Category Archives: Pregnancy and birth

April 27, 2016

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Cervical microbiome during cancer, distinct gut microbiome in kidney stone formers? (unclear due to vaguely formulated control group), culturing marine microbes in artificial seawater, codon usage to predict pathogenicity.

Events

Science Diplomats to present ‘Trust Your Gut: How Helpful Bacteria Impact Health’ – Free talk given 3 times at Yale in May

Pregnancy and birth

News & Views: Immunology: Mum’s microbes boost baby’s immunity – Mihir Pendse & Lora V. Hooper – Nature

Human respiratory microbiome

Culture based: Microbiology of peritonsillar abscess in the South Estonian population – Risto Vaikjärv – Microbial Ecology in Health and Disease

Human reproductive tract microbiome

Cervical Microbiome and Cytokine Profile at Various Stages of Cervical Cancer: A Pilot Study – Astride Audirac-Chalifour – PLOS ONE

Human gut microbiome

Note that the control group is poorly described: Evidence for a distinct gut microbiome in kidney stone formers compared to non-stone formers – Joshua M. Stern – Urolithiasis

Review: Macrobiota — helminths as active participants and partners of the microbiota in host intestinal homeostasis – William C Gause – Current Opinion in Microbiology

Review: The possible mechanisms of the human microbiome in allergic diseases – Kagan Ipci – European Archives of Oto-Rhino-Laryngology

Review: Towards a functional hypothesis relating anti-islet cell autoimmunity to the dietary impact on microbial communities and butyrate production – David Endesfelder – Microbiome

Animal and bioreactor models

Biochar, Bentonite and Zeolite Supplemented Feeding of Layer Chickens Alters Intestinal Microbiota and Reduces Campylobacter Load – Tanka P. Prasai – PLOS ONE

Applying theories of microbial metabolism for induction of targeted enzyme activity in a methanogenic microbial community at a metabolic steady state – Jutta Speda – Applied Microbiology and Biotechnology

A humanized microbiota mouse model of ovalbumin-induced lung inflammation – Marie-Claire Arrieta – Gut Microbes

Plant, root, and soil microbiome

Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria – Edward W. Davis II – PeerJ Preprint

Water and extremophile microbiome

Artificial Seawater Media Facilitate Cultivating Members of the Microbial Majority from the Gulf of Mexico – Michael W. Henson – mSphere

Salinity shapes microbial diversity and community structure in surface sediments of the Qinghai-Tibetan Lakes – Jian Yang – Scientific Reports

Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations – Alexander J. Probst – Environmental Microbiology

Metabolome-mediated biocryomorphic evolution promotes carbon fixation in Greenlandic cryoconite holes – J.M. Cook – Environmental Microbiology

Pollution and waste microbiology

Microbial density and diversity in constructed wetland systems and the relation to pollutant removal efficiency – Yang Zhang – Water Science & Technology

A mesophilic anaerobic digester for treating food waste: process stability and microbial community analysis using pyrosequencing – Lei Li – Microbial Cell Factories

Microbial ecology

Inhibitory interactions promote frequent bistability among competing bacteria –
Erik S. Wright – Nature Communications

Bioinformatics and metagenomics

Protocol: Big Data, Evolution, and Metagenomes: Predicting Disease from Gut Microbiota Codon Usage Profiles – Maja Fabijani – Data Mining Techniques for the Life Sciences

Review: High definition for systems biology of microbial communities: metagenomics gets genome-centric and strain-resolved – Dmitrij Turaev – Current Opinion in Biotechnology

Microbes in the news

Elizabethkingia: The bacteria strain that could kill you. Or cure malaria. Small Science: Genomic data is showing us how little we know – Lisa Margonelli – Houston Chronicle

New Anti-Biofilm Nano Coating Prevents Bacterial Growth on Metal Surfaces – Azo Nano

Quick mapping of our microbiomes and metabolomes – Science Daily

Viral Skin Infections – Tomislav Meštrović – News Medical

Bacteria pill is ‘better than statins’ in the war on cholesterol, say researchers – Joe Smith – Mirror UK

Bacterial virulence is stimulated by burns – EurekAlert

Science, publishing, and career

Meet The New CEO Of The $22 Billion Genomics Company You’ve Never Heard Of: Francis deSouza to lead Illumina – Christina Farr – Fast Company

What Happened When I Pushed Myself to Interview More Women: Increasing the breadth of sources in journalism – John R. Platt – Motherboard

The quiet revolutionary: How the co-discovery of CRISPR explosively changed Emmanuelle Charpentier’s life. The microbiologist spent years moving labs and relishing solitude. Then her work on gene-editing thrust her into the scientific spotlight – Alison Abbott – Nature

Speak up about subtle sexism in science: Female scientists face everyday, often-unintentional microaggression in the workplace, and it won’t stop unless we talk about it – Tricia Serio – Nature

Bik’s Picks

Effects of a Closed Space Environment on Gene Expression in Hair Follicles of Astronauts in the International Space Station – Masahiro Terada – PLOS ONE

April 26, 2016

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Gut microbiome in preterm infants, the bee microbiome, monitoring of surfaces in the ISS, and a database-independent approach to OTU picking.

Jobs and events

Assistant/Associate Professor in Microbiome Studies – University of Arizona

I am one of the judges! 2016 MoBio Microbiome Awards – Deadline May 31

General microbiome

Comment: A multi-omic future for microbiome studies – Janet K. Jansson – Nature Microbiology

Pregnancy and birth

Gut Microbiome Developmental Patterns in Early Life of Preterm Infants: Impacts of Feeding and Gender – Xiaomei Cong – PLOS ONE

Human oral microbiome

Microbiota-based Signature of Gingivitis Treatments: A Randomized Study – Shi Huang – Scientific Reports

Complementary clinical effects of red complex bacteria on generalized periodontitis in a caucasian population – E Lanza – Oral Diseases

Human blood ‘microbiome’

(also stool microbiome) Alteration of the serum microbiome composition in cirrhotic patients with ascites – Alba Santiago – Scientific Reports

Human gut microbiome

Lactobacillus rhamnosus GG Intake Modifies Preschool Children’s Intestinal Microbiota, Alleviates Penicillin-Associated Changes, and Reduces Antibiotic Use – Katri Korpela – PLOS ONE

Fecal Microbiota Transplantation Using Upper Gastrointestinal Tract for the Treatment of Refractory or Severe Complicated Clostridium difficile Infection in Elderly Patients in Poor Medical Condition: The First Study in an Asian Country – Tae-Geun Gweon – Gastroenterology Research and Practice

Review: A healthy gastrointestinal microbiome is dependent on dietary diversity – Mark L. Heiman – Molecular Metabolism

Review: Mediterranean diet and faecal microbiota: a transversal study – Isabel Gutiérrez-Díaz – Food & Function

Editorial to a special Issue: Gut Microbiota and Metagenomic Advancement in Digestive Disease – Jinsheng Yu – Gastroenterology Research and Practice

Review: Efficacy and Mechanisms of Action of Fecal Microbiota Transplantation in Ulcerative Colitis: Pitfalls and Promises From a First Meta-Analysis – F. Scaldaferri – Transplantation Proceedings

Animal and other models

Sex steroid deficiency–associated bone loss is microbiota dependent and prevented by probiotics – Jau-Yi Li – the Journal of Clinical Investigation

Commentary: From the gut to the strut: where inflammation reigns, bone abstains – Jameel Iqbal – The Journal of Clinical Investigation

Acute dextran sulfate sodium (DSS)-induced colitis promotes gut microbial dysbiosis in mice – Peris Mumbi Munyaka – Journal of Basic Microbiology

Effects of low-level dietary microalgae supplementation on the distal intestinal microbiome of farmed rainbow trout Oncorhynchus mykiss (Walbaum) – Philip P Lyons – Aquaculture Research

The evolution of cooperation within the gut microbiota – Seth Rakoff-Nahoum – Nature

Gut microbiota-associated bile acid deconjugation accelerates hepatic steatosis in ob/ob mice – Mi-Young Park – Journal of Applied Microbiology

Effect of in ovo administration of an adult-derived microbiota on establishment of the intestinal microbiome in chickens – Adriana A. Pedroso – American Journal of Veterinary Research

Animal microbiome

First Comparative Analysis of the Community Structures and Carbon Metabolic Pathways of the Bacteria Associated with Alvinocaris longirostris in a Hydrothermal Vent of Okinawa Trough – Qing-lei Sun – PLOS ONE

The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions – Philipp Engel – mBio

Masters thesis, pdf: Geographic influences on the skin microbiome of humpback whales – Kevin Charles Bierlch – Duke University

Plant, root, and soil microbiome

Metabarcoding of Bacteria Associated with the Acute Oak Decline Syndrome in England – Melanie Sapp – MDPI Forests

Conservation tillage increases soil bacterial diversity in the dryland of northern China – Ziting Wang – Agronomy for Sustainable Development

Temporal dynamic of parasite-mediated linkages between the forest canopy and soil processes and the microbial community – Ana Mellado – New Phytologist

A watering manipulation in a semiarid grassland induced changes in fungal but not bacterial community composition – Theresa A. McHugh – Pedobiologia

Vertical micro-distribution of microbial communities living in Sphagnum fallax – Lihong Song – Inter-Research Aquatic Microbial Ecology

Bacterial Rhizosphere Biodiversity from Several Pioneer Desert Sand Plants Near Jizan, Saudi Arabia – Jorge R. Osman – The Open Conference Proceedings Journal

Water microbiome

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

Proteomic Stable Isotope Probing Reveals Taxonomically Distinct Patterns in Amino Acid Assimilation by Coastal Marine Bacterioplankton – Samuel Bryson – mSystems

Phylogenetic structure of bacterial assemblages co-occurring with Ostreopsis cf. ovata bloom – Silvana Vanucci – Harmful Algae

Persistence, loss and appearance of bacteria upstream and downstream – Lisa Dann – Marine and Freshwater Research

Ammonia-oxidizing archaea and bacteria in water columns and sediments of a highly eutrophic plateau freshwater lake – Yuyin Yang – Environmental Science and Pollution Research

Doctoral thesis: Characterization and comparison of microbial communities from different tourist ports in Mediterranean Sea and evaluation of applicability of bioremediation treatments – Enrica Bullita – Università di Cagliari

Built environment microbiome

Four-year bacterial monitoring in the International Space Station—Japanese Experiment Module “Kibo” with culture-independent approach – Tomoaki Ichijo – MPJ Microgravity

Food microbiology

The microbiological quality of pasteurized milk sold by automatic vending machines – Apostolos S. Angelidis – Letters in Applied Microbiology

Waste and pollution microbiology

Seasonal monitoring of bacteria and archaea in a full-scale thermophilic anaerobic digester treating food waste-recycling wastewater: correlations between microbial community characteristics and process variables – Joonyeob Lee – Chemical Engineering Journal

Effect of increased load of high-strength food wastewater in thermophilic and mesophilic anaerobic co-digestion of waste activated sludge on bacterial community structure – Hyun Min Jang – Water Research

Performance of a new suspended filler biofilter for removal of nitrogen oxides under thermophilic conditions and microbial community analysis – Li Han – Science of The Total Environment

Viruses and phages

Deciphering the virus-to-prokaryote ratio (VPR): insights into virus–host relationships in a variety of ecosystems – Kaarle J. Parikka – Biological Reviews

Metagenomics, phylogeny, and bioinformatics

Application of a Database-Independent Approach To Assess the Quality of Operational Taxonomic Unit Picking Methods – Patrick D. Schloss – mSystems

Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C) – Matthew Z. DeMaere – PeerJ Preprint

From Sample to Multi-Omics Conclusions in under 48 Hours – Robert A. Quinn – mSystems

Microbes in the news

An emerging fungal disease is killing snakes in the US – Anand Jagatia – Microbe Post

Gut feeling: Research examines link between stomach bacteria, PTSD – Science Daily

Converting perchlorate into oxygen: Students colonise Mars with E. coli bacteria – Alpha Galileo

Are multidrug-resistant bacteria spread through sewage water? – Universität Bonn

Fermentation festival leads to rapid response system at Center for Microbiome Innovation – Science Codex

Changes in ‘microbiome’ during canine atopic dermatitis could lead to antibiotic-free therapies for human and canine disease – EurekAlert

More Than A Gut Feeling: Can Gut Microbiome Be Used To Treat Mental Disorders? – Catherine Cabral-Isabedra – Tech Times

Gut microbiome alteration may improve survival in graft-versus-host disease – Corinne Foley – 2MinuteMedicine

Your lungs are full of microorganisms … and that’s a good thing – Ian Hall – The Conversation

The new trillion-dollar market opportunity: Video with Jessica Richman – Anne Stych – BizJournals

Malaria, mosquitoes, and microbiota control – Jason Tetro – PopSci

Some Nonantibiotics Disrupt Biofilms in Endometritis Cases – Alexandra Beckstett – The Horse

A serious stomach bug: Norovirus costs billions of dollars of lost productivity – Ike Swetlitz – STAT News

April 23, 2016

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Pint of Science, oral microbiome dynamics, rheumatoid arthritis, mineral turnover in the rhizosphere, and the subzero microbiome.

Events

Pint of Science San Francisco Bay Area (also in other cities all over the world): 23-25 May 2016, combining beer and science

Pregnancy and birth

Microbiome and Fetus: A Relationship for Life – Janet Teodori – Journal of Prenatal & Perinatal Psychology & Health

The Tree(s) of Life: The Human Placenta and My Journey to Learn More about It – Carolyn B. Coyne – PLOS Pathogens

Human oral microbiome

Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome – Niklas Grassl – Genome Biology

Human vaginal microbiome

Effects of low dose estrogen therapy on the vaginal microbiomes of women with atrophic vaginitis – Jian Shen – Scientific Reports

Human gut microbiome

Plasmid metagenomics reveals multiple antibiotic resistance gene classes among the gut microbiomes of hospitalised patients – Tossawan Jitwasinkul – Journal of Global Antimicrobial Resistance

Bifidobacteria Abundance-Featured Gut Microbiota Compositional Change in Patients with Behcet’s Disease – Jun Shimizu – PLOS ONE

An expansion of rare lineage intestinal microbes characterizes rheumatoid arthritis – Jun Chen – Genome Medicine

Microbial Culturomics to Map Halophilic Bacterium in Human Gut: Genome Sequence and Description of Oceanobacillus jeddahense sp. Nov. – Khelaifia Saber – OMICS

Review: Bugging inflammation: role of the gut microbiota – Sj Shen – Clinical & Translational Immunology

Review: Modulating Composition and Metabolic Activity of the Gut Microbiota in IBD Patients – Mario Matijašić – MDPI Int J Mol Sci

Animal models

Effect of Dietary Carboxymethyllysine on glucose and insulin sensitivity, cecal fatty acids and the plasma metabolome in mice fed the Total Western Diet – Robert Edwin Ward – The FASEB Journal

Animal microbiome

The Microbiome of Animals: Implications for Conservation Biology – Simon Bahrndorff – International Journal of Genomics

Review: Herbivore dung as food for dung beetles: elementary coprology for entomologists – Peter Holter – Ecological Entomology

Plant, root, and soil microbiome

Plant–Microbiota Interactions as a Driver of the Mineral Turnover in the Rhizosphere – R. Alegria Terrazas – Advances in Applied Microbiology

Dynamics of endophytic bacteria in plant in vitro culture: quantification of three bacterial strains in Prunus avium in different plant organs and in vitro culture phases – Mona Quambusch – Plant Cell, Tissue and Organ Culture (PCTOC)

Evaluating the lingering effect of livestock grazing on functional potentials of microbial communities in Tibetan grassland soils – Mengmeng Wang – Plant and Soil

Nitrogen fertilization affects bacteria utilizing plant-derived carbon in the rhizosphere of beech seedlings – Silvia Gschwendtner – Plant and Soil

Temporal dynamic of parasite-mediated linkages between the forest canopy and soil processes and the microbial community – Ana Mellado – New Phytologist

Rhizosphere priming effect on soil organic carbon decomposition under plant species differing in soil acidification and root exudation – Xiaojuan Wang – New Phytologist

Water and extremophile microbiome

Viral metabolic reprogramming in marine ecosystems – Bonnie L Hurwitz – Current Opinion in Microbiology

Review: The subzero microbiome: Microbial activity in frozen and thawing soils – Mrinalini P. Nikrad – FEMS Microbiology Ecology

Gene expression profiling of microbial activities and interactions in sediments under haloclines of E. Mediterranean deep hypersaline anoxic basins – Virginia P Edgcomb – The ISME Journal

Waste and pollution microbiology

Effect of thermal pretreatment on the biogas production and microbial communities balance during anaerobic digestion of urban and industrial waste activated sludge – Hajer Ennouri – Bioresource Technology

The Arsenite Oxidation Potential of Native Microbial Communities from Arsenic-Rich Freshwaters – Stefano Fazi – Microbial Ecology

Microbial communities from different subsystems in biological heap leaching system play different roles in iron and sulfur metabolisms – Yunhua Xiao – Applied Microbiology and Biotechnology

Community Structure in Methanogenic Enrichments Provides Insight into Syntrophic Interactions in Hydrocarbon-Impacted Environments – S. Jane Fowler – Frontiers in Microbiology

Food microbiology

The Potential of the Incorporation of Essential Oils and Their Individual Constituents to Improve Microbial Safety in Juices: A Review – Evandro Leite de Souza – Comprehensive Reviews in Food Science and Food Safety

Bioinformatics and metagenomics

The Metagenomic Pizza: a simple recipe to introduce bioinformatics to the layman – Marie-Claude Blatter – EMBnet

MOCAT2: a metagenomic assembly, annotation and profiling framework – Jens Roat Kultima – Bioinformatics

Temporal microbiome road-maps guided by perturbations – Beatriz García-Jiménez – bioRxiv

Fundamental Limits of Pooled-DNA Sequencing – A. Najafi – ArXiv

A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity – Nam-Phuong Nguyen – NPJ Biofilms

Microbial Ecology

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

Viruses and phages

Giant viruses at the core of microscopic wars with global impacts – Adrien Villai – Current Opinion in Virology

Environmental surveillance of viruses by tangential flow filtration and metagenomic reconstruction – V Furtak – Eurosurveillance

Metabolomics

Review: Microbial metabolism of dietary components to bioactive metabolites: opportunities for new therapeutic interventions – Linda S. Zhang – Genome Medicine

Microbes in the news

Your office is a veritable petri dish of bacteria – Sarah Kaplan – The Washington Post

We’re home to trillions of cells that aren’t ours and they’re keeping us alive – Katherine Ellen Foley – Quartz

These oral bacteria are linked to an increased chance of getting pancreatic cancer – Laurie McGinley – The Washington Post

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 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 12, 2016, part 1

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Too many alerts to go through after taking one day off, so here is part one. An updated tree of life, acute appendicitis, rhizosphere of a living fossil plant, Antarctic surface snow, and effects of Superstorm Sandy on creek water.

Jobs and events

Senior Scientist with significant track record in microbiome research – The National Institute for Biological Standards and Control, South Mimms, UK

General microbiome

A new view of the tree of life – Laura A. Hug – Nature Microbiology

Pregnancy and birth

The Gestational Vaginal Microbiome and Spontaneous Preterm Birth among Nulliparous African American Women – Deborah B. Nelson – American Journal of Perinatology

Early colonization of functional groups of microbes in the infant gut – Van T. Pham – Environmental Microbiology

The gut resistome is highly dynamic during the first months of life – Christian JH von Wintersdorff – Future Medicine

Human skin microbiome

Review: Skin Biomes – N. Fyhrquist – Current Allergy and Asthma Reports

Human respiratory microbiome

Review: Next Generation Sequencing and the Microbiome of Chronic Rhinosinusitis – A Primer for Clinicians and Review of Current Research, Its Limitations, and Future Directions – Jake Jervis Bardy – Ann Otol Rhinol Laryngol

Human oral microbiome

The salivary microbiome for differentiating individuals: proof of principle – Sarah L. Leake – Microbes and Infection

Concordance of HOMIM and HOMINGS technologies in the microbiome analysis of clinical samples – Jean-Luc C. Mougeot – Journal of Oral Microbiology

Human gut microbiome

There are no Enterotypes: Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle – Anastassia Gorvitovskaia – Microbiome

Experiment with n=1: Understanding the Impact of Omega-3 Rich Diet on the Gut Microbiota – Blanca S. Noriega – Case Reports in Medicine

First Occurrence of Severe Extraintestinal Manifestations of Crohn’s Disease Following Faecal Microbiota Transplantation – Niels Teich – Journal of Crohn’s and Colitis

Acute appendicitis in children is associated with a local expansion of Fusobacteria – Matthew B. Rogers – Clinical Infectious Diseases

Hypothesis: Gut Microbiota Diversity and Human Diseases: Should We Reintroduce Key Predators in Our Ecosystem? – Alexis Mosca – Frontiers in Microbiology

Not endorsing, because highly controversial and not well founded: Bread and Other Edible Agents of Mental Disease – Paola Bressan and Peter Kramer – Frontiers in Human Neuroscience

Review: The human gut microbiome in health: establishment and resilience of microbiota over a lifetime – Kacy Greenhalgh – Environmental Microbiology

Review: Cytotoxicity of Nanoparticles Contained in Food on Intestinal Cells and the Gut Microbiota – Esther E. Fröhlich – MDPI International Journal of Molecular Sciences

Review: The Role of the Gut Microbiota in Childhood Obesity – Pihl Andreas Friis – Childhood Obesity

Animal models

Gnotobiotic Rodents: An In Vivo Model for the Study of Microbe–Microbe Interactions – Rebeca Martín – Frontiers in Microbiology

Depletion of Cultivatable Gut Microbiota by Broad-Spectrum Antibiotic Pretreatment Worsens Outcome After Murine Stroke – Katarzyna Winek – Stroke

Plant, root, and soil microbiome

Common mycorrhizal networks and their effect on the bargaining power of the fungal partner in the arbuscular mycorrhizal symbiosis – Heike Bückinga – Communicative & Integrative Biology

Rhizosphere Microbiomes of European + Seagrasses Are Selected by the Plant, But Are Not Species Specific – Catarina Cúcio – Frontiers in Microbiology

Specific Microbial Communities Associate with the Rhizosphere of Welwitschia mirabilis, a Living Fossil – Angel Valverde – PLOS ONE

Impact of alien pines on local arbuscular mycorrhizal fungal communities – evidence from two continents – Antonio Gazol – FEMS Microbiology Ecology

Differences in stability of seed-associated microbial assemblages in response to invasion by phytopathogenic microorganisms – Samir Rezki – PeerJ

Using Ancient Traits to Convert Soil Health into Crop Yield: Impact of Selection on Maize Root and Rhizosphere Function – Jennifer E. Schmidt – Frontiers in Plant Science

Partitioning of Functional and Taxonomic Diversity in Surface-Associated Microbial Communities – Alexandra J. Roth-Schulze – Environmental Microbiology

Temporal dynamics of sediment bacterial communities in monospecific stands of Juncus maritimus and Spartina maritima – Daniel F R Cleary – Plant Biology

Thorough high-throughput sequencing analyses unravels huge diversities of soil parasitic protists – Stefan Geisen – Environmental Microbiology

Water and extremophile microbiome

Temporal and Spatial Dynamics of Archaeal Communities in Two Freshwater Lakes at Different Trophic Status – Yuyin Yang – Frontiers in Microbiology

Metagenomic Analysis of Bacterial Communities of Antarctic Surface Snow – Anna Lopatina – Frontiers in Microbiology

Partitioning of Functional and Taxonomic Diversity in Surface-Associated Microbial Communities – Alexandra J. Roth-Schulze – Environmental Microbiology

Impact of an intense water column mixing (0-1500m) on prokaryotic diversity and activities during an open-ocean convection event in the NW Mediterranean Sea – T. Severin – Environmental Microbiology

Aquatic bacterial community is restructured by hydric dynamics associated with Superstorm Sandy – Nikea Ulrich – Applied and Environmental Microbiology

Metagenomic analysis of lacustrine viral diversity along a latitudinal transect of the Antarctic Peninsula – Daniel Aguirre de Cárcer – FEMS Microbiology Ecology

Response of bacterial communities from California coastal waters to alginate particles and an alginolytic Alteromonas macleodii strain – Maximilian Mitulla – Environmental Microbiology

Waste and pollution microbiology

Partitioning of Viruses in Wastewater Systems and Potential for Aerosolization – Mari Titcombe Lee – Environmental Science & Technology Letters

Seasonality of antibiotic prescriptions for outpatients and resistance genes in sewers and wastewater treatment plant outflow – Serena Caucci – FEMS Microbiology Ecology

Spatial and temporal variability of bacterial communities within a combined sewer system – Henriette Stokbro Jensen – MicrobiologyOpen

Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters – Rasmus Hansen Kirkegaard – The ISME Journal

Bioinformatics

Not endorsing: Motif-Based Text Mining of Microbial Metagenome Redundancy Profiling Data for Disease Classification – Yin Wang – BioMed Research International

More microbiology

Host-Derived Sialic Acids Are an Important Nutrient Source Required for Optimal Bacterial Fitness In Vivo – Nathan D. McDonald – mBio

Review: Network-based metabolic analysis and microbial community modeling – Cesar Cardona – Current Opinion in Microbiology

Review: DNA-sensing inflammasomes: regulation of bacterial host defense and the gut microbiota – Si Ming Man – Pathogens and Disease

Microbes in the news

Most of the Tree of Life is a Complete Mystery. We know certain branches exist, but we have never seen the organisms that perch there – Ed Yong – The Atlantic

Wealth of unsuspected new microbes expands tree of life – Science Daily

Can more fiber restore microbiome diversity? – Science Daily

Science, publishing, and career

Research Funding: the Case for a Modified Lottery – Ferric C. Fang and Arturo Casadevall – mBio

 

April 8, 2016

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Bacterial mucin degradation in CF, gastric mucosa vs gastric juice, cockroaches, penguins, estimating post-mortem interval, and effects of sound on growth of E. coli.

Pregnancy and birth

Perinatal microbial exposure may influence aortic intima-media thickness in early infancy – Kate McCloskey – International Journal of Epidemiology

Human skin microbiome

A method for culturing Gram-negative skin microbiota – Ian A. Myles – BMC Microbiology

Human respiratory microbiome

Haemophilus parainfluenzae as a marker of the upper respiratory tract microbiota changes under the influence of preoperative prophylaxis with or without postoperative treatment in patients with lung cancer
Urszula Kosikowska – BMC Microbiology

Evidence and role for bacterial mucin degradation in cystic fibrosis airway disease – Jeffrey M Flynn – BioRxiv

Human oral microbiome

Identification of microorganisms in biofluids of individuals with periodontitis and chronic kidney disease using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry – Levy Anderson César Alves – Rapid Communications in Mass Spectrometry

Review: Host-Microbiome Cross-talk in Oral Mucositis – RM Vasconcelos – Journal of Dental Research

Human stomach microbiome

Comparison of Gastric Microbiota Between Gastric Juice and Mucosa by Next Generation Sequencing Method – Jihee Sung – Journal of Cancer Prevention

Human gut microbiome

Long-Term Green Tea Supplementation Does Not Change the Human Gut Microbiota – Pilou L. H. R. Janssens – PLOS ONE

Fecal bacterial microbiome diversity in chronic HIV-infected patients in China – Yang Sun – Emerging Microbes & Infections

Review: Gut microbiome and lipid metabolism: from associations to mechanisms – Wang, Zheng – Current Opinion in Lipidology

Review: Mood by microbe: towards clinical translation – Timothy G. Dinan – Genome Medicine

Animal models

Microbial-Derived Metabolites Reflect an Altered Intestinal Microbiota during Catch-Up Growth in Undernourished Neonatal Mice – Geoffrey A Preidis – Journal of Nutrition

Reduced Epithelial Na+/H+ Exchange Drives Gut Microbial Dysbiosis and Promotes Inflammatory Response in T Cell-Mediated Murine Colitis – Daniel Laubitz – PLOS ONE

Animal microbiome

Gut Bacterial Community of the Xylophagous Cockroaches Cryptocercus punctulatus and Parasphaeria boleiriana – Mercedes Berlanga – PLOS ONE

Age-Related Differences in the Gastrointestinal Microbiota of Chinstrap Penguins (Pygoscelis antarctica) – Andrés Barbosa – PLOS ONE

Plant, root, and soil microbiome

Functional breadth and home-field advantage generate functional differences among soil microbial decomposers – Nicolas Fanin – Ecology

Greater carbon allocation to mycorrhizal fungi reduces tree nitrogen uptake in a boreal forest – Niles J. Hasselquist – Ecology

Shifts in plant foliar and floral metabolomes in response to the suppression of the associated microbiota – Albert Gargallo-Garriga – BMC Plant Biology

Does arsenic play an important role in the soil microbial community around a typical arsenic mining area? – Fan Wu – Environmental Pollution

Groundwater–surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover – James C. Stegen – Nature Communications

Waste and pollution microbiology

Altitude-scale variation in nitrogen-removal bacterial communities from municipal wastewater treatment plants distributed along a 3600-m altitudinal gradient in China – Lihua Niu – Science of The Total Environment

Performance Assessment of Full-Scale Wastewater Treatment Plants Based on Seasonal Variability of Microbial Communities via High-Throughput Sequencing – Tang Liu – PLOS ONE

Review: Microbial Ecology and Evolution in the Acid Mine Drainage Model System – Li-Nan Huang – Trends in Microbiology

Forensic microbiology

Potential use of bacterial community succession for estimating post-mortem interval as revealed by high-throughput sequencing – Juanjuan Guo – Scientific Reports

Musical microbes

Effects of sound exposure on the growth and intracellular macromolecular synthesis of E. coli k-12 – Shaobin Gu – PeerJ

Functional foods

Special issue on Pre- and Probiotics in Gastroenterology Practice – Clinical Gastroenterology

Microbes in the news

Saving the Tasmanian devil with microbiome research – Yuanyuan Cheng, Carolyn Hogg & Kathy Belov – BioMedCentral Blog

Bacteria used to extract precious metals from e-waste in NUS study – Straits Times

Fighting Indoor Air Pollution with Plant Root Bacteria – Launch UMD

Latest #spacemicrobes Paper is Out… Built Environment Strains Grown on the ISS – David Coil – MicroBEnet

UChicago and Evelo Biosciences sign licensing deal for microbiome-based cancer immunotherapy – PR Newswire

Journal Club: Crowdfunding Science: all that we learned during our first crowdfunding campaigns – Katherine Dahlhausen – MicroBEnet

Maldonado-Contreras recognized by American Gastroenterological Association for gut microbiome research – Megan Bard – University of Massachusetts

Satire: Pope Francis To Award Sainthood To All Microbiome Researchers – The Allium HT: Tomer Altman

Microbes and art

Celling point: scientist makes Darwin’s Origin of Species with bacteria. Molecular biologist Dr Simon Park has made a very unusual edition of the classic text, using bacteria to create the cover – The Guardian

The Microverse: Children books about microbes. Cool titles, such as Escher Surfs the Sewer, and Vibri Finds Her Glow.

April 6, 2016

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C-section and gut colonization, N. flavescens in celiac patients, Lactobacillus in the gut, bird or whiskey, bacteria attached to phytodetritus, microbiology in the classroom, and CRISPR to decipher and shape bacterial diversity. And a bad article about women in space.

Event

Microbiome: How Commensal Bacteria Can Be Our Friends – A Talk by Dr. Deepshika Ramanan – April 14, Genspace Brooklyn, NY, Genspace

Organizing 2017 Microbes of the Built Environment conference, call for community input – Lynn Schriml – MicroBEnet

Pregnancy and birth

Cesarean section changes neonatal gut colonization – Jakob Stokholm – Journal of Allergy and Clinical Immunology

Human respiratory microbiome

Bacterial–viral load and the immune response in stable and exacerbated COPD: significance and therapeutic prospects – Silvestro Ennio D’Anna – International Journal of Chronic Obstructive Pulmonary Disease

Human gut microbiome

Metagenomics Reveals Dysbiosis and a Potentially Pathogenic N. flavescens Strain in Duodenum of Adult Celiac Patients – Valeria D’Argenio – American Journal of Gastroenterology

Th17 responses and natural IgM antibodies are related to gut microbiota composition in systemic lupus erythematosus patients – Patricia López – Scientific Reports

Mining metagenomic whole genome sequences revealed subdominant but constant Lactobacillus population in the human gut microbiota – Maddalena Rossi – Environmental Microbiology Reports

Diminution of the gut resistome after a gut microbiota-targeted dietary intervention in obese children – Guojun Wu – Scientific Reports

DGGE: The Effect of Probiotic Treatment on Patients Infected with the H7N9 Influenza Virus – Xinjun Hu – PLOS ONE

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

Review: Diet, Microbiota, Obesity, and NAFLD: A Dangerous Quartet – Mariana Verdelho Machado – MDPI International Journal of Molecular Sciences

Animal models

Airway bacteria drive a progressive COPD-like phenotype in mice with polymeric immunoglobulin receptor deficiency – Bradley W. Richmond – Nature Communications

Reproduction and Growth in a Murine Model of Early Life-Onset Inflammatory Bowel Disease – Eniko Nagy – PLOS ONE

Intake of Meat Proteins Substantially Increased the Relative Abundance of Genus Lactobacillus in Rat Feces – Yingying Zhu – PLOS ONE

Colitis susceptibility in p47 phox−/− mice is mediated by the microbiome – E. Liana Falcone – Microbiome

Review: Multiscale analysis of the murine intestine for modeling human diseases – Jesse Lyons – Integrative Biology

Animal microbiome

The bird, not the whiskey: Activity of urealytic microorganisms in the gastrointestinal tract of the black grouse Lyrurus tetrix – M. V. Vecherskii – Doklady Biological Sciences

Plant, root, and soil microbiome

Zinc treatment increases the titre of ‘Candidatus Liberibacter asiaticus’ in huanglongbing-affected citrus plants while affecting the bacterial microbiomes – M.Q. Zhang – Journal of Applied Microbiology

Species Specificity of Bacteria Associated to the Brown Seaweeds Lobophora (Dictyotales, Phaeophyceae) and Their Potential for Induction of Rapid Coral Bleaching in Acropora muricata – Christophe Vieira – Frontiers in Microbiology

Water and extremophile microbiome

Aerobic Vinyl Chloride Metabolism in Groundwater Microcosms by Methanotrophic and Etheneotrophic Bacteria – Margaret Findlay – Environmental Science & Technology

Pyrosequencing analysis of bacterial communities in Lake Bosten, a large brackish inland lake in the arid northwest of China – Lei Zhang – Canadian Journal of Microbiology

Dynamic of bacterial communities attached to lightened phytodetritus – Morgan Petit – Environmental Science and Pollution Research

Waste and pollution microbiology

Detection of the Antimicrobial Triclosan in Environmental Samples by Immunoassay – Ki Chang Ahn – Environmental Science & Technology

Lactic acid fermentation from food waste with indigenous microbiota: Effects of pH, temperature and high OLR – Jialing Tang – Waste Management

Use of PCR-DGGE based molecular methods to assessment of microbial diversity during anaerobic treatment of antibiotic combinations – Sevcan Aydin – Bioresource Technology

Microbial Ecology

Host behaviour–parasite feedback: an essential link between animal behaviour and disease ecology – Vanessa O. Ezenwa – Proceedings of the Royal Society B

Myxococcus xanthus: Positively Frequency-Dependent Interference Competition Maintains Diversity and Pervades a Natural Population of Cooperative Microbes – Olaya Rendueles – Current Biology

Review: Deciphering and shaping bacterial diversity through CRISPR – Alexandra E Briner – Current Opinion in Microbiology

Microbes and education

Nice set of papers in ASM’s Journal of Microbiology and Biology Education:

Microbes in the news

The Scary Thing About a Virus That Kills Farmed Fish – Ed Yong – The Atlantic

Seres Therapeutics: All You Need To Know About What Will Be The First Prescription Microbiome Company – Seeking Alpha

Type IV pili: Appendages Help Microbes Survive Harsh Conditions – Charles Q. Choi – Astrobiology

Not endorsing this article. Microbiotas of men and women are not that different, not much published data on effects of space flight on gut microbiome, and I did not like the suggestion that women will get sick more often. Also, antibiotics ain’t gonna help if women have breast cancer.
Gender generates biological challenges for long duration spaceflight – Evan Gough

So long lithium, hello bacteria batteries? – ScienMag (not to be confused with Science)

Microbes in the news

Targeting the gut microbiome to fight heart disease – American Society for Microbiology

Science, publishing, and career

The Immoral Landscape? Scientists Are Associated with Violations of Morality – Bastiaan T. Rutjens – PLOS ONE

April 2, 2016

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Yes, it is technically already April 3, but I only got to do the daily roundup late tonight, so I did not quite get it done in time. C-section and weight influence on infant colonization, dachshunds, crops selecting fungi, post-mortem microbial transmigration

Pregnancy and birth

Birth mode-dependent association between pre-pregnancy maternal weight status and the neonatal intestinal microbiome – Noel T. Mueller – Scientific Reports

Study provides evidence that “vaginal seeding” of infants born by caesarean partially restores microbiota – Amali Lokugamage – BMJ

Relationship between milk microbiota, bacterial load, macronutrients and human cells during lactation – Alba Boix-Amoros – Frontiers in Microbiology

Mode of Delivery Determines Neonatal Pharyngeal Bacterial Composition and Early Intestinal Colonization – David E. Brumbaugh – Journal of Pediatric Gastroenterology & Nutrition

Effect of Formula Containing Lactobacillus Reuteri DSM 17938 on Fecal Microbiota of Infants Born by Cesarean-Section – Rodenas, Clara L. Garcia – Journal of Pediatric Gastroenterology & Nutrition

Human oral microbiome

Mucosal and salivary microbiota associated with recurrent aphthous stomatitis – Yun-ji Kim- BMC Microbiology

Assessment of oral malodor and tonsillar microbiota after gargling with benzethonium chloride – Yuki Iwamura – Journal of Oral Science

Potential screening and early diagnosis method for cancer: Tongue diagnosis – Shuwen Han – International Journal of Oncology

In vitro: A dual-species microbial model for studying the dynamics between oral streptococci and periodontal pathogens during biofilm development on titanium surfaces by flow cytometry – Anita Manti – Research in Microbiology

Human gut microbiome

Changes in fecal microbiota and metabolomics in a child with juvenile idiopathic arthritis (JIA) responding to two treatment periods with exclusive enteral nutrition (EEN) – Lillemor Berntson – Clinical Rheumatology

Renal Failure due to Excessive Intake of Almonds in the Absence of Oxalobacter formigenes – Yngvar Lunde Haaskjold – The American Journal of Medicine

Reanalysis of published data, no apparent new findings: Host genetics is associated with the gut microbial community membership rather than the structure – Peihua Zhao – Molecular BioSystems

Review: Modulatory Effects of Gut Microbiota on the Central Nervous System: How Gut Could Play a Role in Neuropsychiatric Health and Diseases – Shadi S Yarandi – Journal of Neurogastroenterology and Motility

Commentary: Can microbiota research change our understanding of neurodegenerative diseases? – Filip Scheperjans – Neurodegenerative Disease Management

Review: Microbes and the mind: emerging hallmarks of the gut microbiota–brain axis
– Kylynda C. Bauer – Cellular Microbiology

Animal models

Distinctly altered gut microbiota in the progression of liver disease – Guoxiang Xie – Oncotarget

Wolbachia confers sex-specific resistance and tolerance to enteric but not systemic bacterial infection in Drosophila – Radhakrishnan B Vasanthakrishnan – BioRxiv

Gut Microbiota and a Selectively Bred Taste Phenotype: A Novel Model of Microbiome-Behavior Relationships – Lyte, Mark – Psychosomatic Medicine

Periodontal dysbiosis linked to periodontitis is associated with cardio-metabolic adaptation to high-fat diet in mice – Maxime Branchereau – American Journal of Physiology Gastrointestinal and Liver Physiology

Protocol: The Gut Microbiome in the NOD Mouse – Jian Peng – Part of the series Methods in Molecular Biology

Animal microbiome

Fecal dysbiosis in miniature dachshunds with inflammatory colorectal polyps – Hirotaka Igarashi – Research in Veterinary Science

Plant, root, and soil microbiome

Differential response of ammonia-oxidizing archaea and bacteria to the wetting of salty arid soil – Yonatan Sher – Journal of Basic Microbiology

Selection of fungi by candidate cover crops – Maria-Soledad Benitez – Applied Soil Ecology

Unravelling Linkages between Plant Community Composition and the Pathogen-Suppressive Potential of Soils – Ellen Latz – Scientific Reports

Water and extremophile microbiome

Characterization of the prokaryotic diversity through a stratigraphic permafrost core profile from the Qinghai-Tibet Plateau – Weigang Hu – Extremophiles

Seasonal and Spatial Changes of Planktonic Bacterial Communities Inhabiting the Natural Thermal Lake Hévíz, Hungary – Gergely Krett – Acta Microbiologica et Immunologica Hungarica

Microbiome of Death

Fluorescently labeled bacteria provide insight on post-mortem microbial transmigration –
Z.M. Burcham – Forensic Science International

Food microbiology

Review: Hygienic characteristics and microbiological hazard identification in horse and donkey raw milk – Giampaolo Colavita – Veterinaria Italiana

Waste and pollution microbiology

Microbial communities in riparian soils of a settling pond for mine drainage treatment – Miaochun Fan – Water Research

Metagenomic analysis shows diverse, distinct bacterial communities in biofilters among different marine recirculating aquaculture systems – Zhitao Huang – Aquaculture International

More microbiology

Evaluation of genetic diversity among strains of the human gut commensal Bifidobacterium adolescentis – Sabrina Duranti – Scientific Reports

Metagenomics and bioinformatics

Not sure if this is a good approach; ignores variation between individual human microbiome strains: Reconstruction of bacterial and viral genomes from multiple metagenomes – Vineet K. Sharma – Frontiers in Microbiology

Metabolomics

Harnessing the power of microbial metabolism – Eduardo Santero – Current Opinion in Microbiology

Microbiology and art

BioArt: Joana Ricou shows the Beautiful Similarities of the Microbiome – Labiotech

Rap song: CosmosID Metagenomics: Exploring the Universe of Microbes – CosmosID – YouTube

Microbes in the news

Mythbusters: Human Microbiota – Caroline Ayinon – Yale Scientific

Introducing the “HomeGenome”. Not endorsing this. Exploring the Microcosm Within. Adventures and insights from the microbiome – Conan Milner – Epoch Times

April Fool’s Day microbiome jokes

Thanks to Microbiome Boost, Donuts May Be Beneficial: when paired with P. tursiops – Tim De Chant – PBS

A microbiology of the built environment April Fools’ joke – Jonathan Eisen – MicroBEnet

And of course my own selection: Human-derived microbial strains used for food and beverage production – Elisabeth Bik – Microbiome Digest

Science, publishing, and career

‘Lab Girl’ Is a Fierce, Uplifting, Must-Read Memoir – Hope Jahren is an acute observer, prickly, and funny as hell. – Elizabeth Royte – Elle

March 31, 2016

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A special mBio issue discussing the Holobiont concept, salivary microbiota in oral cancer, truffles, sinuses in germ-free mice, and Wolbachia in cave spiders.

General microbiome

Special Issue: The Holobiont Concept- mBio
Introduction to the Hologenome Special Series – Margaret McFall-Ngai
Microbes Drive Evolution of Animals and Plants: the Hologenome Concept – Eugene Rosenberg
Speciation by Symbiosis: the Microbiome and Behavior – J. Dylan Shropshire
Holes in the Hologenome: Why Host-Microbe Symbioses Are Not Holobionts – Angela E. Douglas

Pregnancy and birth

Research Highlight: Baby steps towards the microbiome – Andrea Du Toit – Nature Reviews Microbiology

Oral microbiome

Changes in the salivary microbiota of oral leukoplakia and oral cancer – Xiaosheng Hu – Oral Oncology

Human respiratory microbiome

Tonsillar microbiota in children with PFAPA (periodic fever, aphthous stomatitis, pharyngitis, and adenitis) syndrome – M. V. Tejesvi – European Journal of Clinical Microbiology & Infectious Diseases

Conference abstract: Nasal Microbiome Composition Is Associated with Chitotriosidase (Chit1) Activity in Adult Hutterites – Catherine Igartua – Annals of the American Thoracic Society

Conference abstract: Gut Microbiota and Allergic Disease. New Insights
Susan V. Lynch- Annals of the American Thoracic Society

Human gut microbiome

Association between intestinal permeability and faecal microbiota composition in Italian children with beta cell autoimmunity at risk for type 1 diabetes – Claudio Maffeis – Diabetes/Metabolism Research and Reviews

Fecal microbial transplants reduce antibiotic-resistant genes in patients with recurrent Clostridium difficile infection – Braden Millan – Clinical Infectious Diseases

Special issue with reviews: Gastric and Gut Microbiota in Health and Disease – Digestive Diseases

Animal models

Effect of a long-term high-protein diet on survival, obesity development and gut microbiota in mice – Pia Kiilerich – American Journal of Physiology

Differences in the paranasal sinuses between germ-free and pathogen-free mice – Ravi Jain – International Forum of Allergy & Rhinology

Effects of taurine on gut microbiota and metabolism in mice – Haining Yu – Amino Acids

Animal microbiome

Research Highlight: Microbiome ‘coral’ations – Ursula Hofer – Nature Reviews Microbiology

Classification of Wolbachia (Alphaproteobacteria, Rickettsiales): No evidence for a distinct supergroup in cave spiders – Michael Gerth – BioRxiv

Not a great title: Metagenomic bacterial community profiles of chicken embryo gastrointestinal tract by using T-RFLP analysis – L. A. Ilina – Doklady Biochemistry and Biophysics

Plant, root, and soil microbiome

Screening of soil bacteria as potential agents for drugs biodegradation: a case study with clofibric acid – Claudia Popa Ungureanu – Journal of Chemical Technology and Biotechnology

Metagenomes provide valuable comparative information on soil microeukaryotes –
Samuel Jacquiod – Research in Microbiology

The Truffle Microbiome: Species and Geography Effects on Bacteria Associated with Fruiting Bodies of Hypogeous Pezizales – Gian Maria Niccolò Benucci – Microbial Ecology

Bioreactor microbiology

The First Space-Related Study of a Kombucha Multimicrobial Cellulose-Forming Community: Preparatory Laboratory Experiments – O. Podolich – Origins of Life and Evolution of Biospheres

Food microbiology

Characterisation of the yeast and mould biota in traditional white pickled cheeses by culture-dependent and independent molecular techniques – Hana Šuranská – Folia Microbiologica

Use of propidium monoazide for selective profiling of viable microbial cells during Gouda cheese ripening – Oylum Erkus – International Journal of Food Microbiology

Bioinformatics and metagenomics

Predicting microbial interactions through computational approaches – Chenhao Li – Methods

Microbes in the news

A Hidden Factor in Stroke Severity: The Microbes in Your Gut : A new study in mice demonstrates that manipulating the microbiome can influence the extent of brain damage caused by a stroke – Jordana Cepelewic – Scientific American

Pushing and Pulling on the Mosquito Microbiome – Kevin Bonham – Scientific American

Sampling an animal shelter – Holly Ganz – MicroBEnet

Intestinal Microbiome of Children with Cystic Fibrosis Promotes Gut Inflammation, Study Finds – Patricia Inacio – Cystic Fibrosis News Today
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