Category Archives: Human oral

December 10, 2014

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Food microbiome

The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types – Jenna M. Lang – PeerJ

Human oral microbiome

Subgingival microbial profiles of Sudanese patients with aggressive periodontitis – H. R. Z. Elabdeen – Journal of Periodontal Research

Human bladder microbiome

Interplay between Bladder Microbiota and Urinary Antimicrobial Peptides: Mechanisms for Human Urinary Tract Infection Risk and Symptom Severity – Vanessa Nienhouse – PLOS ONE

Human gut microbiome

Immunomodulatory Properties of Streptococcus and Veillonella Isolates from the Human Small Intestine Microbiota – Bartholomeus van den Bogert – PLOS ONE

Animal models of microbiome research

The Gut Commensal Bacteroides thetaiotaomicron Exacerbates Enteric Infection through Modification of the Metabolic Landscape – Meredith M. Curtis – Cell Host & Microbe

Gut Microbiota-Produced Succinate Promotes C. difficile Infection after Antibiotic Treatment or Motility Disturbance – Jessica A. Ferreyra – Cell Host & Microbe

Regionally Distinct Alterations in the Composition of the Gut Microbiota in Rats with Streptozotocin-Induced Diabetes – Roland Wirth – PLOS ONE

Animal microbiome

Environmentally Determined Differences in the Murine Lung Microbiota and Their Relation to Alveolar Architecture – Yeojun Yun – PLOS ONE

Bacteria and Methanogens Differ along the Gastrointestinal Tract of Chinese Roe Deer (Capreolus pygargus) – Zhipeng Li – PLOS ONE

Transcriptomic Immune Response of the Cotton Stainer Dysdercus fasciatus to Experimental Elimination of Vitamin-Supplementing Intestinal Symbionts – Eugen Bauer – PLOS ONE

Metabolomics

Stool Phospholipid Signature is Altered by Diet and Tumors – Julie M. Davies – PLOS ONE

Pathogens’ Exploitation of the Intestinal Food Web
Tu Anh Pham N., Trevor D. Lawley – Cell Host & Microbe

Could resistant starch be the redeemer of dietary carbohydrate? – M Denise Robertson – Practical Diabetes

A New Insight into the Physiological Role of Bile Salt Hydrolase among Intestinal Bacteria from the Genus Bifidobacterium – Piotr Jarocki – PLOS ONE

Metagenomics

Maths on microbes: adding microbial ecophysiology to metagenomics – Wilfred F. M. Röling – Microbial Biotechnology

Functional optimization of gene clusters by combinatorial design and assembly – Michael J Smanski – Nature Biotechnology

More microbiology

Microbiology: Ditch the term pathogen – Arturo Casadevall & Liise-anne Pirofski – Nature

New sequencing technique: MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island – Philip M Ashton – Nature Biotechnology

Microbes in the news

NASA ISS On-Orbit Status 5 December 2014: Microbiome Experiment – SpaceRef

Bacteria’s Game of ‘Telephone’ Foils Microbiologists’ Eavesdropping – Kim Krieger – UConnToday

Science, publishing, career

The Point When Science Becomes Publicity – James Hamblin – The Atlantic

No Lovin’ Feeling… for Science Fair – Claire Wapole – Huffington Post

How to cope when things go wrong in academia – Julie Gould – Nature Jobs

Scientific Peer Review Is Broken. We’re Fighting to Fix It With Anonymity – The Founders of PubPeer – Wired.com

Not sure how old this is, but I liked the graph: The illustrated guide to a Ph.D. – Matt Might

Ocean biology: Marine dreams – Chris Woolston – Nature

New postdoc report covers familiar ground – Beryl Lieff Benderly, Jim Austin – Science Careers

Bik’s Picks

Injectable 3-D vaccines could fight cancer, infectious diseases – ScienceDaily

Glittering Nobel Gown Represents Scientist’s Work – Joanne Manaster – Scientific American

This Commuter Bus Runs On Poop- A U.K.-based biogas plant has developed a 40-seater than runs on converted sewage and food waste – Corinne Iozzio – Smithsonian

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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 8, 2014

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Human microbiome general

The human microbiome: opportunities and challenges for clinical care – Geraint B. Rogers – Internal Medicine Journal

Evaluative Profiling of Arsenic Sensing and Regulatory Systems in the Human Microbiome Project Genomes – Raphael D Isokpehi – Microbiology Insights

Human oral microbiome

* High resolution taxonomic profiling of the subgingival microbiome for biomarker discovery and periodontitis diagnosis – Szymon P. Szafranski – Applied and Environmental Microbiology

Human gut microbiome

Crosstalk at the mucosal border: importance of the gut microenvironment in IBS – Lena Öhman – Nature Reviews Gastroenterology & Hepatology

Antimicrobial resistance characteristics and fitness of Gram negative faecal bacteria from volunteers treated with minocycline or amoxicillin – Miranda Kirchner – Frontiers in Microbiology

Decrease in lactobacilli in the intestinal microbiota of celiac children with a gluten-free diet, and selection of potentially probiotic strains – María J. Lorenzo Pisarello – Canadian Journal of Microbiology

Safety assessment of genetically modified rice expressing human serum albumin from urine metabonomics and fecal bacterial profile – Xiaozhe Qi – Food and Chemical Toxicology

Pregnancy and birth microbiome

Placental Microbiome and Its Role in Preterm Birth – Bin Cao – NeoReviews

High A. vaginae and G. vaginalis vaginal loads are associated with preterm birth – Florence Bretelle – Clinical Infectious Diseases

Cesarean Section and Chronic Immune Disorders – Astrid Sevelsted – Pediatrics

Animal and other models of microbiome research

Intestinal epithelial ​MyD88 is a sensor switching host metabolism towards obesity according to nutritional status – Amandine Everard – Nature Communications

Bugs and Food: A Recipe for Cancer? – Christina L. Ohland, Christian Jobin – Cell Metabolism

The current provided by oxygen-reducing microbial cathodes is related to the composition of their bacterial community – Mickaël Rimboud – Bioelectrochemistry

Animal microbiome

The putative functional ecology and distribution of archaeal communities in sponges, sediment and seawater in a coral reef environment – Ana R.M. Polónia – Molecular Ecology

Plant microbiome

* The role of bacteria and mycorrhiza in plant sulfur supply – Jacinta M. Gahan and Achim Schmalenberger – Frontiers in Plant Science

Arctic fungal communities associated with roots of Bistorta vivipara do not respond to the same fine-scale edaphic gradients as the aboveground vegetation – Sunil Mundra – New Phytologist

Soil and sediment microbiome

Impacts of altered precipitation regimes on soil communities and biogeochemistry in arid and semi-arid ecosystems – Uffe N. Nielsen – Global Change Biology

* Effects of tree identity dominate over tree diversity on the soil microbial community structure – Andrea Scheibe – Soil Biology and Biochemistry

Smooth brome invasion increases rare soil bacterial species prevalence, bacterial species richness and evenness – Candace L. Piper – Journal of Ecology

The interactive effects of elevated ozone and wheat cultivars on soil microbial community composition and metabolic diversity – Xuelian Bao – Applied Soil Ecology

Seasonal variations of the composition of microbial biofilms in sandy tidal flats: Focus of fatty acids, pigments and exopolymers – Claire Passarelli – Estuarine, Coastal and Shelf Science

Pharmaceuticals in the environment: Biodegradation and effects on natural microbial communities. A Review – Anna Barra Caracciolo – Journal of Pharmaceutical and Biomedical Analysis

Water microbiome

Successional Change in Microbial Communities of Benthic Phormidium-Dominated Biofilms – Katie A. Brasell – Microbial Ecology

Microbiome of the built environment

Characterizing airborne fungal and bacterial concentrations and emission rates in six occupied children’s classrooms – D. Hospodsky – Indoor Air

Food microbiology

Analysis of the bacterial community in aged and aging pit mud of Chinese Luzhou-flavour liquor by combined PCR-DGGE and quantitative PCR assay – Huipeng Liang – Journal of the Science of Food and Agriculture

Phages and viruses

Emerging methods to study bacteriophage infection at the single-cell level – Vinh T. Dang and Matthew B. Sullivan – Frontiers in Microbiology

Metabolomics

* The Community Ecology of Microbial Molecules – Robert A. Quinn, Theodore Alexandrov – Journal of Chemical Ecology

Ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry for rapid analysis of the metabolites of morroniside produced by human intestinal bacteria – Min Zhao – Journal of Chromatography B

Small-intestinal or colonic microbiota as a potential amino acid source in animals – Werner G. Bergen – Amino Acids

Techniques

Comparative assessment of next-generation sequencing, denaturing gradient gel electrophoresis, clonal restriction fragment length polymorphism and cloning-sequencing as methods for characterizing commercial microbial consortia – A.D. Samarajeewa – Journal of Microbiological Methods

Microbes in the news

Now We Know Some Creepy Things About How Penicillin Destroys Bacteria – Esther Inglis-Arkell – IO9

Arctic bacteria converts mercury – Kristian Sjøgren – ScienceNordic

Should I Eat Greek Yogurt? – Mandy Oaklander – Time

CSU team examines dairy-cattle microorganisms to improve food safety – Kristen Browning-Blas – Bovine Vet Online

Glyphosate used with GMO crops under attack for disrupting microbiome: Science or a gut feeling? – David Warmflash – Genetic Literacy Project

#BacteriaHysteria: Why it’s time to detox your desk: Average worker comes into contact with more than 10 MILLION disease-causing bacteria lurking on their keyboard, phone and mouse – Lizzie Parry – Daily Mail

Bik’s Picks

The Yearbook: Our list of newsmakers this year – Manasi Vaidya & Shraddha Chakradhar – Nature Medicine

Notable advances 2014 – Amanda Keener – Nature Medicine

Let’s face it, for robots, falling down is easy. But how do you teach them to land safely? – Maki Naro – Popular Science

Force-feeding a human to a snake is not science (and is also super dumb) – Rachel Feltman – Washington Post

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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 2, 2014

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General microbiome

Microbiome, holobiont and the net of life – Emiliano Salvucci – Critical Reviews in Microbiology

Pregnancy and birth

Infectious Causes of Necrotizing Enterocolitis – Sarah A. Coggins – Clinics in Perinatology

Human oral microbiome

Solving the etiology of dental caries – Aurea Simón-Soro, Alex Mira – Trends in Microbiology

Oral Microbiota in Crevices Around Dental Implants: Profiling of Oral Biofilm – Takuichi Sato – Interface Oral Health Science

Human respiratory microbiome

* Temporal profiling of the bacterial and fungal communities in ΔF508 adult cystic fibrosis sputum – Andrew Nelson – PeerJ Preprint

Human gut microbiome

* Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production – Gary D Wu – Gut

Microbiome of death

* Initial insights into bacterial succession during human decomposition – Embriette R. Hyde – International Journal of Legal Medicine

Animal and other models of microbiome research

Natural killer T cells play a necessary role in modulating of immune-mediated liver injury by gut microbiota – Jianing Chen – Scientific Reports

Effect of stoned olive pomace on rumen microbial communities and polyunsaturated fatty acids biohydrogenation: an in vitro study – Grazia Pallara – BMC Veterinary Research

Successional changes in the chicken cecal microbiome during 42 days of growth are independent of organic acid feed additives – Brian B Oakley – BMC Veterinary Research

Animal microbiome

The role of host phylogeny varies in shaping microbial diversity in the hindguts of lower termites – Vera Tai – Applied and Environmental Microbiology

Plant microbiome

Relocation, high-latitude warming and host genetic identity shape the foliar fungal microbiome of poplars – Miklós Bálint – Molecular Ecology

Soil and sediment microbiome

Distribution of sediment bacterial and archaeal communities in plateau freshwater lakes – Jingxu Zhang – Applied Microbiology and Biotechnology

Effects of Phragmites invasion on soil microbial activity and structure in a brackish marsh – Keunyea Song – Plant and Soil

Water microbiome

* High temporal and spatial diversity in marine RNA viruses implies that they have an important role in mortality and structuring plankton communities – Julia A. Gustavsen – Frontiers in Microbiology

Impact of atmospheric deposition on the metabolism of coastal microbial communities

Sandra Martínez-García – Estuarine, Coastal and Shelf Science

Assessment of Bacterial and Archaeal Community Structure in Swine Wastewater Treatment Processes – Marcio Luis Busi Da Silva – Microbial Ecology

Food microbiology

Evaluation of microbial diversity in the pilot-scale beer brewing process by culture-dependent and culture-independent method – Masayuki Takahashi- Journal of Applied Microbiology

Pre- and probiotics

Recent developments in prebiotics to selectively impact beneficial microbes and promote intestinal health – Robert A. Rastall , Glenn R. Gibson – Current Opinion in Biotechnology

* The domestication of the probiotic bacterium Lactobacillus acidophilus – Matthew J. Bull – Scientific Reports

Microbes in the news

Mining industry could benefit from Wheatbelt discovery of salt and acid tolerant bacteria – Lucinda Jose – ABC Australia

Science, publishing, and career

The never-ending Ph.D. – By Adam Ruben – Science Careers

Clueless Reporter from the Mirror Bases Story on Withdrawn OMICS Publishing Group Article – Jeffrey Beall – ScholaryOA

The Next Enlightenment: Sharing Science With the World – Marietta DiChristina – Huffington Post

Bik’s Picks

Actor Alan Alda Challenges Scientists to Explain ‘What is Sleep?’ – Laura Geggel – LiveScience

Ability to consume alcohol may have shaped primate evolution – Sarah C. P. Williams – Science News

#Shirtgate inspires a Kickstarter for shirts covered in (science) ladies – Rachel Feltman – Washington Post

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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 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 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 17, 2014

Posted on by

Microbiome in pregnancy and birth

16S rRNA Gene Sequencing, Multilocus Sequence Analysis, and Mass Spectrometry Identification of the Proposed New Species “Clostridium neonatale” – Philippe Bouvet – Journal of Clinical Microbiology

Human oral microbiome

Shaping the oral microbiota through intimate kissing – Remco Kort – Microbiome

Distinct composition of the oral indigenous microbiota in South Korean and Japanese adults – Toru Takeshita – Scientific Reports

Periodontal and peri-implant microbiota in patients with healthy and inflamed periodontal and peri-implant tissues – Long-Fei Zhuang – Clinical Oral Implants Research

An in vivo comparison of internal bacterial colonization in two dental implant systems: Identification of a pathogenic reservoir – Joanne Mawhinney – Acta Odontologica Scandinavica

Oral pathogens in children with respiratory disease – Yumiko Endo – Pediatric Dental Journal

Severity-Related Changes of Bronchial Microbiome in Chronic Obstructive Pulmonary Disease – Marian Garcia-Nuñez – Journal of Clinical Microbiology

Human vaginal microbiome

Diversity of vaginal microbial communities and role of PAP smear in its detection – Neha Batra – International Journal of Current Microbiology and Applied Sciences

Human microbiome – other and general

The conjunctival microbiome in health and trachomatous disease: a case control study – Yanjiao Zhou – Genome Medicine

What is a host? Incorporating the Microbiota into the ‘Damage-Response Framework’ – Arturo Casadevall and Liise-anne Pirofski – Infection and Immunity

Plant microbiome

Plant–insect interactions under bacterial influence: ecological implications and underlying mechanisms – Akiko Sugio – Journal of Experimental Botany

Soils and sediments microbiome

Bacterial community composition and biogeochemical heterogeneity in PAH-contaminated riverbank sediments – Gloria P. Johnston, Laura G. Leff – Journal of Soils and Sediments

Diversity of acidophilic prokaryotes at two acid mine drainage sites in Turkey – Pınar Aytar – Environmental Science and Pollution Research

Ammonia-oxidizing archaea versus bacteria in two soil aquifer treatment systems – Kun Ding – Applied Microbiology and Biotechnology

Water microbiome

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

454 Pyrosequencing reveals diversity of Bdellovibrio and like organisms in fresh and salt water – Nan Li – Antonie van Leeuwenhoek

Metabolomics

Molecular details of a starch utilization pathway in the human gut symbiont Eubacterium rectale – Darrell W. Cockburn – Molecular Microbiology

Immunology

Prevention and cure of rotavirus infection via TLR5/NLRC4–mediated production of IL-22 and IL-18 – Benyue Zhang – Science

Microbes in the news

Worm Defies Tradition, Stores Gut Bacteria in Gills Instead – Elizabeth Preston – Discover Magazine

Here’s How Many Bacteria Spread Through One Kiss – Mandy Oaklander – Time

How Bacteria In The Gut Help Fight Off Viruses – Michaeleen Doucleff – Goats and Soda – NPR

This could be the most important scientific breakthrough in our lifetimes – Bengt Saelensminde – MoneyWeek

Probing the Microbial Mysteries of Wine – Iratxe Zarraonaindia and Jack A. Gilbert – Microbe

Self-destructing drone is made of fungus, bacteria, and wasp spit – Lee Mathews – Geek.com

Bik’s Picks

Scientists Descend into Massive Crater in Yamal Peninsula in Siberia: Bermuda Triangle Mystery Solved? – Rhodi Lee – Tech Times

Lightning expected to increase by 50 percent with global warming – Science Daily

Sometimes a Shirt is More Than Just a Shirt.. – Isis the Scientist

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