 2014: from monoclonals to the microbiome – Peter G Gibson, Paul S Foster – The Lancet Respiratory Medicine

Human gut microbiome

Development of Fecal Microbiota Transplantation Suitable for Mainstream Medicine – Alexander Khoruts – Clinical Gastroenterology and Hepatology

The role of the gut and microbes in the pathogenesis of spondyloarthritis – Mark Asquith – Best Practice & Research Clinical Rheumatology

From lifetime to evolution: timescales of human gut microbiota adaptation – Sara Quercia – Frontiers in Microbiology

Animal and other models of microbiome research

Development of aminoglycoside and β-lactamase resistance among intestinal microbiota of swine treated with lincomycin, chlortetracycline, and amoxicillin – Jian Sun – Frontiers in Microbiology

Model systems to analyze the role of miRNAs and commensal microflora in bovine mucosal immune system development – Guanxiang Liang – Molecular Immunology

Gut Microbial Colonization Orchestrates TLR2 Expression, Signaling and Epithelial Proliferation in the Small Intestinal Mucosa – Nives Hörmann – PLOS ONE

The effects of elevated CO2 concentration on competitive interaction between aceticlastic and syntrophic methanogenesis in a model microbial consortium – Souichiro Kato – Frontiers in Microbiology

Animal microbiome

Aerobic cloacal and pharyngeal bacterial flora in six species of free-living birds – J. Stenkat – Journal of Applied Microbiology

Plant microbiome

Expanding genomics of mycorrhizal symbiosis – Alan Kuo – Frontiers in Microbiology

Soil and sediment microbiome

* Impact of interspecific interactions on antimicrobial activity among soil bacteria – Olaf Tyc – Frontiers in Microbiology

* Application of ancient DNA to the reconstruction of past microbial assemblages and for the detection of toxic cyanobacteria in subtropical freshwater ecosystems – Gabriela Martínez de la Escalera – Molecular Ecology

Characterisation of the soil microbial community of cultivated and uncultivated vertisol in Australia under several management regimes – Karuna Shrestha – Agriculture, Ecosystems & Environment

Wastewater reuse in irrigation: A microbiological perspective on implications in soil fertility and human and environmental health – Cristina Becerra-Castro – Environment International

Kotuikan Formation assemblage: a diverse organic-walled microbiota in the Mesoproterozoic Anabar succession, northern Siberia – Natalya G. Vorob’eva – Precambrian Research

Water microbiome

Diurnal expression of SAR11 proteorhodopsin and 16S rRNA genes in coastal North Atlantic waters – Raphaël Lami, David L. Kirchman – Aquatic Microbial Ecology

Leaf-litter-associated fungi and bacteria along temporal and environmental gradients in boreal streams – Jenny Bergfur, Carina Sundberg – Aquatic Microbial Ecology

Seasonal variation in marine-snow-associated and ambient-water prokaryotic communities in the northern Adriatic Sea – Jana Vojvoda – Aquatic Microbial Ecology

Microbial eukaryote diversity in the marine oxygen minimum zone off northern Chile – Darren J. Parris – Frontiers in Microbiology

* Resolving the abundance and air-sea fluxes of airborne microorganisms in the North Atlantic Ocean – Eva Mayol – Frontiers in Microbiology

Microbial contributions to coupled arsenic and sulfur cycling in the acid-sulfide hot spring Champagne Pool, New Zealand – Katrin Hug – Frontiers in Microbiology

Food microbiology

* Unpasteurised commercial boza as a source of microbial diversity – Andrea Osimani – International Journal of Food Microbiology

Metabolomics

* Prediction and quantification of bioactive microbiota metabolites in the mouse gut –
Gautham V. Sridharan – Nature Communications

An isotope-labeled chemical derivatization method for the quantitation of short-chain fatty acids in human feces by liquid chromatography–tandem mass spectrometry – Jun Han – Analytica Chimica Acta

Metagenomics / Bioinformatics

Key roles for freshwater Actinobacteria revealed by deep metagenomic sequencing – Rohit Ghai – Molecular Ecology

* BiomeNet: A Bayesian Model for Inference of Metabolic Divergence among Microbial Communities – Mahdi Shafiei – PLOS Computational Biology

Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships – Maggie C. Y. Lau – Frontiers in Microbiology

Techniques

Microbial Contamination in Next Generation Sequencing: Implications for Sequence-Based Analysis of Clinical Samples – Michael J. Strong – PLOS Pathogens

Comparing High-throughput Platforms for Sequencing the V4 Region of SSU-rDNA in Environmental Microbial Eukaryotic Diversity Surveys – Frédéric Mahé – Journal of Eukaryotic Microbiology

More microbiology papers

The Red Queen Model of Recombination Hotspots Evolution in the Light of Archaic and Modern Human Genomes – Yann Lesecque – PLOS Genetics

Association between Footwear Use and Neglected Tropical Diseases: A Systematic Review and Meta-Analysis – Sara Tomczyk – PLOS Neglected Tropical Diseases

Impact of wash cycle time, temperature and detergent formulation on the hygiene effectiveness of domestic laundering – M. Honisch – Journal of Applied Microbiology

Microbes in the news

Contaminated samples point the finger at the wrong suspects – Dalmeet Chawla – Imperial College London

Analyzing COPD Patients’ Sputum And Microbiota Composition Might Improve Treatment – Isaura Santos – Lung Disease News

Willy Burgdorfer, Who Found Bacteria That Cause Lyme Disease, Is Dead at 89 – William Yardley – The New York Times

Plants talk to each other using an internet of fungus – Nic Fleming – BBC

Bacteria on Russian ‘sex satellite’ survive reentry – Alec Luhn – The Guardian

Body’s bacteria may keep our brains healthy – Elizabeth Pennisi – Science Magazine

Hand dryers ‘splatter’ users with bacteria, scientists warn – Sarah Knapton – Telegraph UK

Unique sense of ‘touch’ gives a prolific bacterium its ability to infect anything – Morgan Kelly – Princeton

Science, publishing and career

Gates Foundation announces world’s strongest policy on open access research – Richard Van Noorden – Nature News Blog

Bogus Journal Accepts Profanity-Laced Anti-Spam Paper – Jeffrey Beal – Scholarly Open Access

* Sh*t My Reviewers Say – Collecting the finest real specimens of reviewer comments since 1456

Ten Simple Rules to Achieve Conference Speaker Gender Balance – Jennifer L. Martin – PLOS ONE

Bik’s Picks

Shedding light on skin color – Ann Gibbons – Science

Flashback Friday: Does garlic protect against vampires? An experimental study – Seriously Science – Discover Magazine

The Secret Life of Passwords – Ian Urbina – New York Times

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Microbiome digest, November 20, 2014

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Human gut microbiome

* Altered Duodenal Microbiota Composition in Celiac Disease Patients Suffering From Persistent Symptoms on a Long-Term Gluten-Free Diet – Pirjo Wacklin – American

Friend and foe: factors influencing the movement of the bacterium Helicobacter pylori along the parasitism–mutualism continuum – Derek Lin and Britt Koskella – Evolutionary Applications

 

Investigation of pH and Temperature Profiles in the GI Tract of Fasted Human Subjects Using the Intellicap® System – Mirko Koziolek – Journal of Pharmaceutical Sciences

Human vaginal microbiome

Vaginal Microbiota and Sexually Transmitted Infections That May Influence Transmission of Cell-Associated HIV – Richard A. Cone – Journal of Infectious Diseases

Animal models of microbiome research

The gut microbiota influences blood-brain barrier permeability in mice – Viorica Braniste – Science Translational Medicine

Association of Obesity with Serum Leptin, Adiponectin, and Serotonin and Gut Microflora in Beagle Dogs – H.-J. Park – Journal of Veterinary Internal Medicine

Animal microbiome

Evaluation of five antibiotics on larval gut bacterial diversity of Plutella xylostella (Lepidoptera: Plutellidae) – Xiao-Li Lin – Insect Science

Soil microbiome

Regional-scale patterns of soil microbes and nematodes across grasslands on the Mongolian plateau: relationships with climate, soil, and plants – Dima Chen – Ecography

Water microbiome

Using a “time machine” to test for local adaptation of aquatic microbes to temporal and spatial environmental variation – Jeremy W. Fox andLawrence D. Harder – Evolution

Role of microorganisms in oceanic anoxic events (OAEs) – Muriel Pacton and Georges E. Gorin – Geology Today

Microbiome of the built environment

* Environmental contamination and hospital-acquired infection: factors that are easily overlooked – C. Beggs – Indoor Air

Bioinformatics

* rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development – Steven F. Stoddard – Nucleic Acids Research

Microbes in the news

Shift in gut bacteria observed in fiber supplement study may offer good news for weight loss – Science Daily – November 18 2014

Altered microbiota linked to GI symptoms in celiac patients on strict diet – Healio.com

Interview with David Sela: Food scientist proposes way to improve health via breast milk – Cecilia Prado – Daily Collegian

* Mother’s Microbes Protect Baby’s Brain – Ruth Williams – The Scientist

Germophobes, spoiler alert: WSU presentation to suggest not all bacteria is bad – Marcia Ratcliff – Winona Daily News

How Gut Bacteria Can Lead to Weight Gain (video) – Melinda Beck – Wall Street Journal

Genes Revealed that May Impact the Colonization of Beneficial Bacteria – Sarah Plumridge – Northwestern.edu

Microbiome Move Over: the Gut Virome Makes Its Debut – Lara C. Pullen – Medscape

Virus Protects Mouse Gut – Tracy Vence – The Scientist

Upcoming events

2014-15: Bioinformatics: Discovering Patterns in Human Microbiome Data (HMD): March 16-18, 2015

Science and Art

If you are looking for Herpes virus pillows: Virus Cushions – Ohh Reindeer

3D printed giant germs help visually impaired see the world of microorganisms – Nanowerk

Doing science experiments on music: Cymatics: Science Vs. Music – Nigel Stanford – Vimeo.com

Bik’s Picks

Magic shoes: How to hear yourself instantly happy – Corrinne Burns – New Scientist

Out of India: Finding the origins of horses, rhinos – Science Daily

Here’s Why Cats Keep Rubbing Against Our Legs (And Why Catnip Makes Them Go Crazy) – Jacueline Howard – The Huffington Post

Here’s Why Dogs Kick Their Legs When You Rub Their ‘Sweet Spot” – Jacueline Howard – The Huffington Post

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Microbiome digest, November 18, 2014

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Pregnancy and birth microbiome

Fetal exposures and perinatal influences on the stool microbiota of premature infants – Diana A. Chernikova – Journal of Maternal-Fetal and Neonatal Medicine

* The Origin of Human Milk Bacteria: Is There a Bacterial Entero-Mammary Pathway during Late Pregnancy and Lactation? – Juan M. Rodríguez – Advances in Nutrition

Human oral microbiome

Dysbiosis and alterations in predicted functions of subgingival microbiome in chronic periodontitis – Mariana E. Kirst – Applied and Environmental Microbiology

Human respiratory microbiome

Analysis of Changes in Diversity and Abundance of the Microbial Community in a Cystic Fibrosis Patient Over a Multi-Year Period – Joshua R. Stokell – Journal of Clinical Microbiology

Human gut microbiome

* Gut Microbes and the Brain: Paradigm Shift in Neuroscience – Emeran A. Mayer – Journal of Neuroscience

Fiber supplementation influences phylogenetic structure and functional capacity of the human intestinal microbiome: follow-up of a randomized controlled trial – Hannah D Holscher – American Journal of Clinical Nutrition

Enteric microbiota leads to new therapeutic strategies for ulcerative colitis – Wei-Xu Chen – World Journal of Gastroenterology

Intestinal microbiota: The explosive mixture at the origin of inflammatory bowel disease? – Roberto Bringiotti – – World Journal of Gastroenterology

Direct Detection and Quantification of Bacterial Genes Associated with Inflammation in DNA Isolated from Stool – Ramon Gomez-Moreno – Advances in Microbiology

Review: The gut microbiome in health and in disease – Shreiner, Andrew B – Current Opinion in Gastroenterology

Animal models of microbiome research

* Composition of Intestinal Microbiota in Immune-Deficient Mice Kept in Three Different Housing Conditions – Christa Thoene-Reineke – PLOS ONE

The Gut Microbiota Modulates Glycaemic Control and Serum Metabolite Profiles in Non-Obese Diabetic Mice – Thomas U. Greiner – PLOS ONE

Animal microbiome

* Convergent Bacterial Microbiotas in the Fungal Agricultural Systems of Insects – Frank O. Aylward – mBio

* Optimization of preservation and processing of sea anemones for microbial community analysis using molecular tools – Joana Rocha – Scientific Reports

Global discovery of colonization determinants in the squid symbiont Vibrio fischeri – John F. Brooks, II – PNAS US

Plant microbiome

It takes an individual plant to raise a community: TRFLP analysis of the rhizosphere microbial community of two pairs of high- and low-metal-accumulating plants – Melanie P. Columbus – Soil Biology and Biochemistry

Soil and sediment microbiome

* Uncoupling of microbial community structure and function in decomposing litter across beech forest ecosystems in Central Europe – Witoon Purahong – Scientific Reports

Different Continuous Cropping Spans Significantly Affect Microbial Community Membership and Structure in a Vanilla-Grown Soil as Revealed by Deep Pyrosequencing – Wu Xiong – Microbial Ecology

Deforestation and cultivation with Maize (Zea mays L.) has a profound effect on the bacterial community structure in soil – Elizabeth Selene Gómez-Acata – Land Degradation & Development

Soil pH Determines Microbial Diversity and Composition in the Park Grass Experiment – Kateryna Zhalnina – Microbial Ecology

Shifts in carbon substrate utilization in sediment microbial communities along the Llobregat River – Anna Freixa – Fundamental and Applied Limnology / Archiv für Hydrobiologie

Salt effects on the soil microbial decomposer community and their role in organic carbon cycling: A review – Kristin M. Rath – Soil Biology and Biochemistry

Water microbiome

* Metagenome Sequencing of the Microbial Community of a Solar Saltern Crystallizer Pond at Cáhuil Lagoon, Chile – Alvaro M. Plominsky – Genome Announcements

Experimental evidence for strong stabilizing forces at high functional diversity of aquatic microbial communities – Francesco Carrara – ESA Ecology

Microbiome of the built environment

* Ecological succession and viability of human-associated microbiota on restroom surfaces – Sean M. Gibbons – Applied and Environmental Microbiology

* Seasonal Variability in Airborne Biotic Contaminants in Swine Confinement Buildings – Priyanka Kumari – PLOS ONE

Metabolomics

Bacterial microcompartments and the modular construction of microbial metabolism – Cheryl A. Kerfeld – Trends in Microbiology

* Suppression of Microbial Metabolic Pathways Inhibits the Generation of the Human Body Odor Component Diacetyl by Staphylococcus spp – Takeshi Hara – PLOS ONE

Bioinformatics

A phylogeny-based sampling strategy and power calculator informs genome-wide
associations studydesign for microbial pathogens – Maha R. Farhat – Genome Medicine

* Poster: Assessment of eukaryotic communities in environmental samples: A workflow comparison for next-generation sequencing data – Kristin Hardge – ePIC

Archaea

Phylogenetically Driven Sequencing of Extremely Halophilic Archaea Reveals Strategies for Static and Dynamic Osmo-response – Erin A. Becker – PLOS Genetics

More microbiology papers

* The commonly used antimicrobial additive triclosan is a liver tumor promoter – Mei-Fei Yueh – PNAS USA

Microbes in the News

Virus linked to mass die-off of sea stars – Craig Welch – The Seattle Times

Bik’s Picks

Wild chimpanzees plan their breakfast time, type, and location – Karline R. L. Janmaat – PNAS USA

Here Are 4 More Vulnerable Fish to Avoid Next Time You’re at the Sushi Bar – Dan Kedmey – Time

Comet landing: Organic molecules detected by Philae – Paul Rincon – BBC News

Correlation instead of causation?: Coffee Creamer, Crackers Linked To Worse Memory – Science2.0

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Microbiome digest, November 11, 2014

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Human oral microbiome

Physiological Adaptations of Key Oral Bacteria – C. W. Ian Douglas – Advances in Microbial Physiology

Human gut microbiome

Development and Survival of Th17 Cells within the Intestines: The Influence of Microbiome- and Diet-Derived Signals – Joseph H. Chewning – The Journal of Immunology

Gut Inflammation and Immunity: What Is the Role of the Human Gut Virome? – Alfredo Focà – Mediators of Inflammation

Animal microbiome

Faecal Microbiota of Forage-Fed Horses in New Zealand and the Population Dynamics of Microbial Communities following Dietary Change – Karlette A. Fernandes – PLOS ONE

The Effect of Phytochemical Tannins-Containing Diet on Rumen Fermentation Characteristics and Microbial Diversity Dynamics in Goats Using 16S rDNA Amplicon Pyrosequencing – B. R. Min – Agriculture, Food & Analytical Bacteriology

Microbial diversity in forestomach and caecum contents of the greater long-tailed hamster Tscherskia triton (Rodentia: Cricetidae) – Akio Shinohara – Mammalian Biology – Zeitschrift für Säugetierkunde

The pathogen Batrachochytrium dendrobatidis disturbs the frog skin microbiome during a natural epidemic and experimental infection – Andrea J. Jani – PNAS USA

Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk – Roberta M. O’Connor – PNAS USA

Arbuscular mycorrhizal fungi communities in a coral cay system (Morrocoy, Venezuela) and their relationships with environmental variables – M.M. Alguacil – Science of the Total Environment

Soil microbiome

Short-term parasite-infection alters already the biomass, activity and functional diversity of soil microbial communities – Jun-Min Li – Scientific Reports

Impact of short-term storage temperature on determination of microbial community composition and abundance in aerated forest soil and anoxic pond sediment samples – Franziska B. Brandt – Systematic and Applied Microbiology

Seasonal influence of climate manipulation on microbial community structure and function in mountain soils – Jérémy Puissant – Soil Biology and Biochemistry

Effect of organic and conventional practices on carbon-substrate utilisation by the soil microbial community in a ‘Cripps Pink’/M7 apple orchard – Andre H Meyer – South African Journal of Plant and Soil

* The Soil Biota Composition along a Progressive Succession of Secondary Vegetation in a Karst Area – Jie Zhao – PLOS ONE

Effects of salinization and crude oil contamination on soil bacterial community structure in the Yellow River Delta region, China – Yong-chao Gao – Applied Soil Ecology

Water microbiome

Community dynamics of prokaryotic and eukaryotic microbes in an estuary reservoir – Zhen Sun – Scientific Reports

Microbial diversity and community structure across environmental gradients in Bransfield Strait, Western Antarctic Peninsula – Camila N. Signori – Frontiers in Microbiology

Metagenomics

Assessment of quality control approaches for metagenomic data analysis – Qian Zhou – Scientific Reports

PaperClip: rapid multi-part DNA assembly from existing libraries – Maryia Trubitsyna – Nucleic Acids Research

Microbial phylogeny

* Assessing the global phylum level diversity within the bacterial domain: A review – Noha H. Youssef – Journal of Advanced Research

Science, publishing, career

Crosspost: Using Google Scholar in Scholarly Workflows – Jonathan Eisen – microBEnet

Hilarious: Overly honest references: “Should we cite the crappy Gabor paper here?” – RetractionWatch – (Note: paper has been removed – see a screenshot here)

Microbes in the news

* Bacteria Hysteria? Deadly bacteria normally found in toilets was discovered in the microwave of these students – The Journal.ie

Bik’s Picks

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication – Michael J. Montague – PNAS USA

UCSF develops site to make sense out of sugar science – Erin Allday – SFGate

Found: The Ideal Fatness for Elephant Seals – Elizabeth Preston – Discover

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