Great news: the videos from the Stanford Microbiome Informatics Symposium talks are up! The symposium was held on May 27, and featured Rob Knight, Justin Sonnenburg, Ami Bhatt, David Relman, and Susan Holmes.
You can see videos of the talks here (click on the tab “Videos”).
Thanks, Somalee Datta, Ami Bhatt, Roger Winkelman and team for making this possible.
Circadian rhythm, resistant starch, mock communities, sea turtle microbiome, tea rhizosphere.
General microbiome
Review: The Metronome of Symbiosis: Interactions Between Microbes and the Host Circadian Clock – Elizabeth A. C. Heath-Heckman – Integrative & Comparative Biology
Human oral microbiome
Microbial Ecosystem Analysis in Root Canal Infections Refractory to Endodontic Treatment – Luiz Carlos Feitosa Henriques – Journal of Endodontics
Human gut microbiome
Impact of dietary resistant starch type 4 on human gut microbiota and immunometabolic functions – Bijaya Upadhyaya – Scientific Reports
Press: Essential Science: Taking on metabolic disorders with starch – Tim Sandle – Digital Journal
Editorial: serologic microbial-associated markers to predict Crohn’s disease behaviour – A. G. Fraser – Alimentary Pharmacology & Therapeutics
Review: Microbiota and Liver – Kazumichi Abe – The Liver in Systemic Diseases
Animal experiments
A Role for Timp3 in Microbiota-Driven Hepatic Steatosis and Metabolic Dysfunction – Maria Mavilio – Cell Reports
Animal microbiome
A first insight into the gut microbiota of the sea turtle Caretta caretta – Khaled F. Abdelrhman – Frontiers in Microbiology
News and views: Co-evolution of marine worms and their chemoautotrophic bacterial symbionts: unexpected host switches explained by ecological fitting? – A. Brune – Molecular Ecology
Bacterial communities of oceanic sea star (Asteroidea: Echinodermata) larvae – Madeline R. Galac – Marine Biology
Gut bacteria differentially affect egg production in the anautogenous mosquito Aedes aegypti and facultatively autogenous mosquito Aedes atropalpus (Diptera: Culicidae) – Kerri L. Coon – Parasites & Vectors
Review: Better with your parasites? Lessons for behavioural ecology from evolved dependence and conditionally helpful parasites – Kelly L. Weinersmith – Animal Behaviour
Plant, root, and soil microbiome
Response of soil properties and microbial communities to agriculture: Implications for primary productivity and soil health indicators – Pankaj Trivedi – Frontiers in Plant Science
Variations of rhizosphere bacterial communities in tea (Camellia sinensis L.) continuous cropping soil by high-throughput pyrosequencing approach – Yanchun Li – Journal of Applied Microbiology
Water and extremophile microbiome
Oil sands tailings ponds harbour a small core prokaryotic microbiome and diverse accessory communities – S.L. Wilson – Journal of Biotechnology
The Ocean Microbiome: Metabolic Engine of the Marine Carbon Cycle – Elizabeth B. Kujawinski – Microbe
Biofilms
Relevant for Cystic Fibrosis: Temperate phages both mediate and drive adaptive evolution in pathogen biofilms – Emily V. Davies – PNAS
Press: Tiny viruses speed-up evolution of bacteria causing infections in cystic fibrosis patients – News Medical
Techniques
Droplet barcoding for massively parallel single-molecule deep sequencing –
Freeman Lan – Nature Communications
Transcriptomics
Comparative transcriptomics across the prokaryotic tree of life – Ofir Cohen – Nucleic Acids Research
Bioinformatics and metagenomics
PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial datasets – Shareef M. Dabdoub – Scientific Reports
Optimization of 16S amplicon analysis using mock communities: implications for
estimating community diversity – Andrew Krohn – PeerJ
Benchmarking of methods for identification of antimicrobial resistance genes in bacterial whole genome data – Philip T. L. C. Clausen – Journal of Antimicrobial Chemotherapy
A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies – Shalabh Thakur – BMC Bioinformatics
Editorial: Nucleic Acids Research annual Web Server Issue in 2016 – Nucleic Acids Research
Happy 4th! Since most folks in the US are firing up the BBQ today, here is a very short Digest. Make sure to read Alexandra Carmichael’s piece on the connection between microbes and Independence Day.
Human gut microbiome
Gut Microbiota Developments With Emphasis on Inflammatory Bowel Disease: Report From the Gut Microbiota for Health World Summit 2016 – Hester Eppinga – Gastroenterology
Review: Targeting the ecology within: The role of the gut–brain axis and human microbiota in drug addiction – Patrick D. Skosnik – Medical Hypotheses
Plant, root, and soil microbiome
Biogeographic distribution patterns of bacteria in typical Chinese forest soils – Zongwei Xia – Frontiers in Microbiology
A diverse soil microbiome degrades more crude oil than specialized bacterial assemblages obtained in culture – Terrence H. Bell – Applied and Environmental Microbiology
Crown galls of grapevine (Vitis vinifera) host distinct microbiota – Hanna Faist – Applied and Environmental Microbiology
Water microbiome
Environmental Breviatea harbour mutualistic Arcobacter epibionts – Emmo Hamann – Nature
Press: Research discovery may lead to new ways to treat bacterial disease. University researchers Marc Strous and Emmo Hamann part of international team exploring how microbes can be both friend and foe – Mark Lowey – UCalgary
Techniques
Effects of Specimen Collection Methodologies and Storage Conditions on the Short-Term Stability of Oral Microbiome Taxonomy – Ting Luo – Applied and Environmental Microbiology
Microbes in the news
The microbes that mark Independence Day – Alexandra Carmichael – uBiome
Subway system laden with harmless bacteria, researchers say. ‘I wouldn’t recommend licking the seats any time soon,’ Harvard professor says – Amina Zafar – CBC News
Bacteria ‘gardeners’ farm algae to harvest when food runs out – Andy Coghlan – New Scientist
More flour recalled as the FDA doubles down on cookie dough warning – Ars Technica
Bacteria Hysteria
Your Cell Phone is Covered in Germs! 5 Tips to Keep It Clean – Ryan Reed – HGTV
Happy Independence Day!
I have mentioned this before, but this website not only contains blog posts, but pages with more static information as well. These pages include lists that I compiled of important papers on particular microbiome topics. I call this my Microbiome Paper Collection, and they are listed as pages (not posts) under the Microbiome Collection button in the grey bar under the picture at the top of this page.
Tonight, I’ve updated the collections on the following topics:
Feel free to browse the Collection pages. The lists are not complete, but should be a good start for an overview of important papers. You can always let me know if I missed a paper by leaving a comment.
Colonic transit time, innovations in artificial gut systems, and how the majority of the human gut microbiome members can be cultured.
Human respiratory microbiome
Nasopharyngeal microbiota composition of children is related to the frequency of upper respiratory infection and acute sinusitis – Clark A. Santee – Microbiome
Metagenomics Study of Viral Pathogens in Undiagnosed Respiratory Specimens
and Identification of Human Enteroviruses at a Thailand Hospital – Yanfei Zhou – American Journal of Tropical Medicine and Hygiene
Review: The respiratory microbiome of HIV-infected individuals – MB Lawani – Expert Review of Anti-infective Therapy
Review: A tale of two sites: how inflammation can reshape the microbiomes of the gut and lungs – Brittan S. Scales – Journal of Leukocyte Biology
Human gut microbiome
Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut – Henrik M. Roager – Nature Microbiology
Behind the paper: How we got captivated by colonic transit time – Henrik Munch Roager – Nature Microbiology Community
Datafying microbes: Malnutrition at the intersection of genomics and global health – Amber Benezra – BioSocieties
Several reviews in the July issue of Therapeutic Advances in Gastroenterology:
The interplay between the microbiome and the adaptive immune response in cancer development – Edda Russo
The intestinal microbiome, barrier function, and immune system in inflammatory bowel disease: a tripartite pathophysiological circuit with implications for new therapeutic directions – Stephen M. Vindigni
Role of the gut microbiota in health and chronic gastrointestinal disease: understanding a hidden metabolic organ – Caitriona M. Guinane
Novel perspectives on therapeutic modulation of the gut microbiota – Justin L. McCarville
Review: The Brain-Body-Microbial Communities: A Crosstalk and Stress Exchange
Beyond the “Gut hypothesis” – Afifi Ma – Abnormal and Behavioural Psychology
Review: The Role of the Microbial Metabolites Including Tryptophan Catabolites and Short Chain Fatty Acids in the Pathophysiology of Immune-Inflammatory and Neuroimmune Disease – Gerwyn Morris – Molecular Neurobiology
Animal experiments
Relationship between the microbiota in different sections of the gastrointestinal tract, and the body weight of broiler chickens – Geon Goo Han – Springer Plus
The upper respiratory tract microbiome and its potential role in bovine respiratory disease and otitis media – Svetlana F. Lima – Scientific Reports
Review: Farewell to Animal Testing: Innovations on Human Intestinal Microphysiological Systems – Tae Hyun Kang – Micromachines
Plant, root, and soil microbiome
Effects of Short-Term Warming and Altered Precipitation on Soil Microbial Communities in Alpine Grassland of the Tibetan Plateau – Kaoping Zhang – Frontiers in Microbiology
Bacterial diversity in the rhizosphere of two phylogenetically closely related plant species across environmental gradients – Xiaofan Na – Journal of Soils and Sediments
Soil microbial communities of three major Chinese truffles in Southwest China – Yu Fu – Canadian Journal of Microbiology
Review: Ecology of nitrogen fixing, nitrifying and denitrifying microorganisms in tropical forest soils – Silvia Pajares – Frontiers in Microbiology
Water and extremophile microbiome
Metagenomic analysis of microbial community of an Amazonian geothermal spring in Peru – Sujay Paul – Genomics Data
Characterization of microbial mat microbiomes in the modern thrombolite ecosystem of Lake Clifton, Western Australia using shotgun metagenomics – John G. Warden – Frontiers in Microbiology
Built environment microbiome
Microbes in the Water Infrastructure: Underpinning Our Society – Takashi Narihiro – Microbes and Environments
Techniques / Metabolomics
Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling – Jennifer T. Lau – Genome Medicine
A Microbiome DNA Enrichment Method for Next-Generation Sequencing Sample Preparation – Erbay Yigit – Current Protocols in Molecular Biology
Sample preparation optimization in fecal metabolic profiling – Olga Deda – Journal of Chromatography B
Viruses and phages
Survival studies of a temperate and lytic bacteriophage in bovine faeces and slurry – Sepo Nyambe – Journal of Applied Microbiology
Microbes in the news
Conference report: Machine Learning Method Differentiates Between Healthy Male, Female Microbiomes: Topological Data Analysis – UC San Diego
A New Role for Marine Archaea. Researchers discover acetogenesis in archaea, suggesting an important role for these little-studied organisms in generating organic carbon below the seafloor – Catherine Offord – The Scientist
Stop worrying about GMOs; it’s that organic granola bar that could make you sick: Listeria – Henry I. Miller – LA Times
USM marine microbiologist Jay Grimes weighs in on vibrio vulnificus – WDAM
Chesterfield Royal scientists send ripples around the NHS – Andy Done-Johnson – Derbyshire Times
Efficiency in the pathology lab: Friend or Foe; the probiotic power of helminths can prevent Crohn’s Disease – Anouk Gouvras – BioMedCentral blog
Supplement may switch off cravings for high-calorie foods – Stephen Feller – UPI
Cravings for high-calorie foods may be switched off by new food supplement – Kate Wighton – Imperial College London
Science, publishing, and career
“He Thinks He’s Untouchable”: Michael Katze, famous for his studies of Ebola and the flu, ran a lab at the University of Washington where intoxication and sexual harassment went unchecked – Azeen Ghorayshi – Buzzfeed
These Beautiful Planets Are Actually Bacteria From Public Places – Photographs by Marco Castelli – Veriy
“Most of the photographs of microbes and bacteria” says Caterina Pacenti, project curator “have a scientific nature, adapted to detect and to emphasize the unique geometries that these are able to form. This time, however, the interest is not to show the invisible or what is hardly visible to the naked eye, but to use the natural shape of bacterial colonies to enlarge and project them into another dimension, reversing all logic and report between big and small, thus loading the planets, the universe and all the work of symbolic values.
Cat
Churchstep
Winners of the 2016 agar art competition – in Pictures – The Guardian Continue reading
NIH’s Lita Proctor writes about the Human Microbiome Project, oral microbiome among Cheyenne and Arapaho, Cystic Fibrosis, responses to resistant starch, the Swan Goose, sugarcane, litter decomposition.
General microbiome
Review: The National Institutes of Health Human Microbiome Project – Lita M. Proctor – Seminars in Fetal and Neonatal Medicine
Pregnancy and birth
Early-Life Events, Including Mode of Delivery and Type of Feeding, Siblings and Gender, Shape the Developing Gut Microbiota – Rocio Martin – PLOS ONE
Human oral microbiome
Oral microbiome diversity among cheyenne and arapaho individuals from Oklahoma – Andrew T. Ozga – American Journal of Physical Anthropology
Human respiratory microbiome
Pyrosequencing Unveils Cystic Fibrosis Lung Microbiome Differences Associated with a Severe Lung Function Decline – Giovanni Bacci – PLOS ONE
Human skin microbiome
The skin microbiome is different in pediatric versus adult atopic dermatitis –
Baochen Shi – Journal of Allergy and Clinical Immunology
Just colony counts: Chlorhexidine avoids skin bacteria recolonization more than triclosan – Juan H. Macias – American Journal of Infection Control
Human gut microbiome
Variable responses of human microbiomes to dietary supplementation with resistant starch – A. Venkataraman – Microbiome
Duodenal bacteria from patients with celiac disease and healthy subjects distinctly affect gluten breakdown and immunogenicity – Alberto Caminero – Gastroenterology
Predominance of Lactobacillus spp. among patients who do not acquire multidrug-resistant organisms – Rafael Araos – Clinical Infectious Diseases
Nutrition and the Microbiome: Special Edition of the Annals of the New York Academy of Sciences
Review: Nutrition and the microbiome – Karin Moelling
Review: Nutrition meets the microbiome: micronutrients and the microbiota – Hans K. Biesalski
Letter: Microbiota and Alcoholic Liver Disease – Peng Chen – Alcoholism: Clinical and Experimental Research
Animal experiments
Sex differences and hormonal effects on gut microbiota composition in mice – Elin Org – Gut Microbes
Animal microbiome
Distinctive gut microbial community structure in both the wild and farmed Swan goose (Anser cygnoides) – Wen Wang – Journal of Basic Microbiology
The gut microbiome of the sea urchin, Lytechinus variegatus from their natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles – Joseph A. Hakim – FEMS Microbiology Ecology
Analysis of microbiota on abalone (Haliotis discus hannai) in South Korea for improved product management – Min-Jung Lee – International Journal of Food Microbiology
Bacterial endosymbionts protect aphids in the field and alter parasitoid community composition – Lukas Rothacher – Ecology
Midgut fungal and bacterial microbiota of Aedes triseriatus and Aedes japonicus shift in response to La Crosse virus infection – Ephantus J. Muturi – Molecular Ecology
Plant, root, and soil microbiome
The importance of C, N and P as driver for bacterial community structure in German beech dominated forest soils – Fabian Bergkemper – Journal of Plant Nutrition and Soil Science
Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome – Rafael Soares Correa de Souza – Scientific Reports
Life in leaf litter: novel insights into community dynamics of bacteria and fungi during litter decomposition – Witoon Purahong – Molecular Ecology
Endophytic microbial diversity of the halophyte Arthrocnemum macrostachyum across plant compartments – M. del R. Mora-Ruiz – FEMS Microbiology Ecology
Conference abstract: High diversity of enzymes in plant-associated microbiomes – Christina A. Müller – New Biotechnology
Review: Plant-Mediated Systemic Interactions Between Pathogens, Parasitic Nematodes, and Herbivores Above- and Belowground – Arjen Biere – Annual Review of Phytopathology
Unearthed! The Amazing Microbiome Exposed: Editor’s Note – Stephen L. Young – Bulletin of the Ecological Society of America
Unearthed! The Amazing Microbiome Exposed: The Arising Researcher – Marnie E. Rout
Unearthed! The Amazing Microbiome Exposed: The Established Researcher – John Klironomos
Water microbiome
Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments – Benjamin J. Tully – Applied and Environmental Microbiology
Built environment microbiome
Evidence of Avian and Possum Fecal Contamination in Rainwater Tanks as Determined by Microbial Source Tracking Approaches – W. Ahmed – Applied and Environmental Microbiology
Factors Influencing Bacterial Diversity and Community Composition in Municipal Drinking Waters in the Ohio River Basin, USA – Lee F. Stanish – PLOS ONE
Microbes in space
Review: Venturing into new realms? Microorganisms in space – Christine Moissl-Eichinger – FEMS Microbiology Reviews
Techniques
Simultaneous purification of DNA and RNA from microbiota in a single colonic mucosal biopsy – Aina E. F. Moen – BMC Research Notes
Microbes in the news
The North American Beaver: Castor canadensis : A look at our local Canadian friend’s microbes – Megan McGrath – Genotek’s The Microbiome Snapshot
Human Microbiome Market : Growth, Development, and Outlook 2014 – 2020 – SB Wire
uBiome Completely Re-Imagines Microbiome Experimentation with New Launch – PR Web
Bacteria prevents mosquitoes from spreading Zika, UW-Madison study says – Wisconsin State Journal
Study sheds more light on how bacteria rapidly causes infectious diseases – News Medical
Gut bacteria spotted eating brain chemicals for the first time – Andy Coghlan – New Scientist
Large Grant to Research on Bacteria in the Nose – Statens Serum Institute
Science, publishing, and career
Great and funny read: Some things you need to know about Google Scholar – Mark Dingemans – Ideophone
Mycorrhizal fungi and CO2, pathogen defense in the gut, Mississippi River plume.
Animal experiments
Defensive Mutualism Rescues NADPH Oxidase Inactivation in Gut Infection – Gratiela Pircalabioru – Cell Host & Microbe
Press: Good gut relationships key in defence against pathogens – Medical Xpress
Plant, root, and soil microbiome
Mycorrhizal association as a primary control of the CO2 fertilization effect – César Terrer – Science
Press: Study finds that plant growth responses to high carbon dioxide depend on symbiotic fungi – EurekAlert
Grassland to woodland transitions: Dynamic response of microbial community structure and carbon use patterns – Courtney A. Creamer – Journal of Geophysical Research
The interaction between arbuscular mycorrhizal fungi and endophytic bacteria enhances plant growth of Acacia gerrardii under salt stress – Abeer Hashem – Frontiers in Microbiology
Water and extremophile microbiome
Mississippi River plume enriches microbial diversity in the northern Gulf of Mexico – Olivia U. Mason – Frontiers in Microbiology
Editorial: Anthropogenic impacts on the microbial ecology and function of aquatic environments – Maurizio Labbate – Frontiers in Microbiology
Unanticipated geochemical and microbial community structure under seasonal ice cover in a dilute, dimictic Arctic lake – Ursel Schuette – Frontiers in Microbiology
Comparative activity and functional ecology of permafrost soils and lithic niches in a hyper-arid polar desert – Jacqueline Goordial – Environmental Microbiology
Metagenomics and bioinformatics
Bioinformatic Characterization of Mosquito Viromes within the Eastern United States and Puerto Rico: Discovery of Novel Viruses – Kenneth G. Frey – Evolutionary Bioinformatics
Review: Reconstructing single genomes from complex microbial communities – Dongwan D. Kang – it-Information Technology
Review: A history of DNA sequence assembly – Eugene W. Myers Jr – it-Information Technology
Review: Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes – Miklós Bálint – FEMS Microbiology Reviews
Microbes in the news
Stanford undergrads cook up a biotech startup to develop new antibiotics for drug-resistant superbugs – Rosemary Mena-Werth – Stanford News
From the Evolution Conference, talk by Danielle Whittaker: Bacteria give bird its sexy smells – Patrick Monahan – Science
Australia’s Melbourne takes selfie of its microbiome – i4U News
The Microbiome and Bronchiolitis: An Unusual Pairing or Is It? – Lewis First – AAP Gateway
An Ounce of (Water) Prevention: microbial fuel degradation – Katherine Vanover – Fuel Market News
New study shows chronic fatigue isn’t just in your head. It may have to do with your gut – Ariana Eunjung Cha – Washington Post
Resistance to antibiotics and to immune system are interconnected in bacteria – EurekAlert
Researchers develop effective strategy for disrupting bacterial biofilms – EurekAlert
How a germ catches a virus – Phys.org
Coming Soon: Gut Bacteria That Actually Cure Your Disease: The $34 billion probiotics market includes some dubious products. This crop looks different – Deena Shanker – Bloomberg
TV weatherman retracts story about toxic bacteria at Northwest Florida beaches – The Destin Log
Bik’s non-microbiology Picks
Former Relman lab member: NASA Astronaut Kate Rubins Prepares for First Trip to Space – Alison Thoet – ABC News
107 Nobel laureates sign letter blasting Greenpeace over GMOs – Joel Achenbach – Washington Post
The Academic Hermit – What are you going to do with your tool?: installation as the Frederick G. Novy Collegiate Professor of Microbiome Research at the University of Michigan – Pat Schloss
Two new papers on multiple sclerosis and breast tissue, cross-respiration, the Boston urban transit microbiome, and plastic debris.
Human respiratory microbiome
Review: The respiratory microbiome of HIV-infected individuals – MB Lawawni – Expert Review of Anti-infective Therapy
Human skin microbiome
The microbiota of breast tissue and its association with tumours – Camilla Urbaniak – Applied and Environmental Microbiology
Human gut microbiome
Alterations of the human gut microbiome in multiple sclerosis – Sushrut Jangi – Nature Communications
Review: Gut microbiota and hematopoietic stem cell transplantation: where do we stand? – D Zama – Bone Marrow Transplantation
Review: The neuropharmacology of butyrate: The bread and butter of the microbiota-gut-brain axis? – Roman M. Stilling – Neurochemistry International
Animal and in vitro experiments
A Commensal Bacterium Promotes Virulence of an Opportunistic Pathogen via Cross-Respiration – Apollo Stacy – mBio
Press: Cross-respiration between oral bacteria leads to worse infections – EurekAlert
Microbiota-Regulated IL-25 Increases Eosinophil Number to Provide Protection during Clostridium difficile Infection – Erica L. Buonomo – Cell Reports
Animal microbiome
Genome-wide survey of gut fungi (Harpellales) reveals the first horizontally transferred ubiquitin gene from a mosquito host – Yan Wang – Molecular Biology and Evolution
In barn swallows: Stress response, gut microbial diversity and sexual signals correlate with social interactions – Iris I. Levin – Biology Letters
Plant, root, and soil microbiome
Plant Host and Geographic Location Drive Endophyte Community Composition in the Face of Perturbation – Natalie Christian – Microbial Ecology
Perspective: Soil immune responses – Jos M. Raaijmakers – Science
Water and extremophile microbiome
Microbes in mercury-enriched geothermal springs in western North America – Gill G. Geese – Science of The Total Environment
Environmental Disturbances Decrease the Variability of Microbial Populations within Periphyton – Cristina M. Herren – mSystems
Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments – Marina N. Mato – Environmental Microbiology
Built environment microbiome
Commentary: Avoiding Pandemic Fears in the Subway and Conquering the Platypus – A. Gonzalez – mSystems
Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment – Tiffany Hsu – mSystems
Press: ‘Bugs’ on the subway: Monitoring the microbial environment to improve public health – EurekAlert
Diversity and Activity of Communities Inhabiting Plastic Debris in the North Pacific Gyre – Jessica A. Bryant – mSystems
Food microbiology
Culture-independent bacterial community profiling of carbon dioxide treated raw milk – Raquel Lo – International Journal of Food Microbiology
Metagenomics and bioinformatics
MetaPalette: a k-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation – David Koslicki – mSystems
Bayesian identification of bacterial strains from sequencing data – Aravind Sankar – Microbial Genomics
MetaTreeMap: An Alternative Visualization Method for Displaying Metagenomic Phylogenic Trees – Maxime Hebrard – PLOS ONE
Proteomics and metabolomics
MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses – Ernesto S. Nakayasu – mSystems
An Integrated Metabolomic and Genomic Mining Workflow To Uncover the Biosynthetic Potential of Bacteria – Maria Maansson – mSystems
Techniques
16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform – Fiona Fouhy – BMC Microbiology
Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies – Se Jin Song – mSystems
Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes – Richard Allen White III – mSystems
A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses – Lindsey A. Moser- mSystems
Fungal identification biases in microbiome projects – Leho Tedersoo – Environmental Microbiology Reports
Microbes in the news
Germs in the Subway Are the Harmless Kind – Nicholas Bakalar – New York Times
An Industrial Microbiologist Who Adds Biofuel to the Fire – Nandita Jayaraj – The Wire India
Interview of Faculty of Clinical Microbiology, Prof. Generalov Igor Ivanovich, at VSMU, Belarus – LinkedIn
A fundraiser to study the turtle microbiome, multiple sclerosis, generalists inside specialist, and visualizing translational activity.
Events
IndieGoGo campaign: TurtleTracts: Study Microbes to Save Sea Turtles – Aubrey Tauer
Also see this blog post: Sneak Peak at our Sea Turtle Microbiome Initiative – Aubrey Tauer
Pregnancy and birth
Gut bacteria and late-onset neonatal bloodstream infections in preterm infants – Phillip I. Tarr – Seminars in Fetal and Neonatal Medicine
Human respiratory microbiome
Commentary: Mode of delivery to the brave new (microbial) world: a defining moment for the respiratory microbiome? – Georgios D. Kitsios – EBioMedicine
Human gut microbiome
Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls – Jun Chen – Scientific Reports
Press: Link between gut bacteria, MS discovered. MS patients show lower levels of good bacteria – Science Daily
Review: Microbiota as Therapeutic Targets – Xavier R.J. – Digestive Diseases
Animal microbiome
The Generalist Inside the Specialist: Gut Bacterial Communities of Two Insect Species Feeding on Toxic Plants Are Dominated by Enterococcus sp. – Cristina Vilanova – Frontiers in Microbiology
Review: The gut microbiome as a virtual endocrine organ with implications for farm and domestic animal endocrinology – T.F. O’Callaghan – Domestic Animal Endocrinology
Plant, root, and soil microbiome
Systemic enrichment of antifungal traits in the rhizosphere microbiome after pathogen attack – Jan-Hendrik Dudenhöffer – Journal of Ecology
A multi-biological assay approach to assess microbial diversity in arsenic (As) contaminated soils – S.R. Stazi – Geomicrobiology Journal
Effects of two fungicide formulations on microbial and macroinvertebrate leaf decomposition under laboratory conditions – Adria A. Elskus – Environmental Toxicology and Chemistry
Book: Plant, Soil and Microbes – Editors: Khalid Rehman Hakeem, Mohd Sayeed Akhtar – Springer
Water and extremophile microbiome
Metagenomics-Guided Mining of Commercially Useful Biocatalysts from Marine Microorganisms – A.R. Uria – Advances in Food and Nutrition Research
Lessons learned from thirty years of geomicrobiological studies of Río Tinto – Ricardo Amils – Research in Microbiology
Metabolic diversity and adaptive mechanisms of iron- and/or sulfur-oxidizing autotrophic acidophiles in extremely acidic environments – Xian Zhang – Environmental Microbiology Reports
Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill – Nina Dombrowski – Nature Microbiology
News and views: Marine microbiology: Community clean up – Rachel Mackelprang – Nature Microbiology
Assessing viral taxonomic composition in benthic marine ecosystems: reliability and efficiency of different bioinformatic tools for viral metagenomic analyses – M. Tangherlini – Scientific Reports
Marine phage genomics: the tip of the iceberg – Blanca Perez Sepulveda – Microbiology Letters
Metabolic networks and proteomics
MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota – Xu Zhang – Microbiome
The use of propidium monoazide in conjunction with qPCR and Illumina sequencing to identify and quantify live yeasts and bacteria – Mansak Tantikachornkiata – International Journal of Food Microbiology
Protocol: Constructing and Analyzing Metabolic Flux Models of Microbial Communities – José P. Faria – Springer Protocols
Viruses and phages
Opinion: The Janus-Face of Bacteriophages across Human Body Habitats – Adam Wahida – PLOS Pathogens
Review: Research on the human virome: where are we and what is next – Shimian Zou – Microbiome
Microbial ecology and techniques
Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia – Roland Hatzenpichler – PNAS
Press: See and sort: Developing novel techniques to visualize uncultured microbial cell activity – Science Daily
High functional diversity stimulates diversification in experimental microbial communities – Alexandre Jousset – Science Advances
Measuring the biodiversity of microbial communities by flow cytometry – Ruben Props – Methods in Ecology and Evolution
Highlight: A timely reminder of technical limitations – James I. Prosser – Microbial Biotechnology
Species-sorting and mass-transfer paradigms control managed natural metacommunities – Susanne Günther – Environmental Microbiology
Microbes in the news
Slimy clumps of bacteria kill thousands. Scientists are fighting back – Usha Lee McFarling – STAT News
Why everyone’s suddenly talking about gut bacteria – Laura Entis – Fortune
Scientists find link between makeup of individual’s microbiome and head and neck cancer – News Medical
Microbiome Digest - Bik's Picks 