Category Archives: Metagenomics & Bioinformatics

December 23, 2015

Posted on by

Dental plaque microbiota shifts during mechanic ventilation, different antibiotics have different effects in mice gut, the Tasmanian devil microbiome, supraglacial communities, and FISH visualization of bacteria.

Microbial detection from almost sterile sites

Absence of Bacteria on Coronary Angioplasty Balloons from Unselected Patients: Results with Use of a High Sensitivity Polymerase Chain Reaction Assay – Gorm Mørk Hansen – PLOS ONE

Pregnancy and birth microbiome

Editorial: Is there a link between viruses and necrotising enterocolitis? – Masako Shimamura – Acta Paediatrica

Human oral microbiome

Microbial profiling of dental plaque from mechanically ventilated patients – Kirsty M Sands – Journal of Medical Microbiology

Discovery and validation of potential bacterial biomarkers for lung cancer – Xinmin Yan – American Journal of Cancer Research

Human gut microbiome

Gut Microbiota Alterations can predict Hospitalizations in Cirrhosis Independent of Diabetes Mellitus – Jasmohan S. Bajaj – Scientific Reports

Editorial: Diarrhoea risk study underlines the difficulties in carrying out research in day care centre settings – Margareta Söderström – Acta Paediatrica

Review: Micromanagement in the gut: microenvironmental factors govern colon mucosal biofilm structure and functionality – Rosemarie De Weirdt – NPJ Biofilms and Microbiomes

Microbiome models

Antibiotic Treatment Affects Intestinal Permeability and Gut Microbial Composition in Wistar Rats Dependent on Antibiotic Class – Monica Vera-Lise Tulstrup – PLOS ONE

Spatial disturbances in altered mucosal and luminal gut viromes of diet-induced obese mice – Min-Soo Kim – Environmental Microbiology

Interaction of mouse splenocytes and macrophages with bacterial strains in vitro: the effect of age in the immune response – A.A. Van Beek – Beneficial Microbes

DGGE: Oral administration of kefiran exerts a bifidogenic effect on BALB/c mice intestinal microbiota – M.F. Hamet – Beneficial Microbes

A Spatially Continuous Model of Carbohydrate Digestion and Transport Processes in the Colon – Arun S. Moorthy – PLOS ONE

Beneficial metabolic effects of selected probiotics on diet-induced obesity and insulin resistance in mice are associated with improvement of dysbiotic gut microbiota – Jeanne Alard – Environmental Microbiology

Editorial: Gutsy Microbes Fly High in the Antiviral War – Javier Robalino – Trends in Microbiology

Animal microbiome

The Tasmanian devil microbiome—implications for conservation and management – Yuanyuan Cheng – Microbiome

Plant, root, and soil microbiome

Rock geochemistry induces stress and starvation responses in the bacterial proteome – Casey C. Bryce – Environmental Microbiology

Isolation, selection and evaluation of antagonistic yeasts and lactic acid bacteria against ochratoxigenic fungus Aspergillus westerdijkiae on coffee beans – G.V. de Melo Pereira – Letters in Applied Microbiology

Low multifunctional redundancy of soil fungal diversity at multiple scales – Akira S. Mori – Ecology Letters

Phosphorus depletion in forest soils shapes bacterial communities towards phosphorus recycling systems – Fabian Bergkemper – Environmental Microbiology

Comparison of bacterial and archaeal communities in depth-resolved zones in an LNAPL body – Maria Irianni-Renno – Applied Microbiology and Biotechnology

Water and extremophile microbiome

Supraglacial bacterial community structures vary across the Greenland ice sheet –
Karen A. Cameron – FEMS Microbiology Ecology

Identification of subannual patterns in microbial community signatures from individual sedimentary laminae using a freeze-coring approach – B. K. Harrison – Limnology and Oceanography

Respiratory quinones in Archaea: phylogenetic distribution and application as biomarkers in the marine environment – Felix J. Elling – Environmental Microbiology

Built environment microbiome

Review: Sources of airborne microorganisms in the built environment – Aaron J. Prussin II – Microbiome

Food microbiology

Abiotic Stress and Phyllosphere Bacteria Influence the Survival of Human Norovirus and Its Surrogates on Preharvest Leafy Greens – Malak A. Esseili – Applied and Environmental Microbiology

Microbiome of death

Microbial ecology of the salmon necrobiome: Evidence salmon carrion decomposition influences aquatic and terrestrial insect microbiomes – Jennifer L. Pechal – Environmental Microbiology

Metagenomics and bioinformatics

Identification and Resolution of Microdiversity through Metagenomic Sequencing of Parallel Consortia – William C. Nelson – Applied and Environmental Microbiology

Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes – Jiarong Guo – Applied and Environmental Microbiology

Techniques

MiL-FISH: Multilabeled Oligonucleotides for Fluorescence In Situ Hybridization Improve Visualization of Bacterial Cells – Mario P. Schimak – Applied and Environmental Microbiology

Microbes in the news

Salmonella traced to pet turtles is spreading once again – Helen Branswell – STAT news

Bacteria resistant to a “last resort” antibiotic have been found in the UK – Frida Garza – Quartz

Gene behavior distinguishes viral from bacterial infections – Laura Sanders – Science News

Near perfect balance in a microbiome paper – hopeful yet no hype – Jonathan Eisen – MicroBEnet

Beneficial bacteria in Hawaiian squid attracted to fatty acids – Phys.org

Conference update: Advances in Human Microbiome Science: Intestinal Diseases – The New York Academy of Sciences

Microbiology and art

Microbiology and Creative Extra Credit – Mark O. Martin – Microbes Rule
Science, publishing, and career

Diversity in Clinical and Biomedical Research: A Promise Yet to Be Fulfilled – Sam S. Oh – PLOS Medicine

Genome-editing revolution: My whirlwind year with CRISPR – Jennifer Doudna – Nature

Science and gender: Scientists must work harder on equality – Meg Urry – Nature

End of year lists

365 days: The science events that shaped 2015. Gene-editing, climate change and Pluto are among the year’s top stories – Monya Baker – Nature

The Coolest Science Stories You May Have Missed in 2015 – Jennifer Ouellette – Gizmodo
[hr]

December 22, 2015

Posted on by

Periodontal disease associated with increased chance for breast cancer, rifaximin treatment of IBS patients, bacteria on surface of 2 different grape varieties in Spain, and a reproducible research workflow in R.

Human oral microbiome

Periodontal Disease and Breast Cancer: Prospective Cohort Study of Postmenopausal Women – Jo L. Freudenheim – Cancer Epidemiology, Biomarkers & Prevention

Distributions of Synergistetes in clinically-healthy and diseased periodontal and peri-implant niches – Xiao-Lin Yu – Microbial Pathogenesis

Human gut microbiome

Modulation of the gut microbiota composition by rifaximin in non-constipated irritable bowel syndrome patients: a molecular approach – Sara Soldi – Clinical and Experimental Gastroenterology

Roles of Sphincter of Oddi Laxity in Bile Duct Microenvironment in Patients with Cholangiolithiasis: From the Perspective of the Microbiome and Metabolome –
Tingbo Liang – Journal of the American College of Surgeons

Book chapter: Influence of Gut Microbiota on Hepatic Lipogenesis and Disease Pathogenesis – Vishal Singh – Hepatic De Novo Lipogenesis and Regulation of Metabolism

Review: Metabolic Interactions in the Gastrointestinal Tract (GIT): Host, Commensal, Probiotics, and Bacteriophage Influences – Luis Vitetta – MDPI Microorganisms

Book chapter: Gut Microbiome and Stress – Winnie-Pui-Pui Liew – Beneficial Microorganisms in Medical and Health Applications

Review: Dietary and Lifestyle Factors Associated with Colorectal Cancer Risk and Interactions with Microbiota: Fiber, Red or Processed Meat and Alcoholic Drinks – Tuan J. – GastroIntestinal Tumors

Models of microbiomes

Effect of chito-oligosaccharides over human faecal microbiota during fermentation in batch cultures – Inmaculada Mateos-Aparicio – Carbohydrate Polymers

Changes in gastric microbiota induced by Helicobacter pylori infection and preventive effects of Lactobacillus plantarum ZDY 2013 against such infection – Mingfang Pan – Journal of Dairy Science

Glycan:glycan interactions: High affinity biomolecular interactions that can mediate binding of pathogenic bacteria to host cells – Christopher J. Day – PNAS

Research highlight: A ‘fit’ microbiota to potentiate cancer immunotherapy – Maria Rescigno – Genome Medicine

Animal microbiome

Ecological Succession in the Honey Bee Gut: Shift in Lactobacillus Strain Dominance During Early Adult Development – Kirk E. Anderson – Host Microbe Interactions

A diverse array of new viral sequences identified in worldwide populations of the Asian citrus psyllid (Diaphorina citri) using viral metagenomics – Shahideh Nouri – Journal of Virology

Co-circulation of three camel coronavirus species and recombination of MERS-CoVs in Saudi Arabia – Jamal S. M. Sabir – Science

Comparison of Fecal Microbial Communities between White and Black Pigs – Robin B. Guevarra – Journal of Applied Biological Chemistry

Plant, root, and soil microbiome

Bacterial diversity of Grenache and Carignan grape surface from different vineyards at Priorat wine region (Catalonia, Spain) – Maria del Carmen Portillo – International Journal of Food Microbiology

Field Application of the Mycorrhizal Fungus Rhizophagus irregularis Increases the Yield of Wheat Crop and Affects Soil Microbial Functionalities – Sanâa Wahbi – American Journal of Plant Sciences

Arbuscular mycorrhizal fungi reduced the ratios of inorganic/organic arsenic in rice grains – H. Li – Chemosphere

Characteristics of rhizosphere and bulk soil microbial communities in rubber plantations in Hainan Island, China – Wang, W. B. – Journal of Tropical Forest Science

Microbial community structure and its temporal changes in Rehmannia glutinosa rhizospheric soils monocultured for different years – Linkun Wu – European Journal of Soil Biology

Exotic Plant Alnus trabeculosa Alters the Composition and Diversity of Native Rhizosphere Bacterial Communities of Phragmites australis – Xueping Chen – Pedosphere

Long-term chronological shifts in bacterial communities and hydrolytic extracellular enzyme activities in the forty years following a land-use change from upland fields to paddy fields – Nan Jiang – Pedobiologia

Water microbiome

Resilience of SAR11 bacteria to rapid acidification in the high latitude open ocean – Manuela Hartmann – FEMS Microbiology Ecology

Selective pressure of temperature on competition and cross-feeding within denitrifying and fermentative microbial communities – Anna Hanke – Frontiers in Microbiology

Bioinformatics

Reproducible Research Workflow in R for the Analysis of Personalized Human Microbiome Data – Benjamin Callahan – Pacific Symposium on Biocomputing

Techniques

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys – William Walters – mSystems

Protocol: Studying Protistan Communities in Hydrocarbon-Contaminated Environments – Julia Johnke – Springer Protocols Handbooks

Microbes in the news

Harmful bacteria can survive in sandwich crackers, cookies for months, UGA study finds – Online Athens

Tomorrow’s Heart Drugs Might Target Gut Microbes – Ed Yong – The Atlantic

Bik’s Picks

Pharmacy delivery vans targeted by thieves seeking painkillers – David Armstrong – STAT news

[hr]

December 21, 2015

Posted on by

Vacuum cleaning, anorexia, chronic fatigue syndrome, celiac disease, and social preferences in mice.

Pregnancy and birth

Potential association of vacuum cleaning frequency with an altered gut microbiota in pregnant women and their 2-year-old children – Ekaterina Avershina – Microbiome

Placental infection with Ureaplasma species is associated with histologic chorioamnionitis and adverse outcomes in moderate and late preterm infants – Emma L. Sweeney – The Journal of Infectious Diseases

Polymicrobial Amniotic Fluid Infection with Mycoplasma/Ureaplasma and Other Bacteria Induces Severe Intra-Amniotic Inflammation Associated with Poor Perinatal Prognosis in Preterm Labor – Noriko Yoneda – American Journal of Reproductive Immunology

The Development of Extremely Preterm Infants Born to Women Who Had Genitourinary Infections During Pregnancy – Alan Leviton – American Journal of Epidemiology

Human skin microbiome

Skin microbiome in melanomas and melanocytic nevi – Alexander Salava- European Journal of Dermatology

Human oral microbiome

Commentary: A New Association for the Oral Metagenome – Nicholas S. Jakubovics – Oral Diseases

Human respiratory microbiome

No evidence for viral sequences in five lepidic adenocarcinomas (former “BAC”) by a high-throughput sequencing approach – Nicolas Berthet – BMC Research Notes

Human gastric and gut microbiome

Gut Dysbiosis in Patients with Anorexia Nervosa – Chihiro Morita – PLOS ONE

Changes in Gut and Plasma Microbiome following Exercise Challenge in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) – Sanjay K. Shukla – PLOS ONE

From an imbalance to a new imbalance: Italian-style gluten-free diet alters the salivary microbiota and metabolome of African celiac children – Danilo Ercolini – Scientific Reports

Bacterial overgrowth and diversification of microbiota in gastric cancer – Wang, Lili – European Journal of Gastroenterology & Hepatology

Review: Endocannabinoids — at the crossroads between the gut microbiota and host metabolism – Patrice D. Cani – Nature Reviews Endocrinology

Review: Disruption of the Gut Microbiome: Clostridium difficile Infection and the Threat of Antibiotic Resistance – Priscilla A. Johanesen – MDPI Genes

Review: Obesity: An overview of possible role(s) of gut hormones, lipid sensing and gut microbiota – Alok Kumar Mishra – Metabolism

Review: Microbiome and Beyond: Non-Viable Food Microbes and Human Health – James W. Daily III – Journal of Medicinal Food

Review: Microbial translocation and microbiome dysbiosis in HIV-associated immune activation – Zevin, Alexander S – Current Opinion in HIV and AIDS

Animal and other models

Calcium supplementation modulates gut microbiota in a prebiotic manner in dietary obese mice – Alice Chaplin – Molecular Nutrition & Food Research

Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries – Joel D. Rudney – Microbiome

Innate immune responses to gut microbiota differ between threespine stickleback populations – Kathryn Milligan-Myhre – Disease Models & Mechanisms

Host microbiota modulates development of social preference in mice – Tim Arentsen – Microbial Ecology in Health and Disease

Gut barrier impairment by high-fat diet in mice depends on housing conditions –
Veronika Maria Müller – Molecular Nutrition & Food Research

A Strategy for the Targeted Metabolomics Analysis of 11 Gut Microbiota-host Co-metabolites in Rat Serum, Urine and Feces by Ultra Performance Liquid Chromatography—Tandem Mass Spectrometry – Waner Hou – Journal of Chromatography A

Editorial: Small but Mighty: Selected Commensal Bacterial Species Determine the Effectiveness of Anti-cancer Immunotherapies – Jose R. Conejo-Garcia – Immunity

Fecal Microbiota Transplant Restores Mucosal Integrity in a Murine Model of Burn Injury – Kuethe, Joshua W – Shock

Animal microbiome

Isolation, identification and fibrolytic characteristics of rumen fungi grown with indigenous methanogen from yaks (Bos grunniens) grazing on the Qinghai-Tibetan Plateau – Ya-Qin Wei – Journal of Applied Microbiology

Molecular characterization of midgut microbiota of Aedes albopictus and Aedes aegypti from Arunachal Pradesh, India – Kamlesh K. Yadav – Parasites & Vectors

Plant, root, and soil microbiome

Soil microbial community structure explains the resistance of respiration to a dry–rewet cycle, but not soil functioning under static conditions – Kate H. Orwin – Functional Ecology

Comparative Analysis of Prokaryotic Communities Associated with Organic and Conventional Farming Systems – Elizaveta Pershina – PLOS ONE

Succession of bacterial communities, coxL genotypes and carbon monoxide oxidation activity in soil microcosms to identify unknown carboxydovore bacteria dominating deciduous forest soil – Isabelle Lalonde – Applied and Environmental Microbiology

Commentary: Disentangling the factors shaping microbiota composition across the plant holobiont – Stéphane Hacquard – New Phytologist

Significant alteration of soil bacterial communities and organic carbon decomposition by different long-term fertilization management conditions of extremely low-productivity arable soil in South China – Weibing Xun – Environmental Microbiology

Water and extremophile microbiome

Physical and chemical controls on habitats for life in the deep subsurface beneath continents and ice – John Parnell – Philosophical Transactions A

Temporal succession in carbon incorporation from macromolecules by particle-attached bacteria in marine microcosms – Xavier Mayali – Environmental Microbiology Reports

Archaeal and bacterial communities across a chronosequence of drained lake basins in arctic alaska – J. Kao-Kniffin – Scientific Reports

Built environment microbiome

Assessment of indoor environmental quality in existing multi-family buildings in North–East Europe – Liuliu Du – Environment International

Alas, no access for me, but sounds cool: Analysis of the incidence fungi in a crypt cemetery – Cecylia Łukaszuk – Journal of the Air & Waste Management Association

Monitoring sulfide-oxidizing biofilm activity on cement surfaces using non-invasive self-referencing microsensors – Liqiu Cheng – Water Research

Metagenomics and bioinformatics

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED – James Kaminski – PLOS Computational Biology

Techniques

Meta3C analysis of a mouse gut microbiome – Martial Marbouty, Lyam Baudry, Axel Cournac, Romain Koszul – BioRxiv

 

Microbes in the news

Podcast: Drugged Gut Microbiome Cuts Heart Risk in Mice – Christopher Intagliata – Scientific American

Are Antibiotics Making People Larger? Overuse of the drugs seems to make us gain weight—even when we don’t take them – James Hamblin – The Atlantic

Petri-Dishing the Dirt for Science and Education at Worcester Polytechnic Institute – PR Web

Men and women deposit different types of bacteria – Tim Sandle – Digital Journal

Mediterranean Diet Impacts Microbiome’s Influence on Heart Disease – Genengnews

Science, publishing, and career

Rejection of rejection: a novel approach to overcoming barriers to publication: Tired of rejections? Cath Chapman and Tim Slade offer a simple way to fight back – The BMJ

365 days: Nature’s 10 – Ten people who mattered this year – Nature

[hr]

December 16, 2015 #2

Posted on by

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

General human microbiome

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

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

Pregnancy and birth (and vaginal microbiome)

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

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

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

Human oral microbiome

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

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

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

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

Human skin microbiome

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

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

Human gut microbiome

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

Model microbiome

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

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

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

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

Necrobiome: the microbiome of death

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

Animal microbiome

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

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

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

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

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

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

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

Plant, root, and soil microbiome

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

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

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

Bioreactor and waste microbiology

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

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

Bioinformatics and metagenomics

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

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

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

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

Microbes in the news

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

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

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

Science, publishing, and career

Plenty of moustaches but not enough women: cross sectional study of medical leaders – Mackenzie R Wehner – BMJ
[hr]

December 15, 2015

Posted on by

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

General microbiome

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

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

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

Pregnancy and birth

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

Human mouth/ear microbiome

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

Human gut microbiome

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

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

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

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

Microbiome models

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

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

Animal microbiome

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

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

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

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

Plant, root, and soil microbiome

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

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

Water and extremophile microbiome

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

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

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

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

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

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

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

Food microbiology

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

Built environment microbiology

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

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

Metagenomics, phages, and bioinformatics

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

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

Techniques

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

Biofilms

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

Microbes in the news

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

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

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

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

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

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

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

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

Science, publishing, and career

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

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

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

Why do scientists like anonymity? Lenny Teytelman – Protocols

[hr]

December 14, 2015

Posted on by

Not a lot of papers today; NCBI’s PubMed alerts has not come out for a couple of days (I will probably get an email tomorrow with 200 new papers…..). Today’s main paper is a not-very microbiological paper on the human gut metagenome.

Human gut microbiome

Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome – Volodymyr Kuleshov – Nature Biotechnology

Review: Microbiota–mitochondria inter-talk: consequence for microbiota–host interaction – Yann Saint-Georges-Chaumet – Pathogens and Disease

Animal microbiome

Toward a better understanding of mechanisms of probiotics and prebiotics action in poultry species – K. M. Ajuwon – Journal of Applied Poultry Research

Microbes in the news

Not sure what is stunning about the diversity they found but: Stunning diversity of gut bacteria uncovered by new approach to gene sequencing devised at Stanford – Jennie Dusheck – Stanford Medicine News Center

Bacteriophage: The Microscopic Black Market – Stefan Rollnick – Huffington Post

Intestinal bacteria are in command – Gemma K. Alderton – Nature Reviews Immunology

The bacteria among us – Jeffrey Perkel – Biotechniques

Antibiotic Use in Food Animals Continues to Rise: Soaring levels of drug use in livestock fuels concern about resistant bacteria, human health – Tom Polansek – Scientific American

Cambridge’s Seres targets ulcerative colitis with new drug based on gut bacteria – Don Seiffert – Boston Business Journal

Altered microbiome burns fewer calories – Study links changes in gut bacteria to lower resting metabolic rate and weight gain in mice – EurekAlert

“How microbial communities interact. It’s kind of like in economics”
Economies of Ail: How Bacteria Flourish – Jo Craven McGinty – Wall Street Journal (subscription required)
Shorter version here that does not require subscription:
Can economics explain our gut microbiome? – Genetic Literacy Project

World’s First Microbiome Fund Swells to €160M With Major Pharma Also Chipping In – LabioTech

Science, publishing, and career

Law ignored, patients at risk: failure to report results of human studies to ClinicalTrials.gov database – Charles Piller – STAT news
[hr]

December 13, 2015

Posted on by

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

Human gut microbiome

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

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

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

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

Animal models

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

Plant, root, and soil microbiome

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

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

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

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

Water and extremophile microbiome

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

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

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

Metagenomics and bioinformatics

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

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

Techniques

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

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

Microbes in the news

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

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

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

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

Bacteria Hysteria

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

[hr]

December 11, 2015

Posted on by

Mammalian corpse decomposition – beautiful work by Jessica Metcalf.

Microbiome of death

Microbial community assembly and metabolic function during mammalian corpse decomposition – Jessica L. Metcalf – Science

Human oral microbiome

Review: Oral microbiome, periodontitis and risk of head and neck cancer – Leonardo Victor Galvão-Moreira – Oral Oncology

Review: The emerging landscape of salivary diagnostics – Yong Zhang – Periodontology 2000

Review: Influence of saliva on the oral microbiota – Philip D. Marsh – Periodontology 2000

Human skin microbiome

OK, not microbial, but entertaining: A comparative clinical study of different hair removal procedures and their impact on axillary odor reduction in men – Anthony Lanzalaco – Journal of Cosmetic Dermatology

Human respiratory microbiome

Correspondence: Potential roles of disordered airway microbiota in patients with severe asthma – Zongxin Ling – Journal of Allergy and Clinical Immunology

Human gut microbiome

Stress and the Microbiota–Gut–Brain Axis in Visceral Pain: Relevance to Irritable Bowel Syndrome – Rachel D. Moloney – CNS Neuroscience & Therapeutics

Review: SLE: Another Autoimmune Disorder Influenced by Microbes and Diet? – Qinghui Mu – Frontiers in Immunology

Review: The Intestinal Microbiome and the Liver Transplant Recipient: What We Know
and What We Need to Know – Iliana Doycheva

Microbiome models

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

Can closed artificial ecosystem have an impact on insect microbial community? A case study of yellow mealworm (Tenebrio molitor L.) – Leyuan Li – Ecological Engineering

Plant, root, and soil microbiome

Increasing aridity reduces soil microbial diversity and abundance in global drylands – Fernando T. Maestre – PNAS

The interaction between iron nutrition, plant species and soil type shapes the rhizosphere microbiome – Youry Pii – Plant Physiology and Biochemistry

Nitrification and Nitrifying Bacteria in a Coastal Microbial Mat – Haoxin Fan – Frontiers in Microbiology

Diversity of Phytophthora Species from Declining Mediterranean Maquis Vegetation, including Two New Species, Phytophthora crassamura and P. ornamentata sp. nov. – Bruno Scanu – PLOS ONE

Algae–bacteria interactions: Evolution, ecology and emerging applications – Rishiram Ramanan – Biotechnology Advances

Water microbiome

Particle-Associated Differ from Free-Living Bacteria in Surface Waters of the Baltic Sea – Angelika Rieck – Frontiers in Microbiology

The global ocean microbiome – Mary Ann Moran – Science

Hypothesis: Fractal Hypothesis of the Pelagic Microbial Ecosystem—Can Simple Ecological Principles Lead to Self-Similar Complexity in the Pelagic Microbial Food Web? – Selina Våge – Frontiers in Microbiology

Food microbiology

Microbiome profiling in fresh-cut products – Chiara Gorni – Trends in Food Science & Technology

FoodMicrobionet: A database for the visualisation and exploration of food bacterial communities based on network analysis – Eugenio Parente – International Journal of Food Microbiology

Bioinformatics and metagenomics

The MG-RAST metagenomics database and portal in 2015 – Andreas Wilke – Nucleic Acids Research

Infection and transplantation

The Interplay of Host Microbiota and Parasitic Protozoans at Mucosal Interfaces: Implications for the Outcomes of Infections and Diseases – Ann-Katrein Bär – PLOS Neglected Tropical Diseases

Viruses and phages

The role of viruses in the evolution of cyanobacteria – S. V. Shestakov – Biology Bulletin Reviews

Microbes in the news

Thousands of unexpected microbes break down our bodies after death – Elizabeth Pennisi – Science
Meet the Necrobiome: The Waves of Microbes That Will Eat Your Corpse – Ed Yong – The Atlantic
Tiny Witnesses: Microbes Can Tell When A Murder Victim Died – Rob Stein – NPR

New Superbug Resistant To All Antibiotics Linked To Imported Meat – Judy Stone – Forbes

Chipotle, E. coli, and more: The surprising truths about food-borne illnesses – Sheila Kaplan – STAT news

What Your Microbiome Wants for Dinner – David R Montgomery and Anne Bikle

Bacteria engineered with synthetic circadian clocks – EurekAlert

Melanoma Meets Microbiome – Kenneth Y. Tsai – NEJM Journal Watch

Can the health of a pregnant woman’s gut influence her baby? – Massey University

Science, publishing, and career

Making the most of the postdoc experience – Lorena Escudero – Frontiers Blog

Should post-publication peer review be anonymous? The PubPeer organisers and two other scholars debate the merits and pitfalls of anonymity in peer review – Times Higher Education

No evidence that gender contributes to personal research funding success in The Netherlands: A reaction to van der Lee and Ellemers – PNAS

[hr]

December 10, 2015

Posted on by

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

General microbiome

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

Human gut microbiome

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

Microbiome models

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

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

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

Plant, root, and soil microbiome

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

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

Water and extremophile microbiome

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

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

Infection and transplantation microbiology

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

Built environment microbiology

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

Bioinformatics and metagenomics

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

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

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

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

Getting the Hologenome Concept Right – Seth Bordenstein – Symbionticism

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

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

Illumina Invests in Four Startups Through Accelerator Program – Genome Web

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

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

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

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

Science, publishing, and career

Blog, tweet, and avoid the pitfalls – Sharon Ann Holgate – Science
[hr]

December 8, 2015

Posted on by

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

General microbiome

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

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

Pregnancy and birth

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

Human respiratory microbiome

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

Human oral microbiome

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

Human skin microbiome

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

Human gut microbiome

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

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

Animal and bioreactor models

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

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

Animal microbiome

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

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

Plant, root, and soil microbiome

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

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

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

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

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

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

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

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

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

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

Water and extremophile microbiome

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

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

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

Waste treatment

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

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

Food microbiology

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

Metagenomics and bioinformatics

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

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

Microbes in the news

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

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

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

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

Fall into Fungi – Alex Alexiev – MicroBEnet

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

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

Cooperating bacteria isolate cheaters – Phys.org

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

Bacteria Hysteria

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

Science, publication, and career

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

[hr]