October 15, 2015

Upcoming Reddit AMA with Jessica Richman, oral microbiome transplants, meta-analysis of the indoor environment, African gut microbiota, corals, lichens, and more.

Events

Ask Me Anything (AMA) with Jessica Richman from uBiome on Reddit. October 16 from 10-11am PT

Human oral microbiome

Towards microbiome transplant as a therapy for periodontitis: an exploratory study of periodontitis microbial signature contrasted by oral health, caries and edentulism – Alex E. Pozhitkov – BMC Oral Health

Human gut microbiome

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease – James D. Lewis – Cell Host & Microbe

Variation in rural African gut microbiota is strongly correlated with colonization by Entamoeba and subsistence – Elise R Morton – BioRxiv

The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids – Jingyuan Fu – Circulation Research

Animal models

Analysis of Bacterial Communities during Clostridium difficile Infection in the Mouse – Ekaterina G. Semenyuk – Infection and Immunity

Structural & Functional Consequences of Chronic Psychosocial Stress on the Microbiome & Host – Aadil Bharwani – Psychoneuroendocrinology

Animal microbiome

Pyrosequencing of the bacteria associated with Platygyra carnosus corals with skeletal growth anomalies reveals differences in bacterial community composition in apparently healthy and diseased tissues – Jenny C. Ng – Frontiers in Microbiology

Plant, root, and soil microbiome

Microbiome change by symbiotic invasion in lichens – Mats Wedin – Environmental Microbiology

Species coexistence in simple microbial communities: unravelling the phenotypic landscape of co-occurring Metschnikowia species in floral nectar – María I. Pozo – Environmental Microbiology

Fungal Biodiversity in the Alpine Tarfala Valley – Claudia Coleine – Microorganisms

Effects of long-term drainage on microbial community composition vary between peatland types – Zuzana Urbanová – Soil Biology and Biochemistry

Geological connectivity drives microbial community structure and connectivity in polar, terrestrial ecosystems – Belinda C. Ferrari – Environmental Microbiology

Soil organic matter quantity and quality shape microbial community compositions of subtropical broadleaved forests – Junjun Ding – Molecular Biology

Built environment microbiome

Microbiota of the indoor environment: a meta-analysis – Rachel I. Adams – Microbiome

Microbial ecology

Private benefits and metabolic conflicts shape the emergence of microbial interdependencies – Sylvie Estrela – Environmental Microbiology

Techniques

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples – Alma E. Parada – Environmental Microbiology

Microbes in the news

Metagenomics Digs Up Microbiome Riches: Researchers Are Consulting Metagenomic Maps and Equipping Themselves with Computational Models and Analytical Tools – GenEnNews

Differences in treatment effect on out-of-balance microbiome in Crohn’s disease – EurekAlert

Pets and Owners May Share MRSA Bacteria – Rachael Rettner – LiveScience

Cultural Riches: Researchers devise new techniques to facilitate growing bacteria collected from the environment – Anna Azvolinsky – The Scientist

This could be our best defense against the antibiotic apocalypse: Carl Zimmer on phage therapy – Lydia Ramsey – Business Insider

Bacteria Hysteria

Millions of mattresses are swarming with bacteria and mould that ‘trigger skin infections, asthma and allergies’ – Fiona Macrae – Daily Mail

Microbiology and art

These Photos Reveal How Magnificent Our World Is On The Micro Level: The award-winning images represent some of the best microphotography from around the world – Jacqueline Howard – Huffington Post

How Lining Yao adapted bacteria into living clothing and biomaterials – Matt Kamen – Wired

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October 12, 2015

A nice and short digest today. Happy Columbus Day!

Human gut microbiome

Relationship Between Microbiota of the Colonic Mucosa vs Feces and Symptoms, Colonic Transit, and Methane Production in Female Patients With Chronic Constipation – Gopanandan Parthasarathy – Gastroenterology

Ecology of bacteria in the human gastrointestinal tract—identification of keystone and foundation taxa – Pål Trosvik and Eric Jacques de Muinck – Microbiome

Review: The Gut Microbiota as a Therapeutic Target in IBD and Metabolic Disease: A Role for the Bile Acid Receptors FXR and TGR5 – Annemarie Baars – Microorganisms

Review: Microbiota in Inflammatory Bowel Disease Pathogenesis and Therapy
Is It All About Diet? – Daniela Elena Serban – Nutrition in Clinical Practice

Review: Role of the Gut Microbiome in Obesity and Diabetes Mellitus – Gillian M. Barlow – Nutrition in Clinical Practice

Animal models

Functional analysis of the relationship between intestinal microbiota and the expression of hepatic genes and pathways during the course of liver regeneration – Hui-Xin Liu – Journal of Hepatology

Metagenomics and Bioinformatics

SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data – Genivaldo Gueiros Z. Silva – Bioinformatics

Viruses and phages

Research Highlight: Phages’ box of tricks for CRISPR – Naomi Attar – Nature Reviews Microbiology

Microbes and art

Microbial masterpieces! Scientists ‘paint’ detailed works of art by growing bacteria from human skin and even faeces in petri dishes – Victoria Woollaston – Daily Mail
http://www.dailymail.co.uk/sciencetech/article-3269542/Microbial-masterpieces-Scientists-paint-detailed-works-art-growing-bacteria-petri-dishes.html

Microbes in the news

University of New Haven professor’s research focuses on ‘horrible’ Lyme disease – Mark Zaretsky – New Haven Register

Repeat from earlier podcast: The Bacterial Cloud We All Carry Could Be As Unique As A Fingerprint – Rob Stein – NPR

Antibiotics ban: California first state to outlaw routine use of bacteria-fighting drugs in livestock – Jessica Calefati – Mercury News

Desperate Families in Delhi as Dengue Overwhelms Hospitals – Nida Najar – New York Times

Novel mathematical method may help reduce development of antibiotic-resistant bacteria – News Medical

Bacteria Hysteria

Concerned about germs on shopping trolley handles? Cleaning gadget beats bacteria – Hannah Bouckley – BT

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October 9, 2015

Microbes and midwives, gut-brain axis, gluten immunopathology, viruses from farm to fork, and handwashing in students.

Pregnancy and birth

Conference abstract: Seeding the infant microbiome: The midwife’s role – Asha McCurley – Women and Birth

Human skin microbiome

Poor hand hygiene by college students linked to more occurrences of infectious diseases, medical visits, and absence from classes – Kayla J. Prater – American Journal of Infection Control

Human gut microbiome

Gut microbiota interacts with brain microstructure and function – José-Manuel Fernandez-Real – The Journal of Clinical Endocrinology & Metabolism

Microbiota–Gut–Brain Axis: Yeast Species Isolated from Stool Samples of Children with Suspected or Diagnosed Autism Spectrum Disorders and In Vitro Susceptibility Against Nystatin and Fluconazole – A. Serda Kantarcioglu

Animal models

Intestinal Microbiota Modulates Gluten-Induced Immunopathology in Humanized Mice – Heather J. Galipeau – American Journal of Pathology

Animal microbiome

Habitat fragmentation is associated to gut microbiota diversity of an endangered primate: implications for conservation – Claudia Barelli – Scientific Reports

Profiling the Succession of Bacterial Communities throughout the Life Stages of a Higher Termite Nasutitermes arborum (Termitidae, Nasutitermitinae) Using 16S rRNA Gene Pyrosequencing – Michel Diouf – PLOS ONE

Built Environment microbiome

Microbial control of dental unit water: Feedback on different disinfection methods experience – Julie Lizon – American Journal of Infection Control

Food microbiology

Review: Fate of Foodborne Viruses in the “Farm to Fork” Chain of Fresh Produce – Dan Li – Comprehensive Reviews in Food Science and Food Safety

Metagenomics

Strain recovery from metagenomes – C Titus Brown – Nature Biotechnology

Science, publishing, and career

Peer Review Resources: tips and suggestions from experienced reviewers as well as externally prepared resources for the beginning peer reviewer – Publons

Funny and informative: So you think you want to run an environmental conservation meeting? Advice on the slings and arrows of outrageous fortune that accompany academic conference planning – E. C. M. Parsons – Journal of Environmental Studies and Sciences

Microbes in the news

UNC-Chapel Hill researchers reveal type of vaginal bacteria that protects women from HIV – EurekAlert

When Evolution Is Infectious – How “probiotic epidemics” help wildlife—and us—survive – Moises Velasquez-Manoff – Nautilus
It takes a village of bacteria to help frogs fight deadly disease, Virginia Tech researchers say – Augusta Free Press

Dirty hospital equipment causes 11 people to become infected with bacteria that could lead to pneumonia – Daily Mail

Cat poop coffee goes biotech – Nature Biotechnology

Bad times for good bacteria: how modern life has damaged our internal ecosystems – The Conversation

Gut microorganisms cause gluten-induced pathology in mouse model of celiac disease – MedicalXpress

Bacteria Hysteria

Sponsored by Dettol: Most teddy bears are covered in food poisoning bacteria, tests reveal – Plymouth Herald
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October 5, 2015

Characterizing and classifying the oral microbiome, homeostasis in the lung microbiome, collecting airborne microbes, and earthworms feeding on microbiomes.

Human oral microbiome

An accurate and efficient experimental approach for characterization of the complex oral microbiota – Wei Zheng – Microbiome

Phylogenetic approaches to microbial community classification – Jie Ning and Robert G. Beiko – Microbiome

DGGE: Stability of saliva microbiota during moderate consumption of red wine – Elvira Barroso – Archives of Oral Biology

Human respiratory tract microbiome

Review: Homeostasis and its Disruption in the Lung Microbiome – Robert P. Dickson – Am J Physiol Lung Cell Mol Physiol

Human gut microbiome

Faecalibacterium prausnitzii subspecies–level dysbiosis in the human gut microbiome underlying atopic dermatitis – Han Song – Journal of Allergy and Clinical Immunology

Animal models

Adaptation of the cecal bacterial microbiome of growing pigs in response to resistant starch type 4 – Barbara U. Metzler-Zebeli – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Landscape Position Influences Microbial Composition and Function via Redistribution of Soil Water across a Watershed – Zhe Du – Applied and Environmental Microbiology

Waste treatment microbiology

Feeding on microbiomes: effects of detritivory on the taxonomic and phylogenetic bacterial composition of animal manures – Manuel Aira – FEMS Microbiology Ecology

Food microbiology

Microbial diversity and dynamics throughout manufacturing and ripening of surface ripened semi-hard Danish Danbo cheeses investigated by culture-independent techniques – Mia Ryssel – International Journal of Food Microbiology

Air / Built environment microbiome

Passive dust collectors for assessing airborne microbial material – Rachel I. Adams – Microbiome

Microbes in the news

Beating parasites wins three scientists Nobel prize for medicine: “I think the microbes might almost deserve it more than I do” – Reuters

Nobel Prize Doctors still spreading word of bacteria find – Cathy O’Leary – The West Australian

Intrapartum antibiotics associated with altered infant gut microbiome – Maren Shapiro and Leah Bressler – 2MinuteMedicine

L’eau de bacteria: A whiff of the future? Biotech firms explore using microorganisms to produce flavors, fragrances – Benjamin Plackett – The Charlotte Observer

uBiome Co-Founder Jessica Richman Scoops Top Prize At IVY Awards, uBiome Is Finalist In MedTech Innovator of 2015 – PR Web

Podcast: Our microbiome and our health. Guests: Gary Wu, Tracy Bale, Frederic Bushman – RadioTimes

Microbiome Monday: Animals and Their BFFs – American Museum of Natural History

Permafrost-eating bacteria: a new twist on thawing Arctic and global warming – Thomas S Bianchi – The Conversation

Microbes may play a major role in cloud formation and wet weather – Richard Gray – Daily Mail

Volkswagen: Diesel transplants reveal likely culprit behind DeiselGate: car microbiomes -featuring Jeferina Gordon, Josephine Candelsman, and Hands Dieter Poetsch – – Morten Blaser – The Megabiome

Bacteria Hysteria

Take care when reusing bags: Reusing carrier bags for a diverse range of contents puts consumers at risk of bacterial contamination – Worthing Herald

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September 25, 2015

A crowd funding project to study mind and microbes, impact of early life gut colonization, microbial aspect to terroir, and khmer sequence analysis.

Crowd funding project: Are our bacteria making us depressed or anxious? – Philip Strandwitz – Experiment.com

Pregnancy and birth

Review: The impact of early life gut colonization on metabolic and obesogenic outcomes: what have animal models shown us? – J. G. Wallace – Journal of Developmental Origins of Health and Disease

Human gut microbiome

Chronic Kidney Disease: The Influence of CKD on Colonic Microbial Metabolism – Ruben Poesen – Journal of the American Society of Nephrology

Review: Could the beneficial effects of dietary calcium on obesity and diabetes control be mediated by changes in intestinal microbiota and integrity? – J. M. G. Gomes – British Journal of Nutrition

Animal models

The microbiota shifts the iron sensing of intestinal cells – Jean-Christophe Deschemin – The FASEB Journal

Plant, root, and soil microbiome

Trophic network architecture of root-associated bacterial communities determines pathogen invasion and plant health – Zhong Wei – Nature Communications

Regional microbial signatures positively correlate with differential wine phenotypes: evidence for a microbial aspect to terroir – Sarah Knight – Scientific Reports

Methanogenic degradation of lignin-derived monoaromatic compounds by microbial enrichments from rice paddy field soil – Souichiro Kato – Scientific Reports

Food microbiology

A diagnosis of the microbiological quality of dehydrated bee-pollen produced in Brazil
A.A.M. De-Melo – Letters in Applied Microbiology

Waste microbiology

The biotransformation of brewer’s spent grain into biogas by anaerobic microbial communities – Dina V. Malakhova – World Journal of Microbiology and Biotechnology

Bioinformatics and metagenomics

The khmer software package: enabling efficient nucleotide sequence analysis – Michael R. Crusoe – F1000 research

Microbes in the news

That Stinky Cheese Is a Result of Evolutionary Overdrive – Carl Zimmer – New York Times

Bacteria are making it harder for would-be murderers – Alexandra Petri – Washington Post

Bacteria Hysteria

Note: research sponsored by Dettol: How your child’s teddy could trigger food poisoning: 80% of cuddly toys harbour harmful bacteria – while one in four are contaminated with faeces – Lizzie Parry – Daily Mail

Science, publishing, and career

How science fairs shaped my career – Rachel Yoho – Science

Bik’s Picks

Scientists discover new system for human genome editing – Phys.org

The truth about pigs – Henry Nicholls – BBC

1 1/2-pound baby born to Utah woman on cruise ship beats odds to survive – Lindsey Whitehurst – Associated Press
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September 10, 2015

Plaque microbiome model to predict caries development, ocular microbiota and Sjögren’s, and aging  fungus cultivating termites.

Events

Free workshop at #UCDavis: “Microbial genomics and transcriptomics hands-on”, Sep 24-25 – Jonathan Eisen – Phylogenomics

Human skin and eye microbiome

TSP-1 Deficiency Alters Ocular Microbiota: Implications for Sjögren’s Syndrome Pathogenesis – Terzulli Marielle – Journal of Ocular Pharmacology and Therapeutics

Human oral microbiome

See “Telltale Mouth Microbes” article below, featuring yours truly: Prediction of Early Childhood Caries via Spatial-Temporal Variations of Oral Microbiota – Fei Teng – Cell Host & Microbe

Human respiratory microbiome

High-throughput sequencing of 16S rDNA amplicons characterizes bacterial composition in bronchoalveolar lavage fluid in patients with ventilator-associated pneumonia – Xiao-Jun Yang – Drug Design, Development and Therapy

Bacteria in the CF Lung: Isolation Drives Diversity – Pablo Manfredi – Cell Host & Microbe

Human reproductive tract microbiome

Cervicovaginal microbiome dysbiosis is associated with proteome changes related to alterations of the cervicovaginal mucosal barrier – H Borgdorff – Mucosal Immunology

Human gut microbiome

The Long-term Efficacy and Safety of Fecal Microbiota Transplant for Recurrent, Severe, and Complicated Clostridium difficile Infection in 146 Elderly Individuals – Agrawal, Manas – Journal of Clinical Gastroenterology

Gut Microbiome Composition in Young Nicaraguan Children During Diarrhea Episodes and Recovery – Sylvia Becker-Dreps – Am J Trop Med Hyg

PhD Thesis: Impaired Gut Microbial Community Development in Undernourished Children – Sathish Subramanian – Washington University

Review: Frenemies: Signaling and Nutritional Integration in Pathogen-Microbiota-Host Interactions – Elizabeth A. Cameron, Vanessa Sperandio – Cell Host & Microbe

Review: Fecal microbiota transplantation as therapy for inflammatory bowel disease: A systematic review and meta-analysis – Ruben J. Colman – Journal of Crohn’s and Colitis

Review: Candida albicans commensalism in the gastrointestinal tract – B. Anne Neville – Yeast Research

Review: Fecal microbiota analysis: an overview of sample collection methods and sequencing strategies – Vincent Thomas – Future Microbiology

Review: The interaction of commensal intestinal bacteria with helminth parasites – Mario M. Zaiss – Parasite Immunology

Animal microbiome

Age polyethism drives community structure of the bacterial gut microbiota in the fungus-cultivating termite Odontotermes formosanus – Hongjie Li – Environmental Microbiology

Diet is the primary determinant of bacterial community structure in the guts of higher termites – Aram Mikaelyan – Molecular Ecology

Isolation of aerobic cultivable cellulolytic bacteria from different regions of the gastrointestinal tract of giant land snail Achatina fulica – Guilherme L. Pinheiro – Frontiers in Microbiology

Plant, soil, and root microbiome

Fungal endophyte Phomopsis liquidambari affects nitrogen transformation processes and related microorganisms in the rice rhizosphere – Bo Yan – Frontiers in Microbiology

Soil fungi for mycoremediation of arsenic pollution in agriculture soils – Manvi Singh
– Journal of Applied Microbiology

Woody plant encroachment, and its removal, impact bacterial and fungal communities across stream and terrestrial habitats in a tallgrass prairie ecosystem – Allison M. Veach – Microbiology Ecology

Review: The role of microorganisms in the ecological functions of soils – T. G. Dobrovol’skaya – Eurasian Soil Science

Water microbiome

Studying composition of bacteriobenthic communities in the sediments of water ecosystems by fatty acid markers – N. G. Sherysheva – Aquatic Microbiology

Extremophiles

Microbial life in Bourlyashchy, the hottest thermal pool of Uzon Caldera, Kamchatka -Nikolay A. Chernyh – Extremophiles

Microbes of the built environment

Metabolomic and high-throughput sequencing analysis – modern approach for the assessment of biodeterioration of materials from historic buildings – Beata Gutarowska – Frontiers in Microbiology

Metagenomics and bioinformatics

Fragmentation and coverage variation in viral metagenome assemblies, and their effect in diversity calculations – Rodrigo García-López – Frontiers in Bioengineering and Biotechnology

Tentacle: distributed quantification of genes in metagenomes – Fredrik Boulund – GigaScience

Potential and pitfalls of eukaryotic metagenome skimming: A test case for lichens
Bastian Greshake – Molecular Ecology Resources

Techniques

Effects of freezing storage on the DNA extraction and microbial evaluation from anaerobic digested sludges – Valeria Romanazzi – BMC Research Notes

Microbes in the news

Telltale Mouth Microbes- The composition of the plaque microbiome can reveal a child’s risk of dental caries months before the decay appears, according to a study. – Jyoti Madhusoodanan – The Scientist

Researcher Succumbs To Cystic Fibrosis, Leaves Unique Investigative Legacy – Charles Moore – Cystic Fibrosis News Today

uBiome Extends Reach of Microbiome Testing Through Global Ambassador Program – PR Web

Get the Poop on Organisms Living in Your Gut With a New Consumer Laboratory Test Offered by American Gut and uBiome – Dark Daily

“A diversity of gifts”: article about the MBL Microbial Diversity course – Jonathan Eisen – Microbe.net

Nanomesh dressings may draw bacteria from chronic wounds – Ben Coxworth – GizMag

Purple bacteria signal zinc deficiency – James Urquhart – Chemistry World

Professor pursues bacteria-to-fuel research abroad: Dr. Galyna Kufryk spent part of the summer studying cyanobacteria at the Institut Pasteur in Paris – Janie Magruder – Grand Canyon University

Bacteria in Overdrive: a key organism in the ocean’s food web will start reproducing at high speed as carbon dioxide levels rise – Robert Perkins – USC Dornsife

Bacteria Hysteria

The Most Bacteria-Infested Places on an Airplane – Rachael Schultz – Shape

Microbes and art

AMNH to present The Secret World Inside You exhibit, 11/4 – Broadway World

Science, publishing, and career

Q&A: The academic satirist: Jorge Cham wowed graduate students with The PhD Movie in 2011 – Zoë Corbyn – Nature

Gender balance: Women are funded more fairly in social science – Paul J. Boyle – Nature
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September 7, 2015

Human skin microbiome

Skin microbiota-associated inflammation precedes autoantibody induced tissue damage in experimental epidermolysis bullosa acquisita – Christoph T. Ellebrecht – Journal of Autoimmunity

Human stomach and gut microbiome

Review: The stomach in health and disease – R H Hunt – Gut

Review: Intestinal microbiota and ulcerative colitis – Toshifumi Ohkusa – Journal of Infection and Chemotherapy

Animal microbiome

Cryptic diversity, reproductive isolation and cytoplasmic incompatibility in a classic biological control success story – Marco Gebiola – Biological Journal of the Linnean Society

Plant, root, and soil microbiome

Fungal community shifts in structure and function across a boreal forest fire chronosequence – Hui Sun – Applied and Environmental Microbiology

Patterns of endemism and habitat selection in coalbed microbial communities
Christopher E. Lawson – Applied and Environmental Microbiology

Geogenic factors as drivers of microbial community diversity in soils overlying polymetallic deposits – Frank Reith – Applied and Environmental Microbiology

Abundance of Antibiotic Resistance Genes in Bacteriophage Following Soil Fertilization With Dairy Manure or Municipal Biosolids, and Evidence for Potential Transduction – Joseph Ross – Applied and Environmental Microbiology

Water microbiome

Human-associated fecal qPCR measurements and simulated risk of gastrointestinal illness in recreational waters contaminated with raw sewage – Alexandria B. Boehm – Environmental Science & Technology Letters

Built environment microbiome

Coexistence of lactic acid bacteria and potential spoilage microbiota in a dairy-processing environment – Giuseppina Stellato – Applied and Environmental Microbiology

Microbes in the news

Goodbye showers-bacteria spray improves health? – Fox2

Researchers expanding use of poliovirus for cancer treatment – Nidhila Masha – Duke Chronicle

Bacteria Advisories Issued for 18 beaches along Texas Coast – KiiiTV

Bacteria could threaten pistachios in NM – Angela Simental – Albuquerque Journal

Possible Key in Virus, Cancer Research Identified – Kathleen Haughney – Labmanager

Bacteria Hysteria

Faecal matter on the TV remote, bodily fluids on bed linens and drinking glasses wiped with a filthy cloth: The dirtiest areas of a hotel room revealed – Chris Kitching – Daily Mail

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September 1, 2015

General microbiome

Perspective: Better together: engineering and application of microbial symbioses – Stephanie G Hays – Current Opinion in Biotechnology

Pregnancy and birth

Maternal use of probiotics during pregnancy and effects on their offspring’s health in an unselected population – Nicole Rutten – European Journal of Pediatrics

Impact of maternal bifidobacteria and the mode of delivery on Bifidobacterium microbiota in infants – S. Sirilun – Beneficial Microbes

Human Milk Oligosaccharides in Premature Infants: Absorption, Excretion and Influence on the Intestinal Microbiota – Mark A. Underwood – Pediatric Research

The influence of impact delivery mode, lactation time, infant gender, maternal age and rural or urban life on total number of Lactobacillus in breast milk Isfahan – Iran – Mansoureh Taghizadeh – Advanced Biomedical Research

Review: Maternal Microbiome and Pregnancy Outcomes That Impact Infant Health: A Review – Anne L Dunlop – Advances in Neonatal Care

Human gut microbiome

Characterization of the gut microbiota of Kawasaki disease patients by metagenomic analysis – Akiko Kinumaki – Frontiers in Microbiology

Review: Microbiome Disturbances and Autism Spectrum Disorders – Cheryl S. Rosenfeld – Drug Metabolism & Disposition

Review: Investigation of Host–Gut Microbiota Modulation of Therapeutic Outcome – Lian Yee Yip – Drug Metabolism & Disposition

Perspective: Could gut microbiota protect against sclerosing cholangitis? – Hanns-Ulrich Marschall – Hepatology

Models of microbiome research

Probiotic Bifidobacterium longum alters gut luminal metabolism through modification of the gut microbial community – Hirosuke Sugahara – Scientific Reports

Microbial community profiles of the colon from steers differing in feed efficiency – Phillip R Myer – Springer Plus

Distinct Shifts in Microbiota Composition during Drosophila Aging Impair Intestinal Function and Drive Mortality – Rebecca I. Clark – Cell Reports

Impact of Fishmeal Replacement in Diets for Gilthead Sea Bream (Sparus aurata) on the Gastrointestinal Microbiota Determined by Pyrosequencing the 16S rRNA Gene – G. Estruch – PLOS ONE

Lean rats gained more body weight than obese ones from a high-fibre diet – Shaoting Li – British Journal of Nutrition

Microbiota RORgulates intestinal suppressor T cells – Ahmed N. Hegazy – Science

Review: Heterogeneity of the gut microbiome in mice: guidelines for optimizing experimental design – Debby Laukens – FEMS Microbiology Reviews

Animal microbiome

Temporal variation selects for diet–microbe co-metabolic traits in the gut of Gorilla spp – Andres Gomez – The ISME Journal

Domestication and cereal feeding developed domestic pig-type intestinal microbiota in animals of suidae – Kazunari Ushida – Animal Science Journal

Rapid Change of Microbiota Diversity in the Gut but Not the Hepatopancreas During Gonadal Development of the New Shrimp Model Neocaridina denticulata – Man Kit Cheung – Marine Biotechnology

Plant, root, and soil microbiome

The Effect of Long-Term Continuous Cropping of Black Pepper on Soil Bacterial Communities as Determined by 454 Pyrosequencing – Wu Xiong – PLOS ONE

A metagenomic window into carbon metabolism at 3 km depth in Precambrian continental crust – Cara Magnabosco – The ISME Journal

A review: What is the spermosphere and how can it be studied? – Séverine Schiltz – Journal of Applied Microbiology

Metagenomics and bioinformatics

glmgraph: An R Package for Variable Selection and Predictive Modeling of Structured Genomic Data – Li Chen – Bioinformatics

Discovery of phosphonic acid natural products by mining the genomes of 10,000 actinomycetes – Kou-San Ju – PNAS

Techniques

Mass Spectrometry-based PhyloProteomics (MSPP): A novel microbial typing Method – Andreas Erich Zautner – Scientific Reports

Microbes and art

Made of Bacteria, This Living Type Morphs Into New Letterforms: Ori Elisar’s project Living Language blurs the lines between designer and mad scientist with his Hebrew symbols grown in petridishes – Meg Miller – FastcoDesign

Microbes in the news

Unusual throat (and mouth) germs linked to schizophrenia, says two new studies – Amy Ellis Nutt – Washington Post

Some Sexually Transmitted Microbes Might Be Good for You – Marissa Fessenden – Smithsonian

How Does Your Microbiome Grow? The reproduction rates of the bacteria in one’s gut may be a good indicator of health or disease – Health Canal

How Do We Build Our Microbiomes? Exhibition “The Secret World Inside You” opens November 7 – American Museum of Natural History

New Yeast And Bacterial Starters Developed For Truly Wild European Wines – Eurasia Review

Bacteria Hysteria

Are your kid’s backpacks a magnet for bacteria? – Anna Zook – WJHL.com

Bik’s Picks

Acoustic shadows help gleaning bats find prey, but may be defeated by prey acoustic camouflage on rough surfaces – Elizabeth L Clare – eLIFE
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