Category Archives: Built Environment Microbiology

April 24, 2016

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Effect of gluten-free diet, broad and accurate taxonomic resolution with multiple genes, ice-nucleating bacteria, indoor bacteria, fungi, and archaea.

Human oral microbiome

Changes in the Oral Moisture and the Amount of Microorganisms in Saliva and Tongue Coating after Oral Ingestion Resumption: A Pilot Study -Natsuki Kishimoto – The Open Dentistry Journal

Human gut microbiome

The influence of a short-term gluten-free diet on the human gut microbiome – Marc Jan Bonder – Genome Medicine

Gut microbiota of Type 1 diabetes patients with good glycaemic control and high physical fitness is similar to people without diabetes: an observational study – C. J. Stewart – Diabetic Medicine

The Influence of Prebiotic Arabinoxylan Oligosaccharides on Microbiota Derived Uremic Retention Solutes in Patients with Chronic Kidney Disease: A Randomized Controlled Trial – Ruben Poesen – PLOS ONE

Minireview: Human microbiome versus food-borne pathogens: friend or foe – Jonathan Josephs-Spaulding – Applied Microbiology and Biotechnology

Opinion: Strain-level dissection of the contribution of the gut microbiome to human metabolic disease – Chenhong Zhang – Genome Medicine

Review: Impact of the gut microbiota on inflammation, obesity, and metabolic disease – Claire L. Boulangé – Genome Medicine

Review: Translational aspects of the microbiome—to be exploited – Edit Mikó – Cell Biology and Toxicology

Animal models

Statement of Retraction. Replication of Obesity and Associated Signaling Pathways Through Transfer of Microbiota From Obese-Prone Rats – Frank A Duca – Diabetes

Gene expression of Lactobacillus plantarum and the commensal microbiota in the ileum of healthy and early SIV-infected rhesus macaques – Benjamin L. Golomb – Scientific Reports

Intestinal Microbiota and Microbial Metabolites Are Changed in a Pig Model Fed a High-Fat/Low-Fiber or a Low-Fat/High-Fiber Diet – Sonja N. Heinritz – PLOS ONE

Plant, root, and soil microbiome

(also filed under New Techniques below) New insights in host-associated microbial diversity with broad and accurate taxonomic resolution – Matthew T. Agler – bioRxiv

Detection of plant growth enhancing features in psychrotolerant yeasts from Patagonia (Argentina) – María Cecilia Mestre – Journal of Basic Microbiology

Discovery and characterization of ionic liquid-tolerant thermophilic cellulases from a switchgrass-adapted microbial community – John M Gladden – Biofuels

Soil biochar amendment shapes the composition of N2O-reducing microbial communities – Johannes Hartera – Science of the Total Environment

Climate change and human activities altered the diversity and composition of soil microbial community in alpine grasslands of the Qinghai-Tibetan Plateau – Yong Zhang – Science of the Total Environment

Water and extremophile microbiome

Ice-nucleating bacteria control the order and dynamics of interfacial water – Ravindra Pandey – Science Advances

Unicellular cyanobacteria Synechocystis accommodate heterotrophic bacteria with varied enzymatic and metal resistance properties – Anas Abdulaziz – Journal of Basic Microbiology

Establishment of a multi-species biofilm model and metatranscriptomic analysis of biofilm and planktonic cell communities – Yuya Nakamura – Applied Microbiology and Biotechnology

Evidence of adaptation, niche separation and microevolution within the genus Polaromonas on Arctic and Antarctic glacial surfaces – Jan Gawor – Extremophiles

Built environment microbiology

Fungal and Bacterial Communities in Indoor Dust Follow Different Environmental Determinants – Fabian Weikl – PLOS ONE

Presence of Archaea in the Indoor Environment and Their Relationships with Housing Characteristics – Sepideh Pakpour – Microbial Ecology

Food microbiology

Enhancing the sweetness of yoghurt through metabolic remodeling of carbohydrate metabolism in Streptococcus thermophilus and Lactobacillus delbrueckii subsp. Bulgaricus – Kim I. Sørensen – Applied and Environmental Microbiology

Microbiota of an Italian Grana like cheese during manufacture and ripening unraveled by 16S rRNA-based approaches – Valentina Alessandria – Applied and Environmental Microbiology

Taxonomy, new techniques, bioinformatics

New insights in host-associated microbial diversity with broad and accurate taxonomic resolution – Matthew T. Agler – bioRxiv

Wedding higher taxonomic ranks with metabolic signatures coded in prokaryotic genomes – Gregorio Iraola – bioRxiv

Reviews: Eco-Evo-Devo: developmental symbiosis and developmental plasticity as evolutionary agents – Scott F. Gilbert – Nature Reviews Genetics

Microbes in the news

How the world’s chillest bacteria make ice. They may be responsible for creating clouds and rain – Alessandra Potenza – The Verge

How The Bacteria In Your Gut Could Be Used To Treat Mental Illness. New research finds that altering gut bacteria in mice changes the way their brains work – Carolyn Gregoire – Huffington Post

Five ‘fake’ water firms in Mombasa shut after tests confirm bacteria – Elkana Jacob – The Star Kenya

Investigators reduce sugar content of yogurt without reducing sweetness: using microbiological methods that predate the era of genetic technologies – Science Daily

How Toronto’s germs are different from those in other cities. New study reveals each community has its own unique blend of fungi and bacteria — a microbial signature – Robin Levinson King – The Star

Microbes and art

Living Art: Meet the Woman Making Sculptures With Bacteria from Her Skin, UK-based artist Mellissa Fisher – Stephanie Leke – Broadly The Vice

April 22, 2016

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General microbiome

Nutrigenomics, the Microbiome, and Gene-Environment Interactions: New Directions in Cardiovascular Disease Research, Prevention, and Treatment
A Scientific Statement From the American Heart Association – Jane F. Ferguson – Circulation: Cardiovascular Genetics

Human skin and eye microbiome

Commentary: Details Matter: Designing Skin Microbiome Studies – Heidi H. Kong – Journal of Investigative Dermatology

Defining the normal “core microbiome” of conjunctival microbial communities – Yusen Huang – Clinical Microbiology and Infection

Supplement with abstracts for the American Academy of Dermatology 74th Annual Meeting – Journal of the American Academy of Dermatology

Supplement with abstracts for the Society for Investigative Dermatology (SID 2016) Annual Meeting – Journal of Investigative Dermatology

Human gut microbiome

Strain-level dissection of the contribution of the gut microbiome to human metabolic disease – Chenhong Zhang – Genome Medicine

Review: Microbiome alterations in HIV infection a review – Brett Williams – Cellular Microbiology

Review? Does Gut Microbiota Affect Endothelial Functions in Chronic Kidney Disease Patients With Type 2 Diabetes Mellitus? – American Journal of Kidney Diseases

Commentary: The return of microbes – Didier Raoult – Clinical Microbiology and Infection

Review: Use your antibiotics wisely. Consequences to the intestinal microbiome – Jorge Cervantes – FEMS Microbiology Letters

Review: The Microbiome, Timing, and Barrier Function in the Context of Allergic Disease – Duane R. Wesemann – Immunity

Animal and in vitro models
Cigarette Smoke Attenuates the Nasal Host Response to Streptococcus pneumoniae and Predisposes to Invasive Pneumococcal Disease in Mice – Pamela Shen – Infection and Immunity

Susceptibility to Ticks and Lyme Disease Spirochetes Is Not Affected in Mice Coinfected with Nematodes – Denny Maaz – Infection and Immunity

Adherence of probiotic bacteria to human colon epithelial cells and inhibitory effect against enteric pathogens – In vitro study – Nowak Adriana – International Journal of Dairy Technology

Microbiota-driven transcriptional changes in prefrontal cortex override genetic differences in social behavior – Mar Gacias – eLIFE

Gut Microbiota Drive Autoimmune Arthritis by Promoting Differentiation and Migration of Peyer’s Patch T Follicular Helper Cells – Fei Teng – Immunity

Preview: Viral Safeguard: The Enteric Virome Protects against Gut Inflammation – Stephanie M. Karst – Immunity

Animal microbiome

Fecal metagenomics for the simultaneous assessment of diet, parasites, and population genetics of an understudied primate – Amrita Srivathsan – Frontiers in Zoology

Comparative analysis of midgut bacterial communities in three aedine mosquito species from dengue-endemic and non-endemic areas of Rajasthan, India – S. S. Charan – Medical and Veterinary Entomology

Minireview: The Sponge Hologenome – Nicole S. Webster – mBio

Water and extremophile microbiome

Response of Antarctic cryoconite microbial communities to light – Elizabeth A. Bagshaw – Microbiology Ecology

Built environment microbiology
The Built Environment Is a Microbial Wasteland – Sean M. Gibbons – mSystems

Food microbiology

Assessment of the microbial diversity during an industrial-scale malting process by a polymerase chain reaction-denaturing gradient gel electrophoresis analysis – Ruilong Li – Journal of the Institute of Brewing (gotta love that name!)

Phages, viruses, and CRISPRs

The diversity-generating benefits of a prokaryotic adaptive immune system – Stineke van Houte – Nature

Microbes in the news
Your city’s microbiome is unique – Christina Procopiou – Newsweek

Human beings – and our offices – are crawling with microbes – Joanna Verran – The Conversation

About Jonathan Eisen: This microbiologist loves bugs, hates hype – and wants you to send him your cat’s poop – Rob Waters – STATnews

Close-up of a dust bunny – Holly Ganz – MicroBE.net

Looking Back, Looking Forward and Phage Hunters: A Q&A with the Student Commencement Speaker – Emily Hellewell – Brigham Young University

Do gut microbes shape our evolution? Researcher proposes that a host’s microbiota can steer its evolution in new directions – Science Daily

Pfizer, Roche Embrace The Microbiome, Leading $43M Bet On Second Genome – Luke Timmerman – Forbes

You’re Home to Trillions of Microbes That Affect Everything From Digestion to Depression – Sydney Lupkin – Vice

Pancreatic Cancer Risk Tied to Specific Mouth Bacteria – Infection Control Today

Science, publishing, and career
Due process in the Twitter age – Marcia McNutt – Science

Peer review: Troubled from the start – Alex Csiszar – Nature

Dirty room-mates make lab mice more useful. Housing lab mice with pet-shop mice gives them more human-like immune systems – Sara Reardon – Nature

UC Davis Storer Lecture series – since 1963 87% of speakers are male – Jonathan Eisen – The Tree of LIfe

April 19, 2016

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A review about breastmilk with a great name, skin microbiome in different populations, a mouse model for Sjögren’s, the office microbiome, Guam reef sponges, the Alaska tundra ecosystem, and taxonomic classification. Note that I will be traveling internationally in the next couple of days due to (another) tragic family situation, so posting will be irregular. But I will try my best!

Pregnancy and birth

Review: Breastfed at Tiffany’s – Thierry Hennet – Trends in Biochemical Sciences

Human skin microbiome

Body Site Is a More Determinant Factor than Human Population Diversity in the Healthy Skin Microbiome – Guillermo I. Perez Perez – PLOS ONE

Pathogenic bacteria profile and antimicrobial susceptibility patterns of ear infection at Bahir Dar Regional Health Research Laboratory Center, Ethiopia – Derese Hailu – SpringerPlus

Human oral microbiome (also see Animal models, below)

Comparison of the Oral Microbiome of Siblings Using Next-generation Sequencing: a Pilot Study – Hyo-Seol Lee – Oral Diseases

Human gastric microbiome

Characterisation of the gastrointestinal mucosa-associated microbiota: a novel technique to prevent cross-contamination during endoscopic procedures – E. R. Shanahan – Alimentary Pharmacology & Therapeutics

Human gut microbiome

Conference Abstract: Walnut Consumption Influences the Human Gut Microbiome – Heather M Guetterman – The FASEB Journal

Conference Abstract: Anemia and Iron Status are Predictors of Gut Microbiome Composition and Metabolites in Infants and Children in Rural Kenya – Daniela Paganini – The FASEB Journal

Recurrent Clostridium difficile infection associates with distinct bile acid and microbiome profiles – J. R. Allegretti – Alimentary Pharmacology & Therapeutics

Effects of sardine-enriched diet on metabolic control, inflammation and gut microbiota in drug-naïve patients with type 2 diabetes: a pilot randomized trial – Mariona Balfegó – Lipids in Health and Disease

Review: From gut dysbiosis to altered brain function and mental illness: mechanisms and pathways – G B Rogers – Molecular Psychiatry

Review: Reshaping the gut microbiota: Impact of low calorie sweeteners and the link to insulin resistance? – Jodi E. Nettleton – Physiology & Behavior

Book chapter, some plagiarism: Impact of Probiotics and Gut Microbiota on Host Behavior – Sarabjit Singh Kanwar – Microbes in Food and Health

Animal models of microbiome research

Mouse model: Altered Mucosal Microbiome Diversity and Disease Severity in Sjögren Syndrome – Cintia S. de Paiva – Scientific Reports

Systemic Characterization of an Obese Phenotype in the Zucker Rat Model Defining Metabolic Axes of Energy Metabolism and Host-Microbial Interactions – Jutarop Phetcharaburanin – Journal of Proteome Research

Metagenomic analysis of antibiotic-induced changes in gut microbiota in a pregnant rat model – Imran Khan – Frontiers in Pharmacology

Inflammasome signaling affects anxiety- and depressive-like behavior and gut microbiome composition – M-L Wong – Molecular Psychiatry

Animal microbiome

The reproductive tracts of two malaria vectors are populated by a core microbiome and by gender- and swarm-enriched microbial biomarkers – Nicola Segata – Scientific Reports

In four shallow and mesophotic tropical reef sponges from Guam the microbial community largely depends on host identity – Georg Steinert – PeerJ

Microbiome analysis and detection of pathogenic bacteria of Penaeus monodon from Jakarta Bay and Bali – Vincensius S.P. Oetama – Marine Pollution Bulletin

Diversity of endosymbiont bacteria associated with a non-filarial nematode group – Stela S. Lazarova – Nematology

Master thesis: Effects of Roundup (glyphosate) on gut microorganisms of farm animals – Charlotte Lynggaard Katholm – Aarhus University

Plant, root, and soil microbiome

Functional composition of plant communities determines the spatial and temporal stability of soil microbial properties in a long-term plant diversity experiment – Tanja Strecker – Oikos

Bacterial communities of the cotton aphid Aphis gossypii associated with Bt cotton in northern China – Yao Zhao – Scientific Reports

Soil microbial community composition and respiration along an experimental precipitation gradient in a semiarid steppe – Cancan Zhao – Scientific Reports

Bioaerosol Deposition to Food Crops near Manure Application: Quantitative Microbial Risk Assessment – Michael A. Jahne – Journal of Environmental Quality

Effects of biofumigation using Brassica juncea and Raphanus sativus in comparison to disinfection using Basamid on apple plant growth and soil microbial communities at three field sites with replant disease – Bunlong Yim – Plant and Soil

Bacterial and eukaryal diversity in soils forming from acid mine drainage precipitates under reclaimed vegetation and biological crusts – Claudia Rojas – Applied Soil Ecology

Assessment of Bacterial Communities and Predictive Functional Profiling in Soils Subjected to Short-Term Fumigation-Incubation – Lin Chen – Microbial Ecology

Archaeal communities in the sediments of different mangrove stands at Dongzhaigang, China – Wei Li – Journal of Soils and Sediments

Metagenomics reveals pervasive bacterial populations and reduced community diversity across the Alaska tundra ecosystem – Eric R. Johnston – Frontiers in Microbiology

Water microbiome

Bacterioplankton biogeography in the Atlantic Ocean: a case study of the distance-decay relationship – Mathias Milici – Frontiers in Microbiology

Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities – Jeffrey Marlow – Frontiers in Microbiology

Metagenomic analysis of sediments under seaports influence in the Equatorial Atlantic Ocean – Tallita Cruz Lopes Tavares – Science of The Total Environment

Dissolution Tests and Microbial Community Analysis Using the Bottom Sediment before and after a Heavy Storm – Ikuo Tsushima – Journal of Water and Environment Technology

Carbohydrate production by microbial mats communities in tidal flat from Bahía Blanca Estuary (Argentina) – E. M. Fernández – Environmental Earth Sciences

Built environment microbiome

Geography and Location Are the Primary Drivers of Office Microbiome Composition – John Chase – mSystems

Waste and pollution microbiology

Population Dynamics of Bulking and Foaming Bacteria in a Full-scale Wastewater Treatment Plant over Five Years – Xiao-Tao Jiang – Scientific Reports

Quantification of microbial load in diesel storage tanks using culture- and qPCR-based approaches – Pedro M. Martin-Sanchez – International Biodeterioration & Biodegradation

Bacterial communities in oil contaminated soils: Biogeography and co-occurrence patterns – Shuo Jiao – Soil Biology and Biochemistry

Methanogen Population of an Oil Production Skimmer Pit and the Effects of Environmental Factors and Substrate Availability on Methanogenesis and Corrosion Rates – Okoro Chuma Conlette – Microbial Ecology

Phages and viruses

Parasite diversity drives rapid host dynamics and evolution of resistance in a bacteria-phage system – Alex Betts – Evolution

Research highlight: More of the world’s a phage – Naomi Attar – Nature Reviews Microbiology

Bioinformatics and metagenomics

Fast and sensitive taxonomic classification for metagenomics with Kaiju – Peter Menzel – Nature Communications

META-pipe – Pipeline Annotation, Analysis and Visualization of Marine Metagenomic Sequence Data – Espen Mikal Robertsen – ArXiv

Fast and sensitive mapping of nanopore sequencing reads with GraphMap – Ivan Sović – Nature Communications

Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity – Beverly E. Flood – Frontiers in Microbiology

Editorial: A tale of two tardigrades – Thomas A. Richards – PNAS

Review: A guide through a family of phylogenetic dissimilarity measures among sites – Sandrine Pavoine – Oikos

Review: Compositional analysis: a valid approach to analyze microbiome high throughput sequencing data – Gregory B Gloor – Canadian Journal of Microbiology

More microbiology

Accessing Nature’s diversity through metabolic engineering and synthetic biology – Jason R. King – F1000 Research

Utilization and control of ecological interactions in polymicrobial infections and community-based microbial cell factories – Vinoth Wigneswaran – F1000 Research

Microbes in the news

Your Invisible Neighbors: Each City Has Unique Microbes – Katherine Du – NPR

Can the bacteria on your skin reveal where you are from? Floors, walls and people in different cities have distinct microbial ‘signatures’ – Abigail Beall – Daily Mail

6 surprising facts about sugar-laden, virus-fighting breast milk – Megan Thielking – STAT News

Gut microbiota development driven by specific enzyme in breast milk – Yvette Brazier – Medical News Today

Mothers’ milk and the infant gut microbiota: An ancient symbiosis – Science Daily

Microbiome-Brain Research to Get $2.8M Boost from NIDA, NCCIH – Genome Web

Earth Day: New insights into coral health hidden in reefs’ microbiomes – National Science Foundation

Downwind safety on the farm. Manure application research aims to improve food safety – American Society of Agronomy

Heartburn Meds Alter the Gut. Acid blockers reduce the diversity of bacteria in the intestines—and that could lead to trouble – Melinda Wenner Moyer – Scientific American

Bacteria that ‘breathes’ iron: Microbes that might change our search for life in space – Dawn Papple – Inquisitr

Microbes and art
This artist uses bacteria as paint: Paint by Microbes – Steph Yin – PopSci

Science, publishing, and career

From #realtimechem to #whywedoresearch: Who are the Tweeting scientists? – Andrew Marsh – Piirus

Tips for Using Social Media to Promote Your Research – Emma Hedington – NPJ Biofilms and Microbiomes

About Joseph Mercola: Known Quack Forced to Refund Customers for Lying About Effects of Tanning Beds – Bryan Menegus – Gizmodo

Bik’s Picks

Meet the woman who makes fake fingers for Japan’s reformed gangsters – Justin McCurry – The Guardian

April 18, 2016

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Tongue coating and halitosis, mucosa and Crohn’s, biography in American forests diazotrophs, and microbes on parchment documents.

Events

Submit your microbial artwork and win the ISMEJ cover competition! – The ISME Journal

Human oral microbiome

Tongue Coating and the Salivary Microbial Communities Vary in Children with Halitosis – Wen Re – Scientific Reports

Human respiratory microbiome

Clinical impact of methicillin-resistant staphylococcus aureus on bacterial pneumonia: cultivation and 16S ribosomal RNA gene analysis of bronchoalveolar lavage fluid – Toshinori Kawanami – BMC Infectious Diseases

Human gut microbiome

Mucosa-attached bacterial community in Crohn’s Disease coheres with the Clinical Disease Activity Index – Holger Schäffler – Environmental Microbiology Reports

Animal microbiome

Impact of gut microbiota on the fly’s germ line – Michael Elgart – Nature Communications

Caribbean corals house shared and host-specific microbial symbionts over time and space – Nathaniel D. Chu – Environmental Microbiology Reports

Plant, root, and soil microbiome

Biogeographic Patterns of Soil Diazotrophic Communities across Six Forests in the North America – Qichao Tu – Molecular Ecology

Unique Organic Matter and Microbial Properties in the Rhizosphere of a Wetland Soil – Daniel I. Kaplan – Environ. Sci. Technol.

Water microbiology

Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments – Elizabeth Trembath-Reichert – PeerJ

Air microbiology

Assessment of microbial communities in PM1 and PM10 of Urumqi during winter – Huange Gou – Environmental Pollution

Waste and pollution microbiology

Geochemical and temporal influences on the enrichment of acidophilic iron-oxidizing bacterial communities – Yizhi Sheng – Applied and Environmental Microbiology

Review: Insights into microbial diversity in wastewater treatment systems: How far have we come? – Isabel Ferrera – Biotechnology Advances

Built environment microbiology

Evaluation of a Parchment Document, the 13th Century Incorporation Charter for the City of Krakow, Poland, for Microbial Hazards – Tomasz Lech – Applied and Environmental Microbiology

Extraction of Aerosol-Deposited Yersinia pestis from Indoor Surfaces To Determine Bacterial Environmental Decay – Ian M. Gut- Applied and Environmental Microbiology

More microbiology

Mechanisms of Bacterial (Serratia marcescens) Attachment to, Migration along, and Killing of Fungal Hyphae – Tal Hover – Applied and Environmental Microbiology

Principles for designing synthetic microbial communities – Nathan I Johns – Current Opinion in Microbiology

Microbes and art

Bacteria Rule Everything Around Me – Geoff Manaugh – BLDG blog

‘Financial Growth’ reveals just how much coins and money can communicate, transfer and exchange – Heidi Hinder

Microbes in the news

In Dutch, with quotes from me: Ineens zit je wel en wee in je darm – Sander Voormolen – NRC

The Endurance of Microbiology: An Interview with Mike Jetten, Mark Martin, Ute Römling, and Victor Torres – Trends in Microbiology

‘We have never been this close’: The campaign to eradicate polio takes a giant step forward – Helen Branswell – STAT News

Antarctica research published – Mike Henson – Thrash Lab

Q&A with Councilor Eva Harris on battle against Zika – American Society of Tropical Medicine and Hygiene

Creating a biobank of the Flagstaff community: Me and my microbiota – Tom Carpenter – AZ Daily Sun

The Human Body’s Complicated Relationship With Fungi – Bret Stetka – WCQS

Queens University student discovers a virus strain – News Observer

Researchers chew over the differences in mouth bacteria in horses – HorseTalk

Newly discovered microbe keeps teeth healthy: Bacteria may offer a new way to prevent cavities – Society for Science

Next job for the microbiome: Tagging criminals – Andrew Porterfield – Genetic Literacy Project

Great Barrier Reef: the scale of bleaching has the most sober scientists worried – James Woodford – The Guardian

Viruses Find Love In A Boiling Place – Inside Science

UB establishes Center for Microbiome Research – University at Buffalo

Cow’s milk has vital prebiotic for a healthy baby’s microbiome – New Scientist

Mainstreaming the Microbiome – Susan K Finston – Biotech blog

Study: Jet Hand Dryers Blast Bacteria Around Bathrooms with Terrifying Force – Ed Jones – Modern Readers

April 13, 2016

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Thematic issue on effect of antibiotics on microbiomes, limited effect of probiotics on stool proteomics, culex mosquito development, ocean acidification, and new technique to determine microbial growth.

General microbiome

Thematic Issue: the effects of anthropogenic use of antibiotics on the microbiomes in various ecosystems and the implications for human health. Guest edited by Prof. Kornelia Smalla, the articles included in this issue are freely available to read til 11th May 2016. Environmental Dimension of Antibiotic Resistance – FEMS Microbiology Ecology
Review: Network-based metabolic analysis and microbial community modeling – Cesar Cardona – Current Opinion in Microbiology

Review: The importance of the microbiome in epidemiologic research – Blake M. Hanson – Annals of Epidemiology

Editorial: Microbiome: Eating for trillions – Derrick M. Chu – Nature

Pregnancy and birth

Preview: Another Reason to Thank Mom: Gestational Effects of Microbiota Metabolites – Seth Rakoff-Nahoum – Cell Host & Microbe

Review: The interplay of host immunity and environment on risk for bacterial vaginosis and associated reproductive health outcomes – Kerry Murphy – The Journal of Infectious Diseases

Human respiratory microbiome

Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype – Leopoldo N. Segal – Nature Microbiology

Human gut microbiome

Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults – Carolin A. Kolmeder – PLOS ONE

Review: The gut microbiota and metabolic disease: current understanding and future perspectives – T. Arora – Journal of Internal Medicine

Animal models

A Host-Produced Autoinducer-2 Mimic Activates Bacterial Quorum Sensing – Anisa S. Ismail – Cell Host & Microbe

Depletion of Butyrate-Producing Clostridia from the Gut Microbiota Drives an Aerobic Luminal Expansion of Salmonella – Fabian Rivera-Chávez – Cell Host & Microbe

Lipocalin 2 Protects from Inflammation and Tumorigenesis Associated with Gut Microbiota Alterations – Alexander R. Moschen – Cell Host & Microbe

Animal microbiome

Culex pipiens Development Is Greatly Influenced by Native Bacteria and Exogenous Yeast – Leonardo M. Díaz-Nieto – PLOS ONE

Plant, root, and soil microbiome

Convergence of soil microbial properties after plant colonization of an experimental plant diversity gradient – Katja Steinauer – BMC Ecology

Bacterial community associated to the pine wilt disease insect vectors Monochamus galloprovincialis and Monochamus alternatus – Marta Alves – Scientific Reports

Relationship between presence of the desert shrub Haloxylon ammodendron and microbial communities in two soils with contrasting textures – Yanfeng Cao – Applied Soil Ecology

Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil – Samiran Banerjee – Soil Biology and Biochemistry

Belowground response to drought in a tropical forest soil. I. Changes in microbial functional potential and metabolism – Nick Bouskill – Frontiers in Microbiology

Water and extremophile microbiome

Spatiotemporal Dynamics of Vibrio spp. within the Sydney Harbour Estuary – Nachshon Siboni – Frontiers in Microbiology

Assimilation of microbial and plant carbon by active prokaryotic and fungal populations in glacial forefields – Thomas Rime – Soil Biology and Biochemistry

Implications of Ocean Acidification for Marine Microorganisms from the Free-Living to the Host-Associated – Paul A. O’Brien – Frontiers in Marine Science

Waste and pollution microbiology

Shifts in microbial community structure and diversity in a MBR combined with worm reactors treating synthetic wastewater – Jia Liu – Journal of Environmental Sciences

Biomineralization of atrazine and analysis of 16S rRNA and catabolic genes of atrazine degraders in a former pesticide mixing site and a machinery washing area – James F. Douglass – Journal of Soils and Sediments

The effect of seasonality upon the development of lotic biofilms and microbial biostabilisation – Holger Schmidt – Freshwater Biology

Review: The importance of sewer biofilms – Henriette Jensen – Water

Food microbiology and functional foods

Lactobacillus plantarum TWK10 Supplementation Improves Exercise Performance and Increases Muscle Mass in Mice – Yi-Ming Chen – MDPI Nutrients

Investigation of the activity of the microorganisms in a Reblochon-style cheese by metatranscriptomic analysis – Christophe Monnet – Frontiers in Microbiology

Review: Prebiotics as a modulator of gut microbiota in paediatric obesity – A. C. Nicolucci – Pediatric Obesity

Techniques

Stable isotope probing with 18O-water to investigate microbial growth and death in environmental samples – Egbert Schwartz – Current Opinion in Biotechnology

Review: A priori Considerations When Conducting High-Throughput Amplicon-Based Sequence Analysis – Aditi Sengupta – Agricultural & Environmental Letters

Microbial ecology

Lack of functional redundancy in the relationship between microbial diversity and ecosystem functioning – Manuel Delgado-Baquerizo

Influence of dormancy on microbial competition under intermittent substrate supply: Insights from model simulations – Konstantin Stolpovsky – FEMS Microbiology Ecology

More microbiology

Metabolic Requirements of Escherichia coli in Intracellular Bacterial Communities during Urinary Tract Infection Pathogenesis – Matt S. Conover – mBio

Biostatistics

Reinventing Biostatistics Education for Basic Scientists – Tracey L. Weissgerber – PLOS Biology

Microbes in the news

MSU professor Gemma Reguera making tiny innovations with a big impact – Erin F. Wasinger – Lansing State Journal

SCSU prof Elizabeth Lewis Roberts discovers fungus, bacteria help grass (really) – Anna Bisaro – New Haven Register

Probiotics for Livestock – Reducing Antibiotic Reliance – Alex Alexiev – MicroBEnet

Taking Cues From Human Nutrition To Reduce Antibiotic Use In Livestock – Amy Mayer – NPR

Why bacteria can’t get any bigger—or smaller – Elizabeth Pennisi – Science

Digestion of lignin in the gut – Science Daily

“Truly exciting”: Probiotic may increase muscle mass, energy & performance – Stephen Daniells – Nutraingredients

Breakthrough at Binghamton furthers development of bacteria-powered energy – The Engineer

Vibrio: Aggressive infectious bacteria species found in Sydney Harbour – Daisy Dumas – Sydney Morning Herald

Science, publishing, and career

Do interventions to reduce misconduct actually work? Maybe not, says new report – Alison McCook – Retraction Watch

$250 million, 300 scientists and 40 labs: Sean Parker’s revolutionary project to ‘solve’ cancer – Ariana Eunjung Cha – Washington Post

Science fairs are as flawed as my solar-powered hot dog cooker – Carl Zimmer – STATnews

The dark side of Guardian comments: part of a series on the rising global phenomenon of online harassment – the Guardian

How one lab challenged a grant rejection and won €5 million – Ewen Callaway – Nature

April 1, 2016 (the serious one)

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Make sure to check out my special April 1st post about the creative use of human-derived microbes in food and beverage production. Today’s serious update is about a twin study on oral microbiota and the effects of host genetics and smoking, microbes in floral nectar along an urbanization gradient, plankton biogeography among alpine lakes, and classification of metagenomics data.

General microbiome

Review: Compositional Data Analysis of the Microbiome: Fundamentals, Tools, and Challenges – Matthew C.B. Tsilimigras – Annals of Epidemiology

Review: Gut Microbiotas and Host Evolution: Scaling Up Symbiosis – Michael Shapira – Trends in Ecology and Evolution

Pregnancy and birth

Conference abstract: Neonatal microbiota in health and disease – P. Panigrahi – International Journal of Infectious Diseases

Human oral microbiome

Analysis of the association between host genetics, smoking, and sputum microbiota in healthy humans – Mi Young Lim – Scientific Reports

Human cervical microbiome

Combined effect of diet and cervical microbiome on the risk of cervical intraepithelial neoplasia – Sang-Soo Seo – Clinical Nutrition

Human gut microbiome

Review: The effect of NOD2 on the microbiota in Crohn’s disease – Mackenzie L Lauro – Current Opinion in Biotechnology

Animal models

Prebiotics and Bioactive Milk Fractions Affect Gut Development, Microbiota and Neurotransmitter Expression in Piglets – Kirsten Berding – Journal of Pediatric Gastroenterology & Nutrition

Isolation of Lactobacillus reuteri from Peyer’s patches and their effects on sIgA production and gut microbiota diversity – Panpan Wang – Molecular Nutrition & Food Research

Plant, root, and soil microbiome

Ectomycorrhizal fungal richness declines toward the host species’ range edge – Richard A. Lankau – Molecular Ecology

Diversity and temporal dynamics of the epiphytic bacterial communities associated with the canopy-forming seaweed Cystoseira compressa (Esper) Gerloff & Nizamuddin – Francesco Paolo Mancuso – Frontiers in Microbiology

Do rhizosphere priming effects enhance plant nitrogen uptake under elevated CO2? –
Ming Nie – Agriculture, Ecosystems & Environment

Evidence for foliar endophytic nitrogen fixation in a widely distributed subalpine conifer – Andrew B. Moyes – New Phytologist

Microbial diversity in the floral nectar of Linaria vulgaris along an urbanization gradient – Jacek Bartlewicz – BMC Ecology

Water and pollution microbiome

Microbial eukaryote plankton communities of high-mountain lakes from three continents exhibit strong biogeographic patterns – Sabine Filker – Molecular Ecology

Nutrient uplift in a cyclonic eddy increases diversity, primary productivity and iron demand of microbial communities relative to a western boundary current – Martina A Doblin – PeerJ preprint

Connectivity between surface and deep waters determines prokaryotic diversity in the North Atlantic Deep Water – Alexander H. Frank – Environmental Microbiology

Chemical multi-contamination drives benthic prokaryotic diversity in the anthropized Toulon Bay – Benjamin Misson – Science of The Total Environment

Phylogenetic clustering of fungal communities in human-disturbed streams – H. Mykrä – Ecosphere

Built environment microbiome

Changes in bacterial composition of biofilm in a metropolitan drinking water distribution system – R. P. Revetta – Journal of Applied Microbiology

Food microbiology

Biodiversity and technological-functional potential of lactic acid bacteria isolated from spontaneously fermented quinoa sourdoughs – L. Ruiz Rodríguez – Journal of Applied Microbiology

Bioreactor microbiology

Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system – Daan R. Speth – Nature Communications

An exploratory study on the influence orange juice on gut microbiota using a dynamic colonic model – Ana Luiza Rocha Faria Duque – Food Research International

Bioinformatics and metagenomics

FOCUS2: agile and sensitive classification of metagenomics data using a reduced database – Genivaldo Silva – BioRxiv

Microbial Ecology

Microbial diversity arising from thermodynamic constraints – Tobias Großkopf – The ISME Journal

Techniques

Genetic circuit design automation: Programming circuitry for synthetic biology –
Alec A. K. Nielsen – Science

Review: Exploring the Secretomes of Microbes and Microbial Communities Using Filamentous Phage Display – Dragana Gagic – Frontiers in Microbiology

Microbes in the news

Your Cat’s Poop Might Help Save Lives: KittyBiome – Lisa Richman – Catster

Pine Bacteria Getting a Closer Look From Scientists – Lorena Anderson – UC Merced

Episode 2: Peek inside a lab trying to create living medicine — from bugs in your gut – Carl Zimmer – STAT News

Poop paper flushed due to possible sample contamination – Shannon Palus – Retraction Watch

About the minimal cell: Breakthrough in synthetic biology is far from ‘playing God’ – New Scientist

Commense Advances Microbiome Platform Targeting Early Childhood Health – Businesswire

New research supports previous findings in the placental microbiome – Baylor College of Medicine

Forensic microbiology from an entomological perspective – SFAM – Microbe Blog
New Potent Nanodrug to Combat Antibiotic-Resistant Infections – University of Arkansas

Vedanta Biosciences Announces License Agreement with RIKEN and other Japanese Institutions for New Immune Boosting Microbiome Technology – Pipeline Review

Brewers Claim They’ve Made Ice-Cold Beer With Vaginal Bacteria; In Theory It Works – Dana Dovey – Medical Daily

Beer brewed with vaginal bacteria is the draft we didn’t ask for – Justina Huddleston – She Knows

Scientists create ‘programming language for bacteria’ – BT.com

‘Listeria on Rye’? Many U.S. Deli Meat Slicers Cut Corners on Cleanliness – Health Day

Retail Deli Slicer Cleaning Frequency — Six Selected Sites, United States, 2012 – Laura G. Brown – CDC Morbidity and Mortality Weekly Report (MMWR)

Science, publishing, and career

Life in the lab, book review of “Lab Girl” by Hope Jahren – Meg Lowman – Science

How to Make Psychology Studies More Reliable – Ed Yong – The Atlantic

Hilda Bastian: She speaks — and draws — truth to scientific power – Karen Weintraub – STAT news

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March 30, 2016

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Microbiome and mood, bone marrow transplantation, archaea in kangaroos, tardigrade genome contamination.

Events

UC Berkeley Event: Archaea and the Three Domains: Classification of Life for Middle School

Microbiome expert to speak at UB –  Martin Blaser is a former president of the Infectious Diseases Society of America, April 6-7 – Charlotte Hsu – University of Buffalo

Pregnancy and birth

Microbiome: Antibiotics and the infant microflora – Kristen Meyer & Kjersti Aagaard – Nature Microbiology

Human mouth microbiome

Accuracy of commercial kits and published primer pairs for the detection of periodontopathogens – Elisabeth Santigli – Clinical Oral Investigations

Human gut microbiome

Gut microbes in correlation with mood: case study in a closed experimental human life support system – L. Li – Neurogastroenterology & Motility

Anti-TNF Therapy Response in Patients with Ulcerative Colitis Is Associated with Colonic Antimicrobial Peptide Expression and Microbiota Composition – Maria K. Magnusson – Journal of Crohn’s and Colitis

Gut microbiota profiling of pediatric NAFLD and obese patients unveiled by an integrated meta-omics based approach – Federica Del Chierico – Hepatology

Commentary: Role of gut flora after bone marrow transplantation – Jonathan U. Peled – Nature Microbiology

Animal microbiome

Differences down-under: alcohol-fueled methanogenesis by archaea present in Australian macropodids – Emily C Hoedt – The ISME Journal

Mussel biofiltration effects on attached bacteria and unicellular eukaryotes in fish-rearing seawater – Eleni Voudanta – PeerJ

Plant, root, and soil microbiome

Tobacco, Microbes, and Carcinogens: Correlation Between Tobacco Cure Conditions, Tobacco-Specific Nitrosamine Content, and Cured Leaf Microbial Community – Audrey D. Law – Microbial Ecology

Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland – Noriko A. Cassman – Scientific Reports

Drinking water microbiome

Flow cytometric examination of bacterial growth in a local drinking water network –
Sam Van Nevel – Water and Environment Journal

Animal microbiome

Breakdown of coevolution between symbiotic bacteria Wolbachia and their filarial hosts – Emilie Lefoulon – PeerJ

Built environment microbiome

Review (but did not make much sense to me): Toward a microbial Neolithic revolution in buildings – David S. Thaler – Microbiome

Bioreactor microbiome

Functional maintenance and structural flexibility of microbial communities perturbed by simulated intense rainfall in a pilot-scale membrane bioreactor – Yuya Sato – Applied Microbiology and Biotechnology

Fungi

News: Microbiology: Fungus produces a toxic surprise – Aaron P. Mitchell – Nature

Candidalysin is a fungal peptide toxin critical for mucosal infection – David L. Moyes – Nature

Biofilms

Spatio-temporal assembly of functional mineral scaffolds within microbial biofilms – Yaara Oppenheimer-Shaanan – NPJ Biofilms

Metagenomics and bioinformatics

Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies – Tom O Delmont – PeerJ

myPhyloDB: a local web server for the storage and analysis of metagenomic data – Daniel K. Manter – Database

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning – Brian Cleary – Nature Biotechnology

Metabolomics

Optimization of metabolomics of defined in vitro gut microbial ecosystems – Dirk K. Wissenbach – International Journal of Medical Microbiology

Microbial ecology

Review: Challenges in microbial ecology: building predictive understanding of community function and dynamics – Stefanie Widder – The ISME Journal

Microbes in the news

Another reason to break the habit: Smoking alters bacterial balance in mouth – EurekAlert

Pseudomonas aeruginosa in shampoos and shower gels made by Gilchrist and Soames – FDA warning letter

Acne bacteria and hot dog cookers: Science projects take center stage at regional fair – Matt Barney – The Joplin Globe

Cave bacteria could control superbugs – News24

The 8-Bit Game That Makes Statistics Addictive – Ed Yong – The Atlantic

Microbes and art

“World’s First” Bacteria-Grown Book Combines Science and Culture – Nathaniel Ainley – The Creators Project

WTF

Polish company to brew beer from Czech model’s vagina bacteria – Ben Hooper – UPI

First Vaginal Beer: Bottled Instinct – Wojciech Mann – IndieGoGo
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March 29, 2016

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Microbiota and stroke outcome, viruses and FMT, Arctic polar deserts, sex and dorm rooms (aren’t you curious?).

Pregnancy and birth

A Study of the Infant Nasal Microbiome Development over the First Year of Life and in Relation to Their Primary Adult Caregivers Using cpn60 Universal Target (UT) as a Phylogenetic Marker – Shelley W. Peterson – PLOS ONE

Human respiratory microbiome (see also above)

Pharyngeal carriage of Neisseria species in the African meningitis belt – Kanny Diallo – Journal of Infection

Human gut microbiome

Commensal microbiota affects ischemic stroke outcome by regulating intestinal γδ T cells – Corinne Benakis – Nature Medicine

Transfer of Viral Communities between Human Individuals during Fecal Microbiota Transplantation – Christel Chehoud – mBio

Correlation between diet and gut bacteria in a population of young adults – Lino Mayorga Reyes – International Journal of Food Sciences and Nutrition

Fecal Microbiota Transfer in Patients With Chronic Antibiotic-Refractory Pouchitis – Andreas Stallmach – American Journal of Gastroenterology

Review: Engineering Human Microbiota: Influencing Cellular and Community Dynamics for Therapeutic Applications – S. Woloszynek – International Review of Cell and Molecular Biology

Review: Metabolic role of lactobacilli in weight modification in humans and animals – Fatima Drissi – Microbial Pathogenesis

Editorial: The Dawning of Microbiome Remediation for Addressing Antibiotic Resistance – Alison Laufer Halpin – Clinical Infectious Diseases

Review: Beyond Antibiotics: New Therapeutic Approaches For Bacterial Infections – Alan R. Hauser – Clinical Infectious Diseases

Correspondence: The Microbiome: A Biological Mechanism Underpinning the Social Gradient of Musculoskeletal Conditions? – Sharon L Brennan-Olsen – Journal of Bone and Mineral Research

Animal models

Effects of chlorpyrifos on the gut microbiome and urine metabolome in mouse (Mus musculus) – Yanping Zhao – Chemosphere

The Effect of Antibiotics on Associated Bacterial Community of Stored Product Mites – Jan Kopecky – PLOS ONE

Animal microbiome

Effects of Host Plant Factors on the Bacterial Communities Associated with Two Whitefly Sibling Species – Ming-Ming Su – PLOS ONE

Microbial Diversity and Parasitic Load in Tropical Fish of Different Environmental Conditions – Philipp Hennersdorf – PLOS ONE

Potential bacterial core species associated with digital dermatitis in cattle herds identified by molecular profiling of interdigital skin samples – Martin W. Nielsen – Veterinary Microbiology

Plant, root, and snow microbiome

Diversity and distribution of the endophytic bacterial community at different stages of Eucalyptus growth – Paulo Sérgio Balbino Miguel – Antonie van Leeuwenhoek

Book: Microbial Inoculants in Sustainable Agricultural Productivity – Springer

Book: Microbial-mediated Induced Systemic Resistance in Plants
Editors: Devendra K. Choudhary, Ajit Varma – Springer

Water, snow, and extremophile microbiome

Microbial communities in a High Arctic polar desert landscape – Clare M. McCann – Frontiers in Microbiology

Responses of methanogenic and methanotrophic communities to warming in varying moisture regimes of two boreal fens – Krista Peltoniemi – Soil Biology and Biochemistry

Oligotyping and metagenome analyses reveal a high-resolution recurrence that frames potential ecological strategies of North Sea bacterioplankton – M. Chafee – Annual DOE JGI Genomics of Energy & Environment Meeting

Long-term increase in snow depth leads to compositional changes in arctic ectomycorrhizal fungal communities – Luis N. Morgado – Global Change Biology

Patterns and variability in geochemical signatures and microbial activity within and between diverse cold seep habitats along the lower continental slope, Northern Gulf of Mexico – Marshall Bowles – Deep Sea Research Part II: Topical Studies in Oceanography

Surface waters in northern Tanzania harbor fecal coliform and antibiotic resistant Salmonella spp. capable of horizontal gene transfer – Beatus Lyimo – African Journal of Microbiology Research

Book chapter: Planktonic Bacterial Communities in Mountain Lake Ecosystems – Masanori Fujii – Structure and Function of Mountain Ecosystems in Japan

Waste and pollution microbiome

Biodegradation of dispersed Macondo crude oil by indigenous Gulf of Mexico microbial communities – Jian Wang – Science of The Total Environment

The effects of various land reclamation scenarios on the succession of soil Bacteria, Archaea, and fungi over the short and long term – Junjian Li – Frontiers in Ecology and Evolution

Illumina MiSeq sequencing reveals long-term impacts of single-walled carbon nanotubes on microbial communities of wastewater treatment systems – Yuanyuan Qu – Bioresource Technology

Predictive functional profiling using marker gene sequences and community diversity analyses of microbes in full-scale anaerobic sludge digesters – Jing Gao – Bioprocess and Biosystems Engineering

Built environment microbiome

Microbial analyses of airborne dust collected from dormitory rooms predict the sex of occupants – Julia C Luongo – Indoor Air

Microbiological characterization of stable resuspended dust – Nora Kováts – Int J Occup Med Environ Health

Food microbiome

Reducing bias in complex microbial community analysis in shrimp based on propidium monoazide combined with PCR-DGGE – Fei Zhao – Food control

A simple and rapid method for detecting living microorganisms in food using laser speckle decorrelation – Jonghee Yoon – arXiv

Viruses and phages

A strange endocytobiont revealed as largest virus – P Scheid – Current Opinion in Microbiology

More microbiology

A generalized spatial measure for resilience of microbial systems – Ryan S. Renslow – Frontiers in Microbiology

Evaluating the efficacy of the new Ion PGM Hi-Q Sequencing Kit applied to bacterial genomes – Felipe L. Pereira – Genomics

In Vitro Selection of RNA-cleaving DNAzymes for Bacterial Detection – Wenqing Zhang – Methods

Architectural transitions in Vibrio cholerae biofilms at single-cell resolution – Knut Drescher – PNAS

Book: New Weapons to Control Bacterial Growth – Editors: Tomas G. Villa, Miguel Vinas – Springer

Microbes in the news

How bacteria, fungi, and mold are finding a home in high-end kitchens
Scientists and chefs find flavor through fermentation – Lindsey J. Smith – The Verge

Could bugs in the gut offer clues for reducing the severity of stroke? – Eric Boodman – STAT news

Microbial cocktails join fecal transplants in IBD treatment trials –
Mark Ratner – Nature Biotechnology News

The Fridge Laser That Detects Bacteria Crawling All Over Food – Rachel Metz – Technology Review

What bacteria lurk in stable dust? – Horsetalk

Humans use ‘sticky molecules’ to hang on to good bacteria in the gut – Stuart Gillespie – University of Oxford

Clostridium botulinum: New Details Emerge on a Notorious Bird-Killing Bacteria – Matt Soniak – Audubon

Swiss study finds E. coli bacteria in ice cubes – The Local

How Dirty Are Public Restrooms, Really? – Stephanie Pappas – Live Science

Gut Microbes Can Evolve From Foe to Friend—And Do It Fast – Ed Yong – National Geographic

Oyster research could lead to food safety strategies – Cookson Beecher – Food Safety News

Why a healthy gut may be the secret to a lean, healthy body – Jennifer Landa – Fox News

Does the 5-Second Rule When You Drop Food Really Work? Here’s What Science Says – Jessica Eggert – Science.Mic

Science, publishing, and career

The seagull of science: Google’s bold bid to transform medicine hits turbulence under a divisive CEO – Charles Piller – STAT news

Andrew Kern on PLoS: Things aren’t what they seem – Storify

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March 24, 2016

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Two papers on antibiotics in early childhood and obesity, diabetic foot ulcers, vertebrate animal microbiomes, cattle hides, kimchi, human archaeological remains, and high inter-center variability in microbiome results.

General microbiome

Review: Stress as a Normal Cue in the Symbiotic Environment – Julia A. Schwartzman – Trends in Microbiology

Pregnancy and birth

Administration of Antibiotics to Children Before Age 2 Years Increases Risk for Childhood Obesity – Frank I. Scott – Gastroenterology

Antibiotic Exposure During the First 6 Months of Life and Weight Gain During Childhood – Jeffrey S. Gerber – JAMA

Editorial: From Bottles to Diapers: How Manipulating and Exploring the Microbiome Is Defining Newborn Care – Jill L. Maron – Clinical Therapeutics

Research highlight: Gut microbiota dysbiosis precedes NEC – Hugh Thomas – Nature Reviews Gastroenterology & Hepatology

Human skin microbiome

One step closer to understanding the role of bacteria in diabetic foot ulcers: characterising the microbiome of ulcers – Karen Smith – BMC Microbiology

Human gut microbiome

Colonic Mucosal Epigenome and Microbiome Development in Children and Adolescents – R. Alan Harris – Journal of Immunology Research

Defining the microbial transcriptional response to colitis through integrated host and microbiome profiling – Nicholas Edward Ilott – The ISME Journal

Targeting colorectal cancer-associated bacteria: a new area of research for personalized treatments – T. Faïs – Gut Microbes

Relative Abundance in Bacterial and Fungal Gut Microbes in Obese Children: A Case Control Study – Borgo Francesca – Childhood Obesity

Review: Can attention to the intestinal microbiota improve understanding and treatment of anorexia nervosa? – Jacquelyn Carr – Expert Review of Gastroenterology & Hepatology

Editorial: Fecal Microbiota Transplantation for Ulcerative Colitis: FoMenTing Change? – Flaviano S. Martins – Digestive Diseases and Sciences

Review: Does the Microbiome Cause B27-related Acute Anterior Uveitis? – James T. Rosenbaum – Ocular Immunology and Inflammation

Microbes in blood

The prognostic significance of bacterial DNA in patients with decompensated cirrhosis and suspected infection – Tony Bruns – Liver International

Animal models

The microbiota-derived metabolite indole decreases mucosal inflammation and injury in a murine model of NSAID enteropathy – Gut Microbes

TLR4-Dependent Secretion by Hepatic Stellate Cells of the Neutrophil-Chemoattractant CXCL1 Mediates Liver Response to Gut Microbiota – Amélie E. Bigorgne – PLOS ONE

Animal microbiome

Vertebrate bacterial gut diversity: size also matters – Jean-Jacques Godon – BMC Ecology

Larval growth rate is associated with the composition of the gut microbiota in the Glanville fritillary butterfly – L. Ruokolainen – Oecologia

Host origin and tissue-microhabitat shaping the microbiota of the terrestrial isopod Armadillidium vulgare – Jessica Dittmer – FEMS Microbiology Ecology

Presence of pathogenic Escherichia coli is correlated with bacterial community diversity and composition on pre-harvest cattle hides – Jessica Chopyk – Microbiome

Plant, root, and soil microbiome

High Diversity Revealed in Leaf Associated Protists (Rhizaria: Cercozoa) of Brassicaceae – Sebastian Ploch – The Journal of Eukaryotic Microbiology

Precipitation shapes communities of arbuscular mycorrhizal fungi in Tibetan alpine steppe – Jing Zhang – Scientific Reports

Spatial and seasonal influences on culturable endophytic mycobiota associated with different tissues of Eugenia jambolana Lam. and their antibacterial activity against MDR strains – Manila Yadav – BMC Microbiology

Response of enzyme activities and microbial communities to soil amendment with sugar alcohols – Huili Yu – Microbiology Open

Bioprospecting plant-associated microbiomes – Christina A. Müller – Journal of Biotechnology

Water and extremophile microbiome

Abundances, diversity and seasonality of (non-extremophilic) Archaea in Alpine freshwaters – Christoph Reitschuler – Antonie van Leeuwenhoek

Anthropogenic effects on bacterial diversity and function along a river-to-estuary gradient in Northwest Greece revealed by metagenomics – Alexandra Meziti – Environmental Microbiology

Heterotrophic Proteobacteria in the vicinity of diffuse hydrothermal venting – Dimitri Meier – Environmental Microbiology

Waste and pollution microbiology

Response and resilience of soil microbial communities inhabiting in edible oil stress/contamination from industrial estates – Vrutika Patel – BMC Microbiology

Built environment microbiology

Diversity of ribosomal 16S DNA- and RNA-based bacterial community in an office building drinking water system – Jenni Inkinen – Journal of Applied Microbiology

Forensic microbiology

Complications in the study of ancient tuberculosis: Presence of environmental bacteria in human archaeological remains – Romy Müller – Journal of Archaeological Science

Food microbiology

Lentibacillus kimchii sp. nov., an extremely halophilic bacterium isolated from kimchi, a Korean fermented vegetable – Young Joon Oh – Antonie van Leeuwenhoek

Computational modeling

Host Selection of Microbiota via Differential Adhesion – Kirstie McLoughlin – Cell Host & Microbe

Techniques

The real cost of sequencing: scaling computation to keep pace with data generation – Paul Muir – Genome Biology

Multicenter quality assessment of 16S ribosomal DNA-sequencing for microbiome analyses reveals high inter-center variability – Andreas Hiergeist –
International Journal of Medical Microbiology

Genotyping bacterial and fungal pathogens using sequence variation in the gene for the CCA-adding enzyme – Paul Franz – BMC Microbiology

Proteomics

Review: Tackling probiotic and gut microbiota functionality through proteomics – Lorena Ruiz – Journal of Proteomics

Microbes in the news

Can we model how viruses move between species? – Nancy Mendoza – Microbe Post

The Virus That Could Cure Alzheimer’s, Parkinson’s, and More – Jon Palfreman – PBS

Report: Laminate wood flooring risk was underestimated by CDC – Jonathan Eisen – MicroBEnet

Microbiota profiles in patients with colorectal cancer differ from healthy individuals – Healio

Science, publishing and career

Set up a ‘self-retraction’ system for honest errors, says Daniele Fanelli – Nature

Incorporating Primary Scientific Literature in Middle and High School Education – Sarah C. Fankhauser – ASM Science

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March 22, 2016

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Eye microbiota and contact lenses, leaf-cutter ant dumps, bacteria help with platinum transformation, metagenomics from a Swedish cave, extreme habitats at home, bacteria on board the ISS, a special issue on Megaviromes, and a recipe for Poop Peeps.

Jobs

Lecturership in Human Microbiome Studies – University of Reading, UK

Pregnancy and birth

Effect of Infant Formula Containing a Low Dose of the Probiotic Bifidobacterium lactis CNCM I-3446 on Immune and Gut Functions in C-Section Delivered Babies: A Pilot Study – L. Baglatzi – Clinical Medicine Insights: Pediatrics

Infection, immunology, and transplantion microbiology

Metagenomic analysis of bloodstream infections in patients with acute leukemia and therapy-induced neutropenia – P. Gyarmati – Scientific Reports

Rifaximin preserves intestinal microbiota balance in patients undergoing allogeneic stem cell transplantation – D Weber – Bone Marrow Transplantation

Gut microbiome–derived metabolites modulate intestinal epithelial cell damage and mitigate graft-versus-host disease – Nathan D Mathewson – Nature Immunology

Crosstalk between microbiota, pathogens and the innate immune responses – Claudia Günther – International Journal of Medical Microbiology

Human oral microbiome

Commentary: Microbiota-derived metabolites modulate tissue homeostasis: relevance to the oral cavity? – Hervé Le Moual – Oral Diseases

Human eye and skin microbiome

Changes in the Eye Microbiota Associated with Contact Lens Wearing – Hakdong Shin – mBio

Human vaginal microbiome

Improvement and automation of a real-time PCR assay for vaginal fluids – E. De Vittori – Forensic Science International

Human gut microbiome

Conference report: Talking about cross-talk: the immune system and the microbiome: A report on the first EMBO conference entitled “Next Gen Immunology—From Host Genome to the Microbiome: Immunity in the Genomic Era”, Feb 2016 – David Zeevi – Genome Biology

Review: An (Anti)-Inflammatory Microbiota: Defining the Role in Inflammatory Bowel Disease? – Burman S. – Digestive Diseases

Review: Gut Microbiota: The Brain Peacekeeper – Chunlong Mu – Frontiers in Microbiology

Review [PDF]: The intestinal microbiota and its role in human health and
disease – Keiko Kataoka – The Journal of Medical Investigation

Editorial: The microbiome as a possible target to prevent celiac disease – Maureen M Leonard – Expert Review of Gastroenterology & Hepatology

Animal models

Mice: Arthritis-induced alveolar bone loss is associated with changes in the composition of oral microbiota – Jôice Dias Corrêa – Anaerobe

Chickens: Dietary High Fluorine Alters Intestinal Microbiota in Broiler Chickens – Qin Luo – Biological Trace Element Research

Tilapia: Abrupt suspension of probiotics administration may increase host pathogen susceptibility by inducing gut dysbiosis – Zhi Liu – Scientific Reports

Animal microbiome

Cellulose-Enriched Microbial Communities from Leaf-Cutter Ant (Atta colombica) Refuse Dumps Vary in Taxonomic Composition and Degradation Ability – Gina R. Lewin – PLOS ONE

Plant, root, and soil microbiome

Relic DNA is abundant in soil and obscures estimates of soil microbial diversity – Paul Carini – bioRxiv

Biological role in the transformation of platinum-group mineral grains – Frank Reith – Nature Geoscience

Associations between ectomycorrhizal fungi and bacterial needle endophytes in Pinus radiata: implications for biotic selection of microbial communities – Megan A. Rúa – Frontiers in Microbiology

Functional composition of plant communities determines the spatial and temporal stability of soil microbial properties in a long-term plant diversity experiment – Tanja Strecker – Oikos

No synergistic effects of water and nitrogen addition on soil microbial communities and soil respiration in a temperate desert – Yan Gui Su – CATENA

The role of phosphorus, magnesium and potassium availability in soil fungal exploration of mineral nutrient sources in Norway spruce forests – Nicholas P. Rosenstock – New Phytologist

Climate and edaphic controllers influence rhizosphere community assembly for a wild annual grass – Erin E. Nuccio – Ecology

Temporal distance decay of similarity of ectomycorrhizal fungal community composition in a subtropical evergreen forest in Japan – Shunsuke Matsuoka – FEMS Microbiology Ecology

Review: The Functioning of Rhizosphere Biota in Wetlands – a Review – Amir Neori – Wetlands

Water and extremophile microbiome

Experimental evidence that microbial activity lowers the albedo of glaciers – M. Musilova – Geochemical Perspectives Letters

Transcriptional analysis of sulfate reducing and chemolithoautotrophic sulfur oxidizing bacteria in the deep subseafloor – William D. Orsi – Environmental Microbiology Reports

Cave microbiome

Metagenomic Analysis from the Interior of a Speleothem in Tjuv-Ante’s Cave, Northern Sweden – Marie Lisandra Zepeda Mendoza – PLOS ONE

Built environment microbiology

Microbial diversity of extreme habitats in human homes – Amy M. Savage – PeerJ preprint

Growth of 48 built environment bacterial isolates on board the International Space Station (ISS) – David A. Coil – PeerJ

Food microbiology

Isolation and identification of biocellulose-producing bacterial strains from Malaysian acidic fruits – Wen Yi W. V – Letters in Applied Microbiology

Bioinformatics, techniques, and metagenomics

Strain-level microbial epidemiology and population genomics from shotgun metagenomics – Matthias Scholz – Nature Methods

Improving the microbial community reconstruction at the genus level by multiple 16S rRNA regions – Shengqin Wang – Journal of Theoretical Biology

A framework for inferring biological communities from environmental DNA – Andrew Olaf Shelton – Ecological Applications

Review: Next-generation sequencing (NGS) in the microbiological world: How to make the most of your money – Antony T. Vincent – Journal of Microbiological Methods

Metagenomics and viruses

A Next-Generation Sequencing Data Analysis Pipeline for Detecting Unknown Pathogens from Mixed Clinical Samples and Revealing Their Genetic Diversity – Yu-Nong Gong – PLOS ONE

Exploring the virome of cattle with non-suppurative encephalitis of unknown etiology by metagenomics – Daniel Wüthrich – Virology

The Intestinal Eukaryotic Virome in Healthy and Diarrhoeic Neonatal Piglets – Oskar E. Karlsson – PLOS ONE

Special issue of Current Opinion in Microbiology: Megaviromes
Review: Giant viruses come of age – Matthias G Fischer
Review: Giant viruses and the origin of modern eukaryotes – Patrick Forterre

To be or not to be alive: How recent discoveries challenge the traditional definitions of viruses and life – Patrick Forterre – Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences

More microbiology

The mystery of plague in medieval Iceland – Chris Callow – Journal of Medieval History

Microbes in the news

HT: Tomer Altman: Poop Peeps: Today we’re going to make Poop Peeps. Marshmallow Peeps that are shaped like the poop emoji.– Matthew Cetta – Nomageddon

Elizabethkingia, the rare and deadly bacteria that’s sickening people in the Midwest, explained – Julia Belluz – Vox

Forest resilience; can microbes help combat climate change issues faster than genetic adaptations? – Armand Séguin

Controversial New Push to Tie Microbes to Alzheimer’s Disease. A journal article says herpes virus and Lyme disease bacteria are behind the mind-robbing illness, but not all researchers are convinced – Melinda Wenner Moyer – Scientific American

Bacteria Are Revolutionizing Biotech–Here’s Why We Need To Talk About It – Catherine Feuillet – Forbes

Contact Lenses Fill Your Eyes With Bacteria – Mandy Oaklander – Time

Killing Bacteria With Gold Nanodisks And Light – Jennifer Hicks – Forbes

Space gives bacteria room to grow – Dan Satherley – NewsHub

Uncovering bacterial role in platinum formation – University of Adelaide

Top Science Fair Projects Put Stream Data, Bacteria to Work – Dan Swanson – News Channel Nebraska

The Daily Startup: Startups Look to ‘New Frontier’ of Microbiomes to Fight Disease – Wall Street Journal

The Human Microbiome Handbook – Edited by Jason Tetro, Emma Allen-Vercoe

New Bioinformatic Approach Enables Strain-Level Microbial Profiling From Metagenomic Data – Genome Web

Ulcerative Colitis Improves in Multidonor Fecal Transplant Trial – Damian McNamara – MedScape

Blog posts by me:

New papers, March 22, 2016 – Elisabeth Bik – MicroBEnet

Extreme environments at home – Elisabeth Bik – MicroBEnet

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