Today’s Picks feature thousand cultured GI tract species, host-microbiome interactions during pregnancy, metagenome assemblies using Hi-C, and the microbiomes of snow leopards and possums.

Human microbiome general

• Special issue of The Cancer Journal – Cancer and Microbiome – The Cancer Journal

Human Gut Microbiome

• The First 1,000 Cultured Species of the Human Gastrointestinal Microbiota – Mirjana Rajilić-Stojanović and Willem M. de Vos – FEMS Microbiology Reviews
• A pilot study of diet and microbiota: interactive associations between fibers and polyphenols with human intestinal bacteria – Adriana Cuervo – Journal of Agricultural and Food Chemistry
• A pilot study on the effect of Lactobacillus casei Zhang on intestinal microbiota parameters in Chinese subjects of different age – L.Y. Kwok – Beneficial Microbes
• Too many antibiotics could spoil your gut – The Irish Times
• Bioengineer is working to make E. coli fight obesity, depression – Deborah Netburn – LA Times

Pregnancy and birth microbiome

• Vaginal microbiome-pregnant host interactions determine a significant proportion of preterm labour – Manju Chandiramani – Fetal and Maternal Medicine Review
• Treatment of genital mycoplasma in colonized pregnant women in late pregnancy is associated with a lower rate of premature labour and neonatal complications – Manon Vouga – Clinical Microbiology and Infection
• Antimicrobial Stewardship in the NICU – Joseph B. Cantey – Infectious Disease Clinics of North America
• Additive Effect between IL-13 Polymorphism and Cesarean Section Delivery/Prenatal Antibiotics Use on Atopic Dermatitis: A Birth Cohort Study (COCOA) – So-Yeon Lee – PLOS ONE
• NIH Accused of Interfering with Ethics Probe. A watchdog group claims that the federal agency improperly influenced the investigation of a study involving the treatment of preterm infants – Bob Grant – The Scientist

Respiratory tract microbiome

• Copy Number Variation of the Beta Defensin Gene Cluster on Chromosome 8p Influences the Bacterial Microbiota within the Nasopharynx of Otitis-Prone Children – Eric A. Jones – PLOS ONE

Mammalian microbiome

• Composition and diversity of the bacterial community in snow leopard (Uncia uncia) distal gut – Honghai Zhang – Annals of Microbiology
• Not all types of host contacts are equal when it comes to E. coli transmission (Mountain brushtail possum) – Michaela D.J. Blyton – Ecology Letters
• Escherichia coli O157:H7 Super-Shedder and Non-Shedder Feedlot Steers Harbour Distinct Fecal Bacterial Communities – Yong Xu – PLOS ONE

Amphibian microbiome

• Amphibian skin may select for rare environmental microbes – Jenifer B Walke – ISME Journal

Insect microbiome

• Microbiota-Induced Changes in Drosophila melanogaster Host Gene Expression and Gut Morphology – Nichole A. Broderick, Nicolas Buchon, Bruno Lemaitre – mBio

Fish microbiome

• Individuals’ diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch) – Daniel I. Bolnick – Ecology Letters

Animal and bioreactor models of gut microbiome

• Circadian Disorganization Alters Intestinal Microbiota – Robin M. Voigt – PLOS ONE
• The HMITM module: a new tool to study the Host-Microbiota Interaction in the human gastrointestinal tract in vitro – Massimo Marzorati – BMC Microbiology
• Microbiome and Colorectal Carcinoma: Insights From Germ-Free and Conventional Animal Models – Tlaskalova-Hogenova, Helena – The Cancer Journal

Environmental microbiome

• Spatial-Temporal Survey and Occupancy-Abundance Modeling To Predict Bacterial Community Dynamics in the Drinking Water Microbiome – Ameet J. Pinto – mBio
• Spatial biodiversity of bacteria along the largest Arctic river determined by next-generation sequencing – Olesya V Kolmakova – FEMS Microbiology Ecology
• Carbon Dioxide and Hydrogen Sulfide Associations with Regional Bacterial Diversity Patterns in Microbially Induced Concrete Corrosion – Alison L. Ling – Environmental Science & Technology
• Diversity of Prokaryotic Community at a Shallow Marine Hydrothermal Site Elucidated by Illumina Sequencing Technology – Valeria Lentini – Current Microbiology
• Temporal Variations in the Abundance and Composition of Biofilm Communities Colonizing Drinking Water Distribution Pipes – John J. Kelly – PLOS ONE
• Screening of Metagenomic and Genomic Libraries Reveals Three Classes of Bacterial Enzymes That Overcome the Toxicity of Acrylate – Andrew R. J. Curson – PLOS ONE
• Metagenomic Analyses Reveal the Involvement of Syntrophic Consortia in Methanol/Electricity Conversion in Microbial Fuel Cells – Ayaka Yamamuro – PLOS ONE

Microbiome and Metabolomics

• Heritability and Clinical Determinants of Serum Indoxyl Sulfate and p-Cresyl Sulfate, Candidate Biomarkers of the Human Microbiome Enterotype – Liesbeth Viaene – PLOS ONE

Phages and viruses

• Beyond Antibiotics – “Today there is renewed interest in phages as warnings intensify that a “post-antibiotic” era looms” – Roger Highfield – Newsweek

Infection, sepsis, and host response

• Developments for improved diagnosis of bacterial bloodstream infections – A. J. M. Loonen – European Journal of Clinical Microbiology & Infectious Diseases

Microbial Ecology papers

• A Critical Time Window for Organismal Interactions in a Pelagic Ecosystem – Kelly J. Benoit-Bird, Margaret A. McManus – PLOS ONE
• What triggers the rising of an intraspecific biodiversity hotspot? Hints from the agile frog – Daniele Canestrelli – Scientific Reports
• Characterizing the effect of population heterogeneity on evolutionary dynamics on complex networks – Shaolin Tan & Jinhu Lü – Scientific Reports
• Maximal Sum of Metabolic Exchange Fluxes Outperforms Biomass Yield as a Predictor of Growth Rate of Microorganisms – Raphy Zarecki – PLOS ONE

Arsenic metabolism

• Speciation of Arsenic in Saliva Samples from a Population of West Bengal, India – Subhamoy Bhowmick – Environmental Science & Technology

Chromosome organization

• Species-Level Deconvolution of Metagenome Assemblies with Hi-C-Based Contact Probability Maps – Joshua N. Burton, Ivan Liachko, Maitreya J. Dunham and Jay Shendure – G3.Genes|Genomes|Genetics
• In vivo single-molecule imaging of bacterial DNA replication, transcription, and repair – Mathew Stracy – FEBS Letters
• Spatial organization of transcription in bacterial cells – Xiaoli Weng – Trends in Genetics

General lab techniques papers

• PCR amplification of repetitive DNA: a limitation to genome editing technologies and many other applications – Carl Maximilian Hommelsheim – Scientific Reports

Dr. Bik’s Picks

• Who Gets to Graduate?“If they come from families in the bottom quartile, they have just a 1 in 6 chance of making it to graduation.” – Paul Tough – NY Times
• Forgive Me, Scientists, for I Have Sinned – “Sometimes I see sunshine on the lawn outside the lab window and realize that I’d rather be outside in the sun” – Adam Ruben – Science
• Impaired Frontal-Basal Ganglia Connectivity in Adolescents with Internet Addiction – Baojuan Li – Scientific Reports
• Making School Lunches Healthier Doesn’t Mean Kids Will Eat Them – A new study found that less than half of students took a vegetable from the lunch line and ate some of it – Olga Khazan – The Atlantic

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