January 11, 2016

Bacteria in breastmilk, nose/skin bacteria preventing pneumococcal infection, biofilms on pig carcasses in flowing water, Jurassic microbial mats, and Comammox Nitrospira-like bacteria in drinking water.

Pregnancy and birth

Characterization of bacterial isolates from the microbiota of mothers’ breast milk and their infants – Kimberly Kozak – Gut Microbes

Review: Association Between the Gut Microbiota and Diet: Fetal Life, Early Childhood, and Further Life – D.A. Kashtanova – Nutrition

Human nose/skin microbiome

Corynebacterium accolens Releases Antipneumococcal Free Fatty Acids from Human Nostril and Skin Surface Triacylglycerols – Lindsey Bomar – mBio

Human gut microbiome

A dysbiotic subpopulation of alcohol-dependent subjects – Philippe de Timary – Gut Microbes

Colorectal cancer: role of commensal bacteria and bystander effects – Xingmin Wang – Gut Microbes

Review: Gut inflammation and microbiome in spondyloarthritis – Jayakanthan Kabeerdoss – Rheumatology International

Review: Gut Microbiota and Celiac Disease – Giovanni Marasco – Digestive Diseases and Sciences

Animal models

Pglyrp-Regulated Gut Microflora Prevotella falsenii, Parabacteroides distasonis and Bacteroides eggerthii Enhance and Alistipes finegoldii Attenuates Colitis in Mice – Roman Dziarski – PLOS ONE

Plant, root, and soil microbiome

Dynamics of viral abundance and diversity in a Sphagnum-dominated peatland: temporal fluctuations prevail over habitat – Flore C. Ballaud – Frontiers in Microbiology

Distribution of Root-Associated Bacterial Communities Along a Salt-Marsh Primary Succession – Miao Wang – Frontiers in Plant Science

Early Jurassic microbial mats – a potential response to reduced biotic activity in the aftermath of the end-Triassic mass extinction event – Olof Peterffy – Palaeogeography, Palaeoclimatology, Palaeoecology

Water and extremophile microbiome

Microbial Biofilm Community Variation in Flowing Habitats: Potential Utility as Bioindicators of Postmortem Submersion Intervals – Jennifer M. Lang – Microorganisms

Effect of water chemistry on zooplanktonic and microbial communities across freshwater ecotones in different macrophyte-dominated shallow lakes – Tomasz Mieczan – Journal of Limnology

Influences of microbial communities on groundwater component concentrations during managed artificial recharge – Wenjing Zhang – Environmental Earth Sciences

Complete metagenome sequencing based microbial diversity insights from Deccan basaltic hot spring of Unkeshwar, Maharashtra, India – Gajanan T. Mehetre – Genomics Data

Perspective: Unraveling the Functions of the Macroalgal Microbiome – Ravindra Pal Singh – Frontiers in Microbiology

Built environment and waste microbiome

Metagenomic Evidence for the Presence of Comammox Nitrospira-Like Bacteria in a Drinking Water System – Ameet J. Pinto – mSphere

Proteolytic bacterial dominance in a full-scale municipal solid waste anaerobic reactor assessed by 454 pyrosequencing technology – Juliana Cardinali-Rezende – Chemosphere

Food microbiology

Microbial dynamics during shelf-life of industrial Ricotta cheese and identification of a Bacillus strain as a cause of a pink discolouration – E. Sattin – Food Microbiology

Microbes in the news

Outbreaks of Salmonellosis from Small Turtles – Maroya Spalding Walters – Pediatrics

Many of these are amazing because of microbes: 17 of the world’s weirdest water features – Marnie Hunter – CNN

Study details how good bacteria might help prevent middle ear infections and pneumonia – EurekAlert

Study: Bacteria, electrons spin in similar patterns. Bacteria streaming through a lattice behave like electrons in a magnetic material – EurekAlert
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December 23, 2015

Posted on December 23, 2015 by eliesbik

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
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December 16, 2015 #2

Posted on December 16, 2015 by eliesbik

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

General human microbiome

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

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

Pregnancy and birth (and vaginal microbiome)

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

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

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

Human oral microbiome

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

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

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

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

Human skin microbiome

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

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

Human gut microbiome

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

Model microbiome

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

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

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

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

Necrobiome: the microbiome of death

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

Animal microbiome

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

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

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

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

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

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

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

Plant, root, and soil microbiome

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

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

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

Bioreactor and waste microbiology

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

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

Bioinformatics and metagenomics

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

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

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

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

Microbes in the news

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

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

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

Science, publishing, and career

Plenty of moustaches but not enough women: cross sectional study of medical leaders – Mackenzie R Wehner – BMJ
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December 11, 2015

Posted on December 11, 2015 by eliesbik

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

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November 25, 2015

Posted on November 25, 2015 by eliesbik

My apologies for 2 missed posts (due to overseas family circumstances). Gut microbiota of infants with botulism, gut microbial diversity in US Midwest population, decomposing pig carcasses, oil-degrading microbes and sunlight.

Events

5th Annual Microbiology of the Built Environment Conference – June 1-3 2016, Boulder, CO

Jobs

Our lab at Stanford University is hiring a Clinical Study Coordinator to be based out of UCSF School of Dentistry. Great position for someone who eventually wants to go to medical or dental school.

Pregnancy and birth

The relationship between early-life environment, the epigenome and the microbiota – Amber V Majnik – Epigenomics

Human oral microbiome

The impact of different DNA extraction methods on the analysis of microbial diversity of oral saliva from healthy youths by polymerase chain reaction-denaturing gradient gel electrophoresis – Ming Chen – Journal of Dental Sciences

Human gut microbiome

Characterizing the fecal microbiota of infants with botulism – T. Brian Shirey – Microbiome

Early-Life Exposure to Antibiotics, Alterations in the Intestinal Microbiome, and Risk of Metabolic Disease in Children and Adults – Sushmita G. Yallapragada – Pediatric Annals

Impact of demographics on human gut microbial diversity in a US Midwest population – Jun Chen – PeerJ Preprint

Review: Feeding the brain and nurturing the mind: Linking nutrition and the gut microbiota to brain development – Manu S. Goyal – PNAS

Review: Metagenomic cross-talk: the regulatory interplay between immunogenomics and the microbiome – Maayan Levy – Genome Medicine

Review: The relationship between early-life environment, the epigenome and the microbiota – Amber V Majnik – Future Medicine

Microbiome models

Gut Commensal E. coli Proteins Activate Host Satiety Pathways following Nutrient-Induced Bacterial Growth – Jonathan Breton – Cell Metabolism

Plant, root, and soil microbiome

From Rare to Dominant: A Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation – Sebastián Fuentes – Applied and Environmental Microbiology

Metabarcoding analysis of Phytophthora diversity using genus specific primers and 454 pyrosequencing – Maria I Prigigallo – Phytopathology

Structures of microbial communities in alpine soils: seasonal and elevational effects – Anna Lazzaro – Frontiers in Microbiology

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

The community structures of prokaryotes and fungi in mountain pasture soils are highly correlated and primarily influenced by pH – Anders Lanzen – Frontiers in Microbiology

Water microbiome

Application of Microfluidic QPCR (MFQPCR) Technique to Monitor Bacterial Pathogens in Beach Water and Complex Environmental Matrices – Muruleedhara Byappanahalli – Environmental Science & Technology Letters

Natural sunlight shapes crude oil-degrading bacterial communities in northern Gulf of Mexico surface waters – Hernando P. Bacosa – Frontiers in MIcrobiology

Bacterioplankton community resilience to ocean acidification: evidence from microbial network analysis – Yu Wang – ICES Journal of Marine Sciences

Microbial Diversity and Bioactive Substances in Disease Suppressive Composts from India – C. M. Mehta – Compost Science & Utilization

Extremophile microbiome

Microbial metagenomics of oil sands tailings ponds: small bugs, big data – Julia M. Foght – Genome

Built environment microbiome

Changes in Microbes of the Built Environment in Early Stages of Urbanization – Maria Gloria Dominguez-Bello

Microbiome of death

The impact of carrion decomposition on the fatty acid methyl ester (FAME) profiles of soil microbial communities in southern Canada – Heloise Breton – Canadian Society of Forensic Science Journal

Metagenomics and bioinformatics

Assembly: a resource for assembled genomes at NCBI – Nucleic Acid Research

Web Resources for Metagenomics Studies – Pravin Dudhagara – Genomics, Proteomics & Bioinformatics

Metagenome Analysis Exploiting High-Throughput Chromosome Conformation Capture (3C) Data – Martial Marbouty – Trends in Genetics

EBI metagenomics in 2016 – an expanding and evolving resource for the analysis and archiving of metagenomic data – Alex Mitchell – Nucleic Acids Research

probeBase—an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016 – Daniel Greuter – Nucleic Acids Research

Microbial ecology / more microbiology

Review: Microbial Invasions: The Process, Patterns, and Mechanisms – Cyrus Alexander Mallon – Trends in Microbiology

Review: Microbial diversity — exploration of natural ecosystems and microbiomes –
Sean M Gibbons – Current Opinion in Genetics & Development

Microbes As Friends, Not Foes: Shifting the Focus from Pathogenesis to Symbiosis – Sheila A. Homburger – The American Biology Teacher

Microbes in the news

Leading Antibiotic Doomsayer Mellows on Infection Armageddon – Michael Byrne – Motherboard
and
I believed we would face an antibiotics apocalypse – until now – Richard James – The Guardian

Tardigrades: Inside the Bizarre Genome of the World’s Toughest Animal – Ed Yong – The Atlantic

C&EN Talks With Microbiome Surveyor Stefanie Kandels-Lewis: The laboratory technician turned fixer kept the Tara Oceans project, an expedition to map the oceans’ microbial populations, afloat for four years – Sarah Everts – C&EN

Kiwi scientists invent stomach ulcer cure – Olivia Wannan – Stuff NZ

A Doctor Wrestles With Whether To Keep Wearing His White Coat – John Henning Schumann – NPR

When will the world wake up to the potential of poo power? – John Vidal – The Guardian

At TEDMED 2015: How microbiome studies could improve the future of humanity – ScopeBlog

Two Types of Diet May Protect Against Type 2 Through Regulation of Gut Microbiota – Diabetes in Control

Symberix lands two SBIRs for GI drug that targets the microbiome – Meghana Keshavan – MedCity News

Diet study overturns all we know about healthy eating – Israel21c

Liberia monitors over 150 Ebola contacts as virus re-emerges – James Harding Giahyue – Reuters

Now We Can Use Microbes to Make Designer Chocolate Flavors – Esther Inglis-Arkell – Gizmodo

Fossils show sign of ancient vampire microbes – Punctures in fossils suggest predation drove the evolution of self-defense systems – Thomas Sumner – Student Science

Science, publishing and career

Stepping Away from the Lab:Emilie, Can I Ask You? Why I made the decision to leave academic research and become an editor.- Cell

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September 24, 2015

Posted on September 24, 2015 by eliesbik

Human genetic variation and microbiome composition, turmeric & travel, Nicotiana recruitment, and microbial stress in the city.

General microbiome

Editorial: Host genetic architecture and the landscape of microbiome composition: humans weigh in – Andrew K Benson – Genome Biology

Host genetic variation impacts microbiome composition across human body sites
Ran Blekhman – Genome Biology

Database of host-pathogen and related species interactions, and their global distribution – Maya Wardeh – Scientific Data

Pregnancy and birth

The role of breast-feeding in infant immune system: a systems perspective on the intestinal microbiome – Paurush Praveen – Microbiome

The role of infection in miscarriage – Sevi Giakoumelou – Human Reproduction Update

Human gut microbiome

The Effect of Probiotics on Gut Microbiota during the Helicobacter pylori Eradication: Randomized Controlled Trial – Bumjo Oh – Helicobacter

Intestinal microbial communities associated with acute enteric infections and disease recovery – Pallavi Singh – Microbiome

Review: Advancing gut microbiome research using cultivation – Morten OA Sommer – Current Opinion in Microbiology

Human urinary tract microbiome

Re: The Microbiome of the Urinary Tract—A Role Beyond Infection – Alan J. Wein – The Journal of Urology

Animal models

Modulation of gut microbiota by berberine and metformin during the treatment of high-fat diet-induced obesity in rats – Xu Zhang – Scientific Reports

A small-molecule antivirulence agent for treating Clostridium difficile infection – Kristina Oresic Bender – Science Translational Medicine

Regulators of Gut Motility Revealed by a Gnotobiotic Model of Diet-Microbiome Interactions Related to Travel – Neelendu Dey – Cell

Animal microbiome

High-throughput DNA sequencing of the moose rumen from different geographical
location reveals a core ruminal methanogenic archaeal diversity and a differential
ciliate protozoal diversity – Suzanne Lynn Ishaq – Microbial Genomics

Microbial populations and fermentation profiles in rumen liquid and solids of Holstein cows respond differently to dietary barley processing – Barbara U. Metzler-Zebeli – Journal of Applied Microbiology

Culture based: Actinomycetes from the South China Sea sponges: isolation, diversity and potential for aromatic polyketides discovery – Zhiyong Li – Frontiers in Microbiology

Longitudinal study of the early-life fecal and nasal microbiotas of the domestic pig – Mackenzie Jonathan Slifierz – BMC Microbiology

Faecal microbiota characterisation of horses using 16 rdna barcoded pyrosequencing, and carriage rate of clostridium difficile at hospital admission – Cristina Rodriguez – BMC Microbiology

Essential Amino Acid Supplementation by Gut Microbes of a Wood-Feeding Cerambycid – Paul A. Ayayee – Environmental Entomology

Plant, root, and soil microbiome

RhizoFlowCell system reveals early effects of micropollutants on aquatic plant rhizosphere – Kalyan Chakravarthy Mynampati – Environmental Pollution

Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by geographic features – Kayla N. Burns – Soil Biology and Biochemistry

Nicotiana Roots Recruit Rare Rhizosphere Taxa as Major Root-Inhabiting Microbes – Muhammad Saleem – Plant Microbe Interactions

Planting increases the abundance and structure complexity of soil core functional genes relevant to carbon and nitrogen cycling – Feng Wang – Scientific Reports

The coupling of the plant and microbial catabolisms of phenanthrene in the rhizosphere of Medicago sativa – Anna Muratova – Journal of Plant Physiology

Contrasting soil bacterial community structure between the phyla Acidobacteria and Proteobacteria in tropical Southeast Asian and temperate Japanese forests – Naohiko T. Miyashita – Genes & Genetic Systems

Review: Ecological importance of soil bacterivores for ecosystem functions – Jean Trap – Plant and Soil

Editorial: Microbial ecology of hydrocarbon-polluted coastal sediments – Robert Duran – Environmental Science and Pollution Research

Waste microbiology

Identification of Bacteria Synthesizing Ribosomal RNA in Response to Uranium Addition During Biostimulation at the Rifle, CO Integrated Field Research Site – Lora R. McGuinness – PLOS ONE

Microbial ecology of hydrocarbon-polluted coastal sediments – Robert Duran – Environmental Science and Pollution Research

Built environment microbiome

Urban stress is associated with variation in microbial species composition-but not richness-in Manhattan – Aspen T Reese – ISME Journal

Microbiome of death

The Search for a Volatile Human Specific Marker in the Decomposition Process – E. Rosier – PLOS ONE

Bioinformatics and metagenomics

In silico identification of bacteriocin gene clusters in the gastrointestinal tract, based on the Human Microbiome Project’s reference genome database – Calum J. Walsh – BMC Microbiology

PhD thesis: Novel methods for comparing and evaluating single and metagenomic assemblies – Christopher M. Hill – University of Maryland

Microbes in the news

Metagenomic Sequencing Shows Changes in Healthy Gut Microbiome Pre- and Post-Antibiotics – Genome Web

Study shows whale microbiome shares characteristics with both ruminants and predators – Phys.org

Researchers isolate the ‘human smell of death’ – Elizabeth Pennisi – Science

Scientists find way to disarm deadly bacteria without destroying the good ones in your gut – Lena H. Sun – Washington Post

Science, publishing, and career

Failure to replicate the STAP cell phenomenon – Alejandro De Los Angeles – @nature

Make academic job advertisements fair to all: Too many university posts are given to men without proper competition – Mathias Wullum Nielsen – Nature

Gender-disparity study faces attack: A paper suggesting a Dutch grant scheme shows bias against women is criticized for a statistical flaw – Chris Woolston

Bik’s Picks

In the name of beauty: phasing out plastic microbeads found in skin scrubs – Nature

How Climate Change Shrank the Tongues of Long-Tongued Bumblebees – Ed Yong

Enamel evolved in the skin and colonized the teeth much later – EurekAlert

Giant Killer Lizards Lived Among Ice-Age Aussies – Discovery
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September 22, 2015

Posted on September 22, 2015 by eliesbik

Effect of hookworm infection on microbiome of celiac subjects, neutrophil ageing, altering the bone niche, and a personal microbial cloud.

Pregnancy and birth

Influence of a combination of probiotics on bacterial infections in very low birthweight newborns – Zlatka Kanic – Wiener klinische Wochenschrift

Microbiome of death

High-throughput nucleotide sequence analysis of diverse bacterial communities in leachates of decomposing pig carcasses – Seung Hak Yang – Genetics and Molecular Biology

Human respiratory tract microbiome

Investigation of bacterial repopulation after sinus surgery and perioperative antibiotics – Leah J. Hauser – International Forum of Allergy & Rhinology

Human oral microbiome

Comparison of Subgingival and Peri-implant Microbiome in Chronic Periodontitis – Zhang, Qian – Chinese Journal of Dental Research

The novel association between red complex of oral microbe and body mass index in healthy Japanese: a population based cross-sectional study – Kanae Matsushita – Journal of Clinical Biochemistry and Nutrition

Human gut microbiome

The relationship between faecal-associated and mucosal-associated microbiota in irritable bowel syndrome patients and healthy subjects – I. Rangel – Alimentary Pharmacology & Therapeutics

Experimental hookworm infection and escalating gluten challenges are associated with increased microbial richness in celiac subjects – Paul Giacomin – Scientific Reports

Effect of administering a multi-species probiotic mixture on the changes in fecal microbiota and symptoms of irritable bowel syndrome: a randomized, double-blind, placebo-controlled trial – Hyuk Yoon – Journal of Clinical Biochemistry and Nutrition

Review: Improving healthspan via changes in gut microbiota and fermentation – Michael J. Keenan – AGE

Review: Gastric Microbiota – Gianluca Ianiro – Helicobacter

Thesis: High-resolution analysis of the human intestinal microbiota stability landscape – Tineka Blake – Aalto University

Animal models

An integrated metabonomics and microbiology analysis of host-microbiota metabolic interactions in rats with Coptis chinensis-induced diarrhea – Yemeng Li – RCS Advances

Microbiota from Obese Mice Regulate Hematopoietic Stem Cell Differentiation by Altering the Bone Niche – Yubin Luo – Cell Metabolism

The levonorgestrel-releasing intrauterine system is associated with delayed endocervical clearance of Chlamydia trachomatis without alterations in vaginal microbiota – E.R. Liechty – Pathogens and Disease

Goldfish: Correlations of Gut Microbial Community Shift with Hepatic Damages and Growth Inhibition of Carassius auratus Induced by Pentachlorophenol Exposure – Haifeng Kan – Environmental Science & Technology

Neutrophil ageing is regulated by the microbiome – Dachuan Zhang – Nature

Animal microbiome

Diversity analysis of diazotrophs associated with corals from Xisha and Sanya, South China Sea – Qingsong Yang – Aquatic Ecosystem Health & Management

Characterization of the Skin Microbiota in Italian Stream Frogs (Rana italica) Infected and Uninfected by a Cutaneous Parasitic Disease – Ermanno Federici – Microbes and Environments

Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression –
Jia Y. Har – Frontiers in Microbiology

Plant, root, and soil microbiome

Endophytic bacterial communities associated with two explant sources of Eucalyptus benthamii Maiden & Cambage – Natalia Pimentel Esposito-Polesi – World Journal of Microbiology and Biotechnology

Endospores, prokaryotes, and microbial indicators in arable soils from three long-term experiments – Paulina Tamez-Hidalgo – Biology and Fertility of Soils

Namib Desert dune/interdune transects exhibit habitat-specific edaphic bacterial communities – Sandra Ronca – Frontiers in Microbiology

Responses of aromatic-degrading microbial communities to elevated nitrate in sediments –
Meiying Xu – Environmental Science & Technology

Climate change and physical disturbance cause similar community shifts in biological soil crusts – Scott Ferrenberg – PNAS

Water / Extremophile microbiome

Patchy-distributed ciliate (Protozoa) diversity of eight polar communities as determined by 454 amplicon pyrosequencing – Jae-Ho Jung – Animal Cells and Systems

Protist communities in a marine oxygen minimum zone off Costa Rica by 454 pyrosequencing – H. Jing – Biogeosciences Discussions

Built environment microbiome

Humans differ in their personal microbial cloud – James F. Meadow – PeerJ

Waste microbiology

Relationship between bacterial diversity and environmental parameters during composting of different raw materials – Xueqin Wang – Bioresource Technology

The sociality of bioremediation: Hijacking the social lives of microbial populations to clean up heavy metal contamination – Siobhan O’Brien, Angus Buckling – EMBO Reports

Culturing oil sands microbes as mixed species communities enhances ex situ model naphthenic acid degradation – Marc A. Demeter – Frontiers in Microbiology

Microbial Ecology

Predicting microbial traits with phylogenies – Marta Goberna and Miguel Verdú – The ISME Journal

Bioinformatics and metagenomics

Metagenomic reconstructions of bacterial CRISPR loci constrain population histories – Christine L Sun – The ISME Journal

CCLasso: correlation inference for compositional data through Lasso – Huaying Fang – Bioinformatics

Computational methodology for predicting the landscape of the human–microbial interactome region level influence – Edgar D. Coelho – Journal of Bioinformatics and Computational Biology

Techniques

Targeted single molecule mutation detection with massively parallel sequencing – Mark T. Gregory – Nucleic Acids Research

Micelle PCR reduces chimera formation in 16S rRNA profiling of complex microbial DNA mixtures – Stefan A. Boers – Scientific Reports

Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis – Thomas Briese – mBio

Microbes in the news

Wherever You Go, Your Personal Cloud Of Microbes Follows – Rob Stein – NPR

Former CEO knew about contamination, wrote “Just ship it”: 28 years for salmonella: Peanut exec gets groundbreaking sentence – Moni Basu – CNN

UGA microbiology researchers identify potential mechanism for neurodegenerative diseases – News Medical

Researchers find novel signature in the brains of children with cerebral malaria – EurekAlert

Science, publishing, and career

About annoying invitations to write papers in questionable journals and strategies how to handle those: You are invited to submit… – David Moher and Anubhav Srivastava – BMC Medicine

Bik’s Picks

8 trillion microbeads pollute U.S. aquatic habitats daily – Jareen Imam – CNN

Science Says This Is the Sound Giraffes Make – Alexandra Sifferlin – Time

I Am the Walrus: What 35,000 Walruses Tell Us About Our Future in Warming World – Miyoko Sakashita – Huffington Post

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August 25, 2015

Posted on August 25, 2015 by eliesbik

Microbiome of Polish Cemetery soil, microbiome and risk of Plasmodium infection, interactions between mouse gut microbiota, host Genetics and diet, and the microbiome of air at three different heights.

The microbiome of death

Microbiological Analysis of Necrosols Collected from Urban Cemeteries in Poland – Ireneusz Całkosiński – BioMed Research International

Book: Carrion Ecology, Evolution, and Their Applications – M. Eric Benbow – CRC Press

Pregnancy and birth

Review: Rate of establishing the gut microbiota in infancy has consequences for future health – Shaillay Dogra – Gut Microbes

Editorial with disturbing title: Can establishment of human microbiome be customized after birth with local traditions of first feed and intimate kissing? – Sarman Singh – Journal of Laboratory Physicians

Human oral microbiome

Alterations of the Subgingival Microbiota in Pediatric Crohn’s Disease Studied Longitudinally in Discovery and Validation Cohorts – Judith Kelsen – Inflammatory Bowel Diseases

Review: Human microbiome: From the bathroom to the bedside – Stephen Malnick, Ehud Melzer – World J Gastrointest Pathophysiol

Human gut microbiota / transcriptomics

Stool microbiota composition is associated with the prospective risk of Plasmodium falciparum infection – Shibu Yooseph – BMC Genomics

Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota – Guanhui Bao – Frontiers in Microbiology

The Fecal Virome of Children with Hand, Foot, and Mouth Disease that Tested PCR Negative for Pathogenic Enteroviruses – Piyada Linsuwanon – PLOS ONE

Review: Gut microbiota and allogeneic transplantation – Weilin Wang – Journal of Translational Medicine

Animal models

Interactions between Gut Microbiota, Host Genetics and Diet Modulate the Predisposition to Obesity and Metabolic Syndrome – Siegfried Ussar – Cell Metabolism

Physical Activity Differentially Affects the Cecal Microbiota of Ovariectomized Female Rats Selectively Bred for High and Low Aerobic Capacity – Tzu-Wen Liu – PLOS ONE

Animal microbiome

Isolation of oxalotrophic bacteria associated with Varroa destructor mites – M. Maddaloni – Letters in Applied Microbiology

Diversity of bacterial communities in the midgut of Bactrocera cucurbitae (Diptera: Tephritidae) populations and their potential use as attractants – Ashok B. Hadapad – Pest Management Science

Midgut bacterial communities in the giant Asian honeybee (Apisdorsata) across four developmental stages: a comparative study – Prakaimuk Saraithong – Insect Science

Bacterial communities associated with four ctenophore genera from the German Bight (North Sea) – Wenjin Hao – FEMS Microbial Ecology

Plant, root, and soil microbiome
(also see study above filed under Microbiome of Death)

The effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon – Wei H. Xu – Frontiers in Microbiology

Archaeal Communities in a Heterogeneous Hypersaline-Alkaline Soil – Yendi E. Navarro-Noya – Archaea

Molecular characterization of microbial communities in the rhizosphere soils and roots of diseased and healthy Panax notoginseng – Zhaoxiang Wu – Antonie van Leeuwenhoek

The diversity changes of soil microbial communities stimulated by climate, soil type and vegetation type analyzed via a functional gene array – Fu Chen – World Journal of Microbiology and Biotechnology

Water microbiome

Carbon fixation by basalt-hosted microbial communities – Beth N. Orcutt – Frontiers in Microbiology

Annual dynamics of North Sea bacterioplankton: Seasonal variability superimposes short-term variation – Judith Lucas – Microbiology Ecology

Ecology and Distribution of Thaumarchaea in the Deep Hypolimnion of Lake Maggiore –
Manuela Coci – Archaea

Viral and grazer regulation of prokaryotic growth efficiency in temperate freshwater pelagic environments – A.S. Pradeep Ram – FEMS Microbiology Ecology

Air / built environment microbiome

Vertical distribution of airborne bacterial communities in an Asian-dust downwind area, Noto Peninsula – Teruya Maki – Atmospheric Environment

Microbiological consequences of indoor composting – Alexandre Naegele – Indoor Air

Extremophiles

Response of the rare biosphere to environmental stressors in a highly diverse ecosystem (Zodletone spring, OK, USA) – Suzanne Coveley – PeerJ

Food microbiology

Wine fermentation microbiome: a landscape from different Portuguese wine appellations – Cátia Pinto – Frontiers in Microbiology

Difference of microbial community stressed in artificial pit muds for Luzhou-flavour liquor brewing revealed by multiphase culture-independent technology – Liqiang Zhang – Journal of Applied Microbiology

Monitoring of Yeast Communities and Volatile Flavor Changes During Traditional Korean Soy Sauce Fermentation – Young-Ran Song – Journal of Food Science

Bioreactor microbiology

Microbial community in a hydrogenotrophic denitrification reactor based on pyrosequencing – Hongyu Wang – Applied Microbiology and Biotechnology

Techniques and other microbiology

Application of iChip to Grow “Uncultivable” Microorganisms and its Impact on Antibiotic Discovery – Rinzhin T. Sherpa – Journal of Pharmacy & Pharmaceutical Sciences

Cultivating the uncultured: growing the recalcitrant cluster-2 Frankia strains – Maher Gtari – Scientific Reports

Isolation of Genetically Tractable Most-Wanted Bacteria by Metaparental Mating – Páraic Ó Cuív – Scientific Reports

Burkholderia bacteria infectiously induce the proto-farming symbiosis of Dictyostelium amoebae and food bacteria – Susanne DiSalvo – PNAS

Science, publishing, and career

A call to arms for women in science – Women’s Agenda
Microbes in the news

The Bacteria That Turn Amoebas Into Farmers – Ed Yong – National Geographic

Testers find twice as many ‘superbugs’ in conventional hamburger as organic ones – Lena H. Sun – Washington Post

Humans carry more antibiotic-resistant bacteria than animals they work with – Medical Xpress
[hr]

August 24, 2015

Posted on August 24, 2015 by eliesbik

Microbiome of death

Soil fungal community shift evaluation as a potential cadaver decomposition indicator –
Monica Chimutsa – Forensic Science International

Pregnancy and birth

Master Thesis – The Association of Necrotizing Enterocolitis with Integrons and Antibiotic Resistance Genes in the Gut Microbiota of Preterm Infants – Eva Lena F. Estensmo – Norwegian University of Life Sciences

Human respiratory microbiome

Regional Isolation Drives Bacterial Diversification within Cystic Fibrosis Lungs – Peter Jorth – Cell Host & Microbe

Quantitative analysis of pathogens in the lower respiratory tract of patients with chronic obstructive pulmonary disease – Huaying Wang – BMC Pulmonary Medicine

Animal microbiome

Evidence-based recommendations on storing and handling specimens for analyses of insect microbiota – Tobin J Hammer – Peer J

Path analyses of cross-sectional and longitudinal data suggest that variability in natural communities of blood-associated parasites is derived from host characteristics and not interspecific interactions – Carmit Cohen – Parasites & Vectors

Plant, root, and soil microbiome

Available nitrogen is the key factor influencing soil microbial functional gene diversity in tropical rainforest – Jing Cong – BMC Microbiology

Disentangling the ‘brown world’ faecal-detritus interaction web: dung beetle effects on soil microbial properties – Eleanor M. Slade – Oikos

Taxon-specific responses of soil microbial communities to different soil priming effects induced by addition of plant residues and their biochars – Peng Su – Journal of Soils and Sediments

Research Highlight: Root recruiting – Mirella Bucci – Nature Chemical Biology

Water microbiome

Habitat and water quality variables as predictors of community composition in an Indonesian coral reef: a multi-taxon study in the Spermonde Archipelago – Ana Rita Moura Polónia – Science of the Total Environment

Waste water microbiology

Persistence of Ebola Virus in Sterilized Wastewater – Kyle Bibby – Environmental Science & Technology Letters

Metagenomics and bioinformatics

MetaObtainer: A Tool for Obtaining Specified Species from Metagenomic Reads of Next-generation Sequencing – Weihua Pan – Interdisciplinary Sciences: Computational Life Sciences

Minimum Information about a Biosynthetic Gene cluster – Marnix H Medema – Nature Chemical Biology

Viruses

A protein domain-based view of the virosphere-host relationship – Aare Abroi – Biochimie

Microbes in the news

Add Lots of Microbes to ‘Me, Myself, and I’ – David Salisbury – Futurity

The Microbiome Is Science’s Hot New Kid – Anand Veeravagu and Tessa Anderman – The Daily Beast

Science Briefs: Topography of spinach leaf shelters bacteria – John Bordsen – Charlotte Observer

Inside N.C. Science: Bugs – and mates – attracted by body odor – Sarah Council – Charlotte Observer

Universal flu vaccine comes closer, scientists say – Michelle Roberts – BBC News

Science, publishing, and career

Here’s what two college doctors say freshman need to know – LaTasha Seliby and Ranit Mishori – Washington Post

Women, minorities still underrepresented in medical specialties – Megan Brooks – Reuters

Bik’s Picks

Japanese Spacecraft Delivers Mice, Booze and More to ISS – Sarah Lewin – NBC News

Biologists Have Spotted the First Wolf Pack in California in 100 Years – Marissa Fessenden – Smithsonian

Get the Bunsen burner out: It’s time to concoct dinner – Nancy Szokan – Washington Post

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Microbiome Digest – Bik's Picks

A daily digest of scientific microbiome papers, by the MD team. Founded by Elisabeth Bik, microbiome and science integrity consultant. Twitter: @microbiomdigest

Category Archives: Microbiome of Death

January 11, 2016

January 5, 2016

December 23, 2015

December 16, 2015 #2

December 11, 2015

November 25, 2015

September 24, 2015

September 22, 2015

August 25, 2015

August 24, 2015