Category Archives: General Microbiome

June 8, 2016

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Obesity and microbiome patterns, universality of human microbial dynamics, intestinal fungal dysbiosis, pre-eclampsia, seaweed ice-ice disease.

Pregnancy and birth

Review: A dormant microbial component in the development of pre-eclampsia – Douglas B Kell – bioRxiv

General human microbiome

Universality of human microbial dynamics – Amir Bashan – Nature

News and Views: Host-microbe interaction: Rules of the game for microbiota – Karoline Faust – Nature

Perspectives: Accounting for reciprocal host–microbiome interactions in experimental science – Thaddeus S. Stappenbeck – Nature

Human gut microbiome

Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome – Marc Sze – bioRxiv

Animal and in vitro experiments

Immunological Consequences of Intestinal Fungal Dysbiosis – Matthew L. Wheeler – Cell Host & Microbe

Editorial: The Fungal Mycobiota: Small Numbers, Large Impacts – Carol A. Kumamoto – Cell Host & Microbe

Research Highlights: Love Thy Neighbor: Sharing and Cooperativity in the Gut Microbiota – Nathan T. Porter – Cell Host & Microbe

Animal microbiome

Overfishing and nutrient pollution interact with temperature to disrupt coral reefs down to microbial scales – Jesse R. Zaneveld – Nature Communications

Restructuring of the sponge microbiome favors tolerance to ocean acidification – M. Ribes – Environmental Microbiology Reports

Plant, root, and soil microbiome

Molecular identification of new bacterial causative agent of ice-ice disease on seaweed Kappaphycus alvarezii – Marlina Achmad – PeerJ Preprint

Effect of temperature (5 °C–25 °C) on epiphytic lactic acid bacteria populations and fermentation of whole-plant corn silage – Yiqin Zhou – Journal of Applied Microbiology

Conventional methanotrophs are responsible for atmospheric methane oxidation in paddy soils – Yuanfeng Cai – Nature Communications

More microbiology

Nondegenerative Evolution in Ancient Heritable Bacterial Endosymbionts of Fungi – Stephen J. Mondo – Molecular Biology and Evolution

Historical Y. pestis Genomes Reveal the European Black Death as the Source of Ancient and Modern Plague Pandemics – Maria A. Spyrou – Cell Host & Microbe

Microbes in the news

Arlington native Alexandra Worden named American Academy of Microbiology fellow – Arlington Wicked Local

Disease Researcher Finds New Home at Valencia — in the Classroom, with Dr. Hemangi Patil – Linda Shrieves Beaty – Valencia College

From the Congress of the European Academy of Neurology in Copenhagen, Denmark: Scientists Gather to Discuss Novel Connections Between Gut Microbiome and Brain Disorders – Patricia Inacio – Multiple Sclerosis News Today

Cooperative and Combative Behaviour in the Human Gut: Probing the Microbiome, with Athena Aktipis – SciCasts

Speeding Up Drug Discovery to Fight Tuberculosis – Seattle researchers created a genetic blueprint of the cunning tuberculosis bacteria, then used it to predict and rank potential drug targets – SystemsBiology

Science, publishing, and career

What does research reproducibility mean? – Steven N. Goodman – Science Translational Medicine

Editorial: Second chances – The line between compliance and misconduct is finer than you might think – Nature

Misconduct: Lessons from researcher rehab – James M. DuBois – Nature

June 7, 2016

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Microbiomes of the lung, red coral, effect of invertebrates on water microbes, and bacteriophages are reservoirs of antibiotic resistance genes.

General microbiome

The vast unknown microbial biosphere – Carlos Pedrós-Alió – PNAS

Human respiratory microbiome

Review: The Lung Microbiome, Immunity, and the Pathogenesis of Chronic Lung Disease – David N. O’Dwyer – The Journal of Immunology

Review/Hypothesis: A Role for the Intestinal Microbiota and Virome in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)? – Navena Navaneetharaja – MDPI Journal of Clinical Medicine

Human gut microbiome

Review: The metabolic role of the gut microbiota in health and rheumatic disease: mechanisms and interventions – Shahla Abdollahi-Roodsaz – Nature Reviews Rheumatology

Animal experiments

Accelerated dysbiosis of gut microbiota during aggravation of DSS-induced colitis by a butyrate-producing bacterium – Qianpeng Zhang – Scientific Reports

Bacterial Adrenergic Sensors Regulate Virulence of Enteric Pathogens in the Gut – Cristiano G. Moreira – mBio

Animal microbiome

Spirochaetes dominate the microbial community associated with the red coral Corallium rubrum on a broad geographic scale – Jeroen A. J. M. van de Water – Scientific Reports

Plant, root, and soil microbiome

Mangrove succession enriches the sediment microbial community in South China – Quan Chen – Scientific Reports

Correlations between the composition of modular fungal communities and litter decomposition-associated ecosystem functions – Witoon Purahong – Fungal Ecology

History Leaves Its Mark on Soil Bacterial Diversity – Jennifer B. H. Martiny – mBio

Water and extremophile microbiome

Alteration of physico-chemical and microbial properties in freshwater substrates by burrowing invertebrates – Carolin Boeker – Limnologica – Ecology and Management of Inland Waters

Effects of the invasive clam Corbicula fluminea (Müller, 1774) on an estuarine microbial community – Adriana Novais – Science of The Total Environment

Delineating ecologically significant taxonomic units from global patterns of marine picocyanobacteria – Gregory K. Farrant – PNAS

Bacterial community composition and structure in an Urban River impacted by different pollutant sources – A. Mark Ibekwe – Science of The Total Environment

Population Dynamics and Community Composition of Ammonia Oxidizers in Salt Marshes after the Deepwater Horizon Oil Spill – Anne Bernhard – Frontiers in Microbiology

Review: Cannibalistic viruses in the aquatic environment: role of virophages in manipulating microbial communities – V. Marie – International Journal of Environmental Science and Technology

Built environment microbiome

Molecular investigation of bacterial communities: Data from two frequently used surfaces in the São Paulo Institute of Tropical Medicine – Tairacan Augusto Pereira da Fonseca – Data in Brief

The prevalence of foodborne pathogenic bacteria on cutting boards and their ecological correlation with background biota – Noor-Azira Abdul-Mutalib – AIMS Microbiology

Metagenomics and viruses

Metagenomic analysis reveals that bacteriophages are reservoirs of antibiotic resistance genes – Jéssica Subirats – International Journal of Antimicrobial Agents

Bioinformatics

SMART: Statistical Metabolomics Analysis—An R Tool – Yu-Jen Liang – Analytical Chemistry

Techniques

Book: Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing – Editors: Ana M. Aransay, José Luis Lavín Trueba – Springer Books

More microbiology

Coupling spatiotemporal community assembly processes to ecosystem function – Emily Graham – PeerJ Preprint

Evolution of the archaeal and mammalian information processing systems: towards an archaeal model for human disease – Zhe Lyu – Cellular and Molecular Life Sciences

Species richness influences wine ecosystem function through a dominant species – Primrose J. Boynton – Fungal Ecology

Microbes in the news
New antimicrobial material joins fight against antibiotic-resistant bacteria – Michael Irving – GizMag

Note: PNAS paper not yet out: Distinguishing Deadly Staph Bacteria from Harmless Strains – Heather Buschman – UC San Diego

Scientists craft an artificial seawater concoction. New recipe facilitates marine microbe cultivation and characterization – EurekAlert

The man who can map the chemicals all over your body: Pieter Dorrestein uses mass spectrometry to eavesdrop on the molecular conversations between microbes and their world – Paul Tullis – Nature

Stockton Kimball Awardee is Noted Bacterial Pathogenesis Researcher – University of Buffalo

MSU doctoral student Jeffrey Simkins awarded National Science Foundation fellowship to research in Australia – Montana State University – KBZK

Vaccine watches bacteria, strikes only when trouble stirs – University of Buffalo

Bacteria hairs make excellent electrical wires – Science Daily

Science, publishing, and career

My paper got published: The Prevalence of Inappropriate Image Duplication in Biomedical Research Publications – Elisabeth M. Bik, Arturo Casadevall, Ferric C. Fang – mBio

May 26, 2016

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Bioinformatics Symposium tomorrow at Stanford with free live stream, development of upper respiratory tract microbiome in infants, coral microbiome in Hawaii, calcified red algae microbiome, and metagenomics pathogen detection tool.

Events

Tomorrow, starts at 8am Pacific Time: Bioinformatics for the Microbiome, Stanford University. Will also be live streamed (and recording will be kept here for a while too) at Stanford Webcast. Due to family circumstances I won’t be able to be there, unfortunately 😦

Targeting the Microbiome – September 19-22, Boston, MA

Report from meeting earlier this week: Frontiers in Human Microbiota Symbiotic Interactions” 3rd Annual Meeting of the Bridging Biomedical Worlds Series

Jobs

Postdoc position in Pat Schloss group – Department of Microbiology & Immunology at the University of Michigan

General microbiome

Bioengineering microbial communities: Their potential to help, hinder and disgust – Diane Sivasubramaniama – Bioengineered

Pregnancy and birth

Development of Upper Respiratory Tract Microbiota in Infancy is Affected by Mode of Delivery – Astrid A.T.M. Bosch – EBioMedicine

Human respiratory microbiome

Long-Term Evolution of Burkholderia multivorans during a Chronic Cystic Fibrosis Infection Reveals Shifting Forces of Selection – Inês N. Silva – mSystems

Study shows how bacteria evolve in lungs of cystic fibrosis patients – Science Daily

Upper airway microbial colonization in patients with neuromuscular disorders – Florian Stehling – Respirology

Human gut microbiome

Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study – Toshitaka Odamaki – BMC Microbiology

Metagenomic characterization of microbial communities in situ within the deeper layers of the ileum in Crohn’s Disease – Chandra Sekhar Pedamallu – CMGH Cellular and Molecular Gastroenterology and Hepatology

Association of Systemic Sclerosis With a Unique Colonic Microbial Consortium – Elizabeth R. Volkmann – Arthritis & Rheumatology

Development of the gut microbiota and mucosal IgA responses in twins and gnotobiotic mice – Joseph D. Planer – Nature

Animal experiments

Impact of a High-Fat or High-Fiber Diet on Intestinal Microbiota and Metabolic Markers in a Pig Model – Sonja N. Heinritz – MDPI Nutrients

Immunological Consequences of Intestinal Fungal Dysbiosis – Matthew L. Wheeler – Cell Host & MIcrobe

Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease – Hiutung Chu – Science

Editorial: Microbiome: Does the brain listen to the gut? – Thomas Kuntz – eLIFE

Animal microbiome

Biogeography of planktonic and coral-associated microorganisms across the Hawaiian Archipelago – Jennifer L. Salerno – FEMS Microbiology Ecology

Codivergence of the primary bacterial endosymbiont of psyllids versus host switches and replacement of their secondary bacterial endosymbionts – Aidan A. G. Hall – Environmental Microbiology

An exploration of the fungal assemblage in each life history stage of the butterfly, Lycaeides melissa (Lycaenidae), as well as its host plant Astragalus canadensis (Fabaceae) – Joshua G. Harrison – Fungal Ecology

Comparison of the fecal microbiota in horses with Equine Metabolic Syndrome (EMS) and metabolically normal controls fed a similar all forage diet – S. Elzinga – Journal of Equine Veterinary Science

Plant, root, and soil microbiome

Characterising the microbiome of Corallina officinalis, a dominant calcified intertidal red alga – Juliet Brodie – FEMS Microbiology Ecology

Relative importance of soil properties and microbial community for soil functionality: insights from a microbial swap experiment – Manuel Delgado-Baquerizo – Functional Ecology

Effect of agricultural practices and coastal constraints on soil microbial functional properties in Mediterranean olive orchards – N. Boukhdoud – European Journal of Soil Science

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

Book Chapter: Bacteria and Non-lichenized Fungi Within Biological Soil Crusts – Stefanie Maier – Biological Soil Crusts: An Organizing Principle in Drylands

Metagenomics, bioinformatics, and techniques

HoloVir: A workflow for investigating the diversity and function of viruses in invertebrate holobionts – Patrick W. Laffy – Frontiers in Microbiology

Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling – Steven Flygare – Genome Biology

Metagenomics pathogen detection tool could change how infectious diseases are diagnosed – EurekAlert

Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing – Matthew Thoendel – Journal of Microbiological Methods

BMPOS: a Flexible and User-Friendly Tool Sets for Microbiome Studies – Victor S. Pylro – Microbial Ecology

Functional foods

Reviewing Classical and Molecular Techniques Regarding Profiling of Probiotic Character of Microorganisms – Christos Stefanis – Current Research in Nutrition and Food Science

Microbes in the news

Polio-free world? Not if scientists refuse to destroy their research specimens – Helen Branswell – STAT news

The secret history of ancient toilets. By scouring the remains of early loos and sewers, archaeologists are finding clues to what life was like in the Roman world and in other civilizations – Chelsea Wald – Nature

Using Gut Bacteria To Save The Planet – John Farrell – Forbes

The Emergent Microbiome: A Revolution for the Life Sciences – Part VI, Diagnostics – Jessica L. Miles and Anthony D. Sabatelli – Lexology

May 24, 2016

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Endophytes in Miscanthus seeds, the microbes of Blood Pond Hell, microbes in indoor dust, and Dada2 sample inference from Illumina data.

General microbiome

Moonshot or mania? – Sally Adee looks behind the hype – New Scientist

Human gut microbiome

Research Highlight: Microbiota trigger inflammation – Ellen F. Carney – Nature Reviews Nephrology

Glycans affect DNA extraction and induce substantial differences in gut metagenomic studies – Emmanouil Angelakis – Scientific Reports

Microbiome of HIV-infected people – Grégory Dubourg – Microbial Pathogenesis

Review: The microbiota and immune response during Clostridium difficile infection – Erica L. Buonomo – Anaerobe

Animal experiments

Snapshot on a Pilot Metagenomic Study for the Appraisal of Gut Microbial Diversity in Mice, Cat, and Man – Coline Plé – Gastroenterology Research and Practice

Plant, root, and soil microbiome

The microbiomes and metagenomes of forest biochars – Genevieve L. Noyce – Scientific Reports

Endophytic bacteria in Miscanthus seed: implications for germination, vertical inheritance of endophytes, plant evolution and breeding – Naomi Cope-Selby – GCB Bioenergy

Impact of Faba Bean-Seed Rhizobial Inoculation on Microbial Activity in the Rhizosphere Soil during Growing Season – Anna Siczek – Int J Mol Sci

Evaluation of Strategies to Separate Root-Associated Microbial Communities: A Crucial Choice in Rhizobiome Research – Tim Richter-Heitmann – Frontiers in Microbiology

Bacterial Diversity and Community Structure in Korean Ginseng Field Soil Are Shifted by Cultivation Time – Ngoc-Lan Nguyen – PLOS ONE

Water and extremophile microbiome

Estimating planktonic diversity through spatial dominance patterns in a model ocean – Alice Soccodato – Marine Genomics

Microbial community profiling of the Chinoike Jigoku (“Blood Pond Hell”) hot spring in Beppu, Japan: isolation and characterization of Fe(III)-reducing Sulfolobus sp. strain GA1 – Yusei Masakia – Research in Microbiology

Near-Bottom Hypoxia Impacts Dynamics of Bacterioplankton Assemblage throughout Water Column of the Gulf of Finland (Baltic Sea) – Peeter Laas – PLOS ONE

Fungal communities in sediments of subtropical Chinese seas as estimated by DNA metabarcoding – Wei Li – Scientific Reports

Built environment microbiology

Characterization of the bacterial and fungal microbiome in indoor dust and outdoor air samples: a pilot study – Blake Hanson – Environmental Science: Processes & Impact

Microbiome Profiling of Drinking Water in Relation to Incidence of Inflammatory Bowel Disease – Jessica D Forbes – Canadian Journal of Microbiology

Infection microbiology

The scanning electron microscope in microbiology and diagnosis of infectious disease – Christine G. Golding – Scientific Reports

Bioinformatics

DADA2: High-resolution sample inference from Illumina amplicon data – Benjamin J Callahan – Nature Methods (OA by author)

MetaTrans: an open-source pipeline for metatranscriptomics – Xavier Martinez – Scientific Reports

An Introduction to Programming for Bioscientists: A Python-based Primer – Berk Ekmekci – Arxiv / PLOS

An Optimized Graph-Based Metagenomic Gene Classification Approach: Metagenomic Gene Analysis – Md Sarwar Kamal – Classification and Clustering in Biomedical Signal Processing

Complex heatmaps reveal patterns and correlations in multidimensional genomic data – Zuguang Gu – Bioinformatics

Unsupervised random forest: a tutorial with case studies – Nelson Lee Afanador – Journal of Chemometrics

Metagenomics

Review: The bright side of microbial dark matter: lessons learned from the uncultivated majority – Lindsey Solden – Current Opinion in Microbiology

Metabolomics

Review: Metabolomics of fecal samples: a practical consideration – Silke Matysik – Trends in Food Science & Technology

Viruses and phages

Targeted virus detection in next-generation sequencing data using an automated e-probe based approach – Marike Visser – Virology

Identification of diverse mycoviruses through metatranscriptomics characterization of the viromes of five major fungal plant pathogens – Shin-Yi Lee Marzano – Journal of Virology

Viruses and bacteria in Th2 biased allergic airway disease – Feng Lan – Allergy

More microbiology

Biofilms: Microbial Shelters Against Antibiotics – Skander Hathroubi – Microbial Drug Resistance

Microbes in the news

Building An Antibiotic To Kill Bad Microbes While Sparing Good Ones – Madeline K. Sofia – NPR

A rallying call for microbiome science national data management – A National Microbiome Data Center is essential for enabling exploration of all the environmental genomic data – EurekAlert

Could Gut Microbiome Be the Holy Grail for Diabetes Treatment? – An Expert Weighs In at International Endocrinology Congress – Business Wire

AOBiome and its Consumer Division, Mother Dirt, Founding members of the Microbiome Coalition, Helps Launch of the National Microbiome Initiative – PR Newswire

Painful pooping may stop panda sex. A gut-wrenching tummy ache can throw cold water on pandas’ love life. Amy Middleton reports. – Amy Middleton – Cosmos Magazine

May 20, 2016

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Updated microbial census, building healthy gut communities, antibiotics might worsen symptoms in transplant patients, another gut-brain connection, and FiveThirtyEight’s Gut Science week.

Events

Bioinformatics for the Microbiome Symposium at Stanford – Friday, May 27

General microbiology

Status of the Archaeal and Bacterial Census: an Update – Patrick D. Schloss – mBio

Suddenly everyone is a microbiota specialist! – Stefan A. Boers – Clinical Microbiology and Infection

Intricacies of assessing the human microbiome in epidemiologic studies – Courtney K. Robinson – Annals of Epidemiology

Pregnancy and birth

Sepsis in preterm infants causes alterations in mucosal gene expression and microbiota profiles compared to non-septic twins – María Cernada – Scientific Reports

From our lab, Editorial: Gut microbiota: How to build healthy growth-promoting gut communities – David A. Relman – Nature Reviews Gastroenterology & Hepatology

Human oral microbiome

Investigating Oral Microbiome Profiles in Children with Cleft Lip and Palate for Prognosis of Alveolar Bone Grafting – Luwei Liu – PLOS ONE

Human skin, eye, and ear microbiome (also see under Animal Experiments below)

Microbiology of Middle Ear Infections: Do You Hear What I Hear? – Donna M. Wolk – Clinical Microbiology Newsletter

Review: Impact of Microbiome on Ocular Health – Abirami Kugadas – The Ocular Surface

Human respiratory microbiome

Azithromycin therapy during RSV bronchiolitis: upper airway microbiome alterations and subsequent recurrent wheeze – Yanjiao Zhou – Journal of Allergy and Clinical Immunology

Human urinary tract microbiome

Research Highlight: Stones: Gut microbiome is unique in kidney stone disease – Rebecca Kelsey – Nature Reviews Urology

Human gut microbiome

Increased Gut Redox and Depletion of Anaerobic and Methanogenic Prokaryotes in Severe Acute Malnutrition – Matthieu Million – Scientific Reports

Topological distortion and reorganized modular structure of gut microbial co-occurrence networks in inflammatory bowel disease – Steven N. Baldassano – Scientific Reports

Hypothesis: Targeting the Ecology Within: The Role of the Gut-Brain Axis and Human Microbiota in Drug Addiction – Patrick D. Skosnik – Medical Hypotheses

Editorial: FMT — enduring strains – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Review: Gut Microbiota and Metabolic Health: The Potential Beneficial Effects of a Medium Chain Triglyceride Diet in Obese Individuals – Sabri Ahmed Rial – MDPI Nutrients

Fecal Microbiota Transplantation

Predictors of Early Failure After Fecal Microbiota Transplantation for the Therapy of Clostridium Difficile Infection: A Multicenter Study – Monika Fischer – The American Journal of Gastroenterology

Animal experiments

Ly6Chi Monocytes Provide a Link between Antibiotic-Induced Changes in Gut Microbiota and Adult Hippocampal Neurogenesis – Luisa Möhle – Cell Reports

Gut bacteria influence the birth of new brain cells in mice – Jessica Hamzelou – New Scientist

Editorial: Microbiota Alterations in Inflammatory Bowel Diseases: From Correlation to Causality – Benoit Chassaing – CMGH Cellular and Molecular Gastroenterology and Hepatology

Commentary: Canine and Human Atopic Dermatitis: Two Faces of the Same Host-Microbe Interaction – Domenico Santoro – Journal of Investigative Dermatology

Longitudinal Evaluation of the Skin Microbiome and Association with Microenvironment and Treatment in Canine Atopic Dermatitis – Charles W. Bradley – Journal of Investigative Dermatology

Plant, root, and soil microbiome

Plant community influence on soil microbial response after a wildfire in Sierra Nevada National Park (Spain) – Gema Bárcenas-Moreno – Science of The Total Environment

Insight into how organic amendments can shape the soil microbiome in long-term field experiments as revealed by network analysis – Ning Ling – Soil Biology and Biochemistry

Mycorrhiza and heavy metal resistant bacteria enhance growth, nutrient uptake and alter metabolic profile of sorghum grown in marginal soil – Faten Dhawi – Chemosphere

Built environment microbiome

Subaerial biofilms on granitic historic buildings: microbial diversity and development of phototrophic multi-species cultures – D. Vázquez-Nion

Pollution and waste microbiology

Microbial diversity and community structure in an antimony-rich tailings dump – Enzong Xiao – Applied Microbiology and Biotechnology

Food microbiology

A method to isolate bacterial communities and characterize ecosystems from food products: Validation and utilization in as a reproducible chicken meat model – Amélie Rouger – International Journal of Food Microbiology

Bioinformatics, proteomics, metabolomics

An adaptive association test for microbiome data: R package MiSPU – Chong Wu – Genome Medicine

Review: The information science of microbial ecology – Aria S Hahn – Current Opinion in Microbiology

Editorial: Proteomic interrogation of the gut microbiota: potential clinical impact – Sven-Bastiaan Haange – Expert Review of Proteomics

Microbial community metabolic modeling: A community data-driven network reconstruction – Christopher S. Henry – Journal of Cellular Physiology

More microbiology

Increased GVHD-related mortality with broad-spectrum antibiotic use after allogeneic hematopoietic stem cell transplantation in human patients and mice – Yusuke Shono – Science Translational Medicine

Some antibiotics may worsen complications in transplant patients – Science Daily

Microbes in the news

Welcome To FiveThirtyEight’s Gut Science Week – Maggie Koerth-Baker

Everybody Is Constipated, Nobody Is Constipated – Maggie Koerth-Baker

What Your Poop Says About You – Christine Laskowski

Probiotics Won’t Fix All Your Health Problems – Katherine Hobson

What Your Poop Says About You – Christine Laskowski

Is Gut Science Biased? – Anna Maria Barry-Jester

How Your Gut Affects Your Mood – Christie Aschwanden – FiveThirtyEight

Your Mouth Has Bacteria “That Could Grow on Mars,” Says a NASA Scientist – Especially if you had cheese sometime recently – Neel V. Patel – Inverse

Science, publishing, and career

Preprints for the life sciences – Jeremy M. Berg – Science

May 17, 2016

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Live blogging from the Michigan Microbial Meeting, microbiomes of Tibetan macaques and Pika, climate gases from SAR11, mycobiome of stored peanuts, and the deep biosphere.

Events

Ongoing now, with live written coverage: Michigan Meeting ““Unseen Partners: Manipulating Microbial Communities that Support Life on Earth.”

Bioinformatics for the Microbiome Symposium – Stanford Medicine – Friday May 27, 2016

Symposium: With a Little Help from My Friends: Microbial Partners in Integrative and Comparative Biology – Jan 4-8 2017, New Orleans

General microbiome

Microbiome Data Science: Understanding Our Microbial Planet – Nikos C. Kyrpides – Trends in Microbiology

Animal experiments

Antiviral effect of vitamin A on norovirus infection via modulation of the gut microbiome
Heetae Lee – Scientific Reports

A single gene of a commensal microbe affects host susceptibility to enteric infection – Mi Young Yoon – Nature Communications

Conference abstract: The Impact of Dietary Soy on Gut Microbiome – India R Gill – The FASEB Journal

Animal microbiome

Marked variation between winter and spring gut microbiota in free-ranging Tibetan Macaques (Macaca thibetana) – Binghua Sun – Scientific Reports

Pika population density is associated with composition and diversity of gut microbiota – Huan Li – Frontiers in Microbiology

Review: The bovine milk microbiota: insights and perspectives from -omics studies – Mol Biosyst

Plant, root, and soil microbiome

Soil pH, total phosphorus, climate and distance are the major factors influencing microbial activity at a regional spatial scale – Haichuan Cao – Scientific Reports

Biochar alters the soil microbiome and soil function: results of next generation amplicon sequencing across Europe – Joseph R. Jenkins – GCB Bioenergy

Biochar as a novel niche for culturing microbial communities in composting – Daquan Sun – Waste Management

Review: Omic Relief for the Biotically Stressed: Metabolomics of Plant Biotic Interactions –
Hezi Tenenboim – Trends in Plant Science

Temperature sensitivity of soil microbial communities: an application of macromolecular rate theory to microbial respiration – Charlotte J. Alster – Biogeosciences

Water and extremophile microbiome

The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol – Jing Sun – Nature Microbiology

News coverage: 
Story behind the paper: Climate gases from SAR11 – Stephen Giovannoni – Nature Microbiology Community Blog
Tiny organisms have huge effect on world’s atmosphere – Science Daily

Bacterial and archaeal communities in the deep-sea sediments of inactive hydrothermal vents in the Southwest India Ridge – Likui Zhang – Scientific Reports

Depth-dependent and seasonal variability in archaeal community structure in the subarctic and subtropical western North Pacific – Ryo Kaneko – Journal of Oceanography

Exploring the interaction patterns among taxa and environments from marine metagenomic data – Ze-Gang Wei – Quantitative Biology

Review: Analysis of Low-Biomass Microbial Communities in the Deep Biosphere – Y. Morono – Advances in Applied Microbiology

Undergraduate thesis: Oases of Microbial Life in the Highest Elevation Fumaroles on Earth – Adam Solon – University of Colorado-Boulder

Food microbiology

Variation in fungal microbiome (mycobiome) and aflatoxins during simulated storage of in-shell peanuts and peanut kernels – Fuguo Xing – Scientific Reports

Microbiology of death

Involvement of microbial mats in early fossilization by decay delay and formation of impressions and replicas of vertebrates and invertebrates – Miguel Iniesto – Scientific Reports

Pollution and waste microbiology

Correlating microbial community profiles with geochemical conditions in a watershed heavily contaminated by an antimony tailing pond – Enzong Xiao – Environmental Pollution

pH modulates arsenic toxicity in Bacillus licheniformis DAS-2 – K. Tripti – Ecotoxicology and Environmental Safety

News coverage: Bacteria discovered to remove arsenic from soil – BK Mishral – Times of India

More microbiology

Immunization with a heat-killed preparation of the environmental bacterium Mycobacterium vaccae promotes stress resilience in mice – Stefan O. Reber – PNAS

News coverage: Immunization with bacteria promotes stress resilience, coping behaviors in mice, CU-Boulder study finds – University of Colorado Boulder

Natural mutations in a Staphylococcus aureus virulence regulator attenuate cytotoxicity but permit bacteremia and abscess formation – Sudip Das – PNAS

Range expansions transition from pulled to pushed waves as growth becomes more cooperative in an experimental microbial population – Saurabh R. Gandhi – PNAS

Microbes and art

Creating art with bacteria at New England Biolabs – Jennie Oemig – Wicked Local Beverly

Microbes in the news

Interviewing the Founder of the World #1 Microbiome Investment fund: Isabelle De Cremoux – Labiotech

How Soil Microbes Fight Climate Change – They’re our microscopic allies in making dirt a major resource for storing excess carbon – Esther Ngumbi – Scientific American

Everything You Need to Know About Obama’s New Microbiome Initiative – Tiny organisms. Big budgets. – Kastalia Medrano – Inverse

Welcome To FiveThirtyEight’s Gut Science Week – Maggie Koerth-Baker – Five Thirty Eight
What Your Poop Says About You – Christine Laskowski – Five Thirty Eight

FAQ on Microbiology of Built Environments from the American Academy of Microbiology – Jonathan Eisen – MicroBEnet

At A Texas Body Farm, Studying The Decay Of Donated Corpses – Kai Kupferschmidt – World Crunch

Children with and without multiple sclerosis have differences in gut bacteria – EurekAlert

Bathroom Reader: A Brief History of the Toilet – Zack Fediay – uBiome Blog

Linfield Wine Lecture Series: Managing Expectations: The Microbiome in Agriculture – Jack Gilbert – Linfield College

Science, publishing, and career

Point of View: Avoiding a lost generation of scientists – Justin Q Taylor – eLIFE

Twitter won’t count links and photos as part of your 140 characters – Dave Gershgorn – PopSci

Bruno Lemaitre on Science and Narcissism – Leonid Schneider – For Better Science

Screen Shot 2016-05-17 at 10.58AM, May 17.jpg

Illustration by Leonid Schneider

May 13, 2016

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Today brought us great news from the White House Office of Science and Technology Policy (OSTP): the National Microbiome Initiative (NMI). Look on Twitter for our tweets tagged with #NMI.

National Microbiome Initiative and news coverage

Fact Sheet: Announcing the National Microbiome Initiative – The White House Office of Science and Technology Policy

Microbes shape our world – and a new White House initiative will figure out how – Rachel Feltman – The Washington Post

Obama administration to launch microbiome initiative, heeding scientists’ calls – David Nather – STAT News

The White House Launches the National Microbiome Initiative: Half a billion dollars are being pledged to study the microbes in humans, crops, soils, oceans, and more – Ed Yong – The Atlantic

Pleasantly surprised by the National Microbiome Initiative – Jonathan Eisen – The Tree of Life

New microbiome center to combine UChicago, Marine Biological Laboratory, Argonne expertise – EurekAlert

Events

Bioinformatics for the Microbiome – Stanford – Friday May 27th, with talks by Rob Knight, Ami Bhatt, Susan Holmes, Tomer Altman, Justin Sonnenberg, Sharon Greenblum, Ben Callahan and more.

Pint of Science Festival, May 23-25, San Francisco: Science talks in the finest watering holes of the Bay Area. Several microbiology talks!

Time is Running Out for “Culture as Medium” exhibit at Baltimore Under Ground Science Space (BUGSS) – Anne M. Estes – Mostly Microbes

Festival of Genomics – 27-29 June 2016 Boston

General microbiome

Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century Challenges – Martin J. Blaser – mBio

“Every Gene Is Everywhere but the Environment Selects”: Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis – Marco Fondi – Genome Biology and Evolution

Pregnancy and birth

News: Antibiotics, gut bugs and the young – Hilary Browne – Nature Reviews Microbiology

Human skin microbiome

Cross your legs before reading this one: Genital anaerobic bacterial overgrowth and the PrePex male circumcision device, Rakai, Uganda – Cindy M. Liu -The Journal of Infectious Diseases

Human gut microbiome

Gut microbiota in early pediatric multiple sclerosis: a case−control study – H. Tremlett – European Journal of Neurology

Review: Dumpster Diving in the Gut: Bacterial Microcompartments as Part of a Host-Associated Lifestyle – Christopher M. Jakobson – PLOS Pathogens

Plant, root, and soil microbiome

The Sphagnum microbiome: new insights from an ancient plant lineage – Joel E. Kostka – New Phytologist

Bioinformatics and metagenomics

PhySortR: a fast, flexible tool for sorting phylogenetic trees in R – Timothy G. Stephens – PeerJ

Microbes in the news
Is a Disrupted Gut Microbiome at the Root of Modern Disease?—with Dr. Justin Sonnenburg – Chris Kresser – Revolution Health Radio

Fatal attachment: How pathogenic bacteria hang on to mucosa and avoid exfoliation – EurekAlert

This MIT professor is using bee poop to map an invisible world – Melia Robinson – TechInsider

Microbes and art

ASM Agar Art 2016 People’s Choice voting – vote for the best contribution.

Science, publishing, and career

Top Medical Journals Give Women Researchers Short Shrift – Lauren Silverman – NPR

May 11, 2016

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Microbiomes in low-income human habitats, graph mining for sequence datasets, and a PhD Comics video on the microbiome.

Events

The Barcelona Debates on The Human Microbiome – June 30th and July 1st, 2016 – Barcelona

2016 Molecular Genetics of Bacteria and Phages Meeting in Madison, Wisconsin – August 8-12

General microbiome

Book: Microbiota of the Human Body – Implications in Health and Disease – Editor: Andreas Schwiertz – Springer

Human skin microbiome

Analysis of Facial Implants for Bacterial Biofilm Formation Using Scanning Electron Microscopy – Thomas J. Walker – JAMA Facial Plastic Surgery

Human gut microbiome

Interconnected microbiomes and resistomes in low-income human habitats – Erica C. Pehrsson – Nature

Review: The human gut microbiota and its interactive connections to diet – C. Milani – Journal of Human Nutrition and Dietetics

Editorial: The Bugs Within Our Body: The Human Microbiota – DJ Philpott – Clinical Pharmacology & Therapeutics

Plant, root, and soil microbiome

Fate of classical faecal bacterial markers and ampicillin-resistant bacteria in agricultural soils under Mediterranean climate after urban sludge amendment – Clarissa Gondim-Porto – Science of the Total Environment

Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi – Stéphane Hacquard – Nature Communications

Gypsum amendment to rice paddy soil stimulated bacteria involved in sulfur cycling but largely preserved the phylogenetic composition of the total bacterial community – Susanne Wörner – Environmental Microbiology Reports

Built environment microbiome

Interconnected microbiomes and resistomes in low-income human habitats – Erica C. Pehrsson – Nature

Metagenomics and bioinformatics

Graph mining for next generation sequencing: leveraging the assembly graph for biological insights – Julia Warnke-Sommer – BMC Genomics

More microbiology

Phenotypic heterogeneity driven by nutrient limitation promotes growth in fluctuating environments – Frank Schreiber – Nature Microbiology

Microbes in the news

Video: The Hidden World of Microbiomes – PhD Comics

Microbiome Monday: What Are You Made Of? – American Museum of Natural History

How dust from the Sahara fuels poisonous bacteria blooms in the Caribbean – Sarah Kaplan – Washington Post

UGA study finds Saharan dust affects marine bacteria, potential pathogen Vibrio
Vibrio can cause serious illness in humans, other marine organisms – EurekAlert

Thank Me Later: New Planet-Saving Bacteria Eats Switchgrass, Makes Biofuel – Tina Casey – Clean Technica

Game-Changing Bacteria Transmits Tuberculosis Through the Skin – HCP Live

Narrow spectrum antibiotic kills pathogens without killing good bacteria – EurekAlert

Dr Paul Blatchford awarded Emerging Researcher Grant – Press Release: Plant and Food Research

The Eye of a Microbial Camera – Nils Schuergers and Tchern Lenn – Natural History Mag

Science, publishing, and career

There’s a huge gender pay gap for STEM careers — just one year after graduation – Brian Resnick – Vox

Young women in STEM fields earn up to one-third less than men – EurekAlert

Bik’s Non-Microbiology Picks

Coral snakes predict the evolution of mimicry across New World snakes – Alison R. Davis Rabosky – Nature Communications

Meet the scientist debunking every dumb food myth on the internet
For every pseudoscientific blog parroting the latest trend, Yvette d’Entremont has a fact-based response – Diana Duong – Chatelaine

Is it safe to eat a newspaper? A Washington Post columnist is about to find out – Damian Garde – STAT news

May 7, 2016

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Drosophila male-killing spiroplasma, chitin in potting soil, temperature constraints for complex life, a book on microbial diversity, and monitoring sewer health.

General microbiome

Review: Design, analysis and application of synthetic microbial consortia – Xiaoqiang Jia – Synthetic and Systems Biotechnology

Review: Metabolic network modeling of microbial interactions in natural and engineered environmental systems – Octavio Perez-Garcia – Frontiers in Microbiology

Opinion: Mirror, mirror on the wall: which microbiomes will help heal them all? – Renuka R. Nayak – BMC Medicine

Hypothesis: Do microbiotas warm their hosts? – Eugene Rosenberg – Gut Microbes

Human respiratory microbiome

Microbiome diversity in the sputum of patients with pulmonary tuberculosis – P. Krishna – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

Literature review: The gut microbiota: a major player in the toxicity of environmental pollutants? – Sandrine P Claus – NPJ Biofilms and Microbiomes

Impact of Hypocaloric Hyperproteic Diet on Gut Microbiota in Overweight or Obese Patients with Nonalcoholic Fatty Liver Disease: A Pilot Study – Zoltan Pataky – Digestive Diseases and Sciences

n=1: Six-week Diet Correction for Body Weight Reduction and Its Subsequent Changes of Gut Microbiota: A Case Report – Bumjo Oh – Clinical Nutrition Research

Conference abstract: Associations Between Physical Activity and the Intestinal Microbiome of College Freshmen – Corrie M Whisner – The FASEB Journal

Animal experiments

Male-Killing Spiroplasma Alters Behavior of the Dosage Compensation Complex during Drosophila melanogaster Embryogenesis – Becky Cheng – Current Biology

Experimental Evolution on a Wild Mammal Species Results in Modifications of Gut Microbial Communities – Kevin D. Kohl – Frontiers in Microbiology

Conference abstract: Soy positively impacts cecal microbiota of ovariectomized rats selectively bred for low aerobic capacity – Tzu-Wen Liu – the FASEB Journal

Animal microbiome

Midgut Transcriptome of the Cockroach Periplaneta americana and Its Microbiota: Digestion, Detoxification and Oxidative Stress Response – Jianhua Zhang – PLOS ONE

Plants, roots, and soil microbiome

Chitin Mixed in Potting Soil Alters Lettuce Growth, the Survival of Zoonotic Bacteria on the Leaves and Associated Rhizosphere Microbiology – Jane Debode – Frontiers in Microbiology

Litter microbial and soil faunal communities stimulated in the wake of a volcanic eruption in a semiarid woodland in Patagonia, Argentina – Paula Berenstecher – Functional Ecology

Richness and bioactivity of culturable soil fungi from the Fildes Peninsula, Antarctica – Zhuang Ding – Extremophiles

Effect of 35 years inorganic fertilizer and manure amendment on structure of bacterial and archaeal communities in black soil of northeast China – Jianli Ding – Applied Soil Ecology

Conference abstract: Multi-omics of the Soil Microbiome – Janet K Jansson – The FASEB Journal

Review: Life cycle specialization of filamentous pathogens — colonization and reproduction in plant tissues – Janine Haueisen – Current Opinion in Microbiology

Review: Interspecific hybridization impacts host range and pathogenicity of filamentous microbes – Jasper RL Depotter – Current Opinion in Microbiology

Water and extremophile microbiome

From climate models to planetary habitability: temperature constraints for complex life – Laura Silva – arXiv preprint

Macroecological drivers of archaea and bacteria in benthic deep-sea ecosystems – Roberto Danovaro – Science Advances

Snowmelt induced hydrologic perturbations drive dynamic microbiological and geochemical behaviors across a shallow riparian aquifer – Robert Danczak – Frontiers in Earth Science

External controls on the distribution, fabrics and mineralization of modern microbial mats in a coastal hypersaline lagoon, Cayo Coco (Cuba) – Anthony Bouton

Richness and bioactivity of culturable soil fungi from the Fildes Peninsula, Antarctica – Zhuang Ding – Extremophiles

Single-Cell Genome and Group-Specific dsrAB Sequencing Implicate Marine Members of the Class Dehalococcoidia (Phylum Chloroflexi) in Sulfur Cycling – Kenneth Wasmund – mBio

Book: Their World: A Diversity of Microbial Environments – Editors: Christon J. Hurst – Springer

Review: Marine microorganisms as a promising and sustainable source of bioactive molecules – G. Romano – Marine Environmental Research

Waste and pollution microbiology

Hydrogeochemistry and coal-associated bacterial populations from a methanogenic coal bed – Elliott P. Barnharta – International Journal of Coal Geology

Review: Does bioleaching represent a biotechnological strategy for remediation of contaminated sediments? – Viviana Fonti – Science of The Total Environment

Review: Microbial sequencing methods for monitoring of anaerobic treatment of antibiotics to optimize performance and prevent system failure – Sevcan Aydin – Applied Microbiology and Biotechnology

Viruses and phages

Editorial overview: The megaviromes – Didier Raoult – Current Opinion in Microbiology

More microbiology

Stochastic Assembly of Bacteria in Microwell Arrays Reveals the Importance of Confinement in Community Development – Ryan H. Hansen – PLOS ONE

RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria – Kelly C Wrighton – The ISME Journal

Research Highlight: A time to gather chromosomes together – Naomi Attar – Nature Reviews Microbiology

Conference abstract: Metabolic Exchange In Microbial Communities – Andrei Osterman – The FASEB Journal

Microbes in the news

Pipe Dreams: Tapping into the Health Information in Our Sewers – Carrie Arnold – Environmental Health Perspectives

Deep sea microbes may be key to oceans’ climate change feedback – Howard Lee – The Guardian

Exploiting Male Killing Bacteria Could Control Insect Pest Species in the Future – SciCasts

Fifty people warned about possible exposure to drug-resistant bacteria at University of Alberta Hospital – Keith Gerein

May 4, 2016

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Note: If you enjoy this blog, I would very much appreciate a comment here below. Without your support, I might not be able to continue MicrobiomeDigest in its current form and frequency. So please, show your love by leaving a sign of support at the end of this blog. Thank you from the bottom of my heart! – Elies

Culturing the unculturables, a review on social bee microbiotas, the needle mycobiome, and an improved phage search tool.

Jobs and events

Faculty Position – Phage Biology and Microbiome Research, McMaster University, Ontario – Science Careers

Postdoctoral Fellow in Mucosal Immunology and Host-Microbiome Interactions
Jill Roberts Institute for Research in Inflammatory Bowel Disease at Weill Cornell Medicine – New York City, United States of America

General microbiome

Review: Microbial contributions to chronic inflammation and metabolic disease – Shanahan, Fergus – Current Opinion in Clinical Nutrition and Metabolic Care

Review: The microbial-mammalian metabolic axis: a critical symbiotic relationship – Chilloux, Julien – Current Opinion in Clinical Nutrition and Metabolic Care

Human gut microbiome

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation – Hilary P. Browne – Nature

(Also oral samples) The role of the gastrointestinal microbiome in infectious complications during induction chemotherapy for acute myeloid leukemia – Jessica R. Galloway-Peña – Cancer

Ecological Effect of Solithromycin on the Normal Human Oropharyngeal and Intestinal Microbiota – Mamun-Ur Rashid – Antimicrobial Agents and Chemotherapy

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

Clostridium difficile Infection in Patients with Inflammatory Bowel Disease – Nancy Fu – Current Infectious Disease Reports

Review: Interplay between diet, gut microbiota, epigenetic events, and colorectal cancer – Scott J. Bultman – Molecular Nutrition & Food Research

Animal microbiome

Cecal microbiota of Tibetan Chickens from five geographic regions were determined by 16S rRNA sequencing – Xueyan Zhou – Microbiology Open

Variability of Bacterial Communities in the Moth Heliothis virescens Indicates Transient Association with the Host – Heike Staudacher – PLOS ONE

Review: Gut microbial communities of social bees – Waldan K. Kwong and Nancy A. Moran – Nature Reviews Microbiology

Plant, root, and soil microbiome

Mineral Type and Solution Chemistry Affect the Structure and Composition of Actively Growing Bacterial Communities as Revealed by Bromodeoxyuridine Immunocapture and 16S rRNA Pyrosequencing – L. C. Kelly – Microbial Ecology

Habitat conditions and phenological tree traits overrule the influence of tree genotype in the needle mycobiome–Picea glauca system at an arctic treeline ecotone – Pascal Eusemann – New Phytologist

Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes
Philip E. Long – Trends in Microbiology

Extremophile microbiome

Twenty-Three Species of Hypobarophilic Bacteria Recovered from Diverse Ecosystems Exhibit Growth under Simulated Martian Conditions at 0.7 kPa – Andrew C. Schuerger – Astrobiology

Bioinformatics

Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains – Yemin Lan – Microbiome

Phages and viruses

Inferring phage-bacteria infection networks from time series data – Luis Jover – bioRxiv preprint

PHASTER: a better, faster version of the PHAST phage search tool – David Arndt – Nucleic Acids Research

Techniques

Digital Droplet Multiple Displacement Amplification (ddMDA) for Whole Genome Sequencing of Limited DNA Samples – Minsoung Rhee – PLOS ONE

Microbial Ecology

A conceptual framework for invasion in microbial communities – Marta Kinnunen – The ISME Journal

Microbes in the news

Most Gut Microbes Can Be Cultured. Contrary to the popular thought that many species are “unculturable,” the majority of bacteria known to populate the human gut can be grown in the lab, scientists show – Jyoti Madhusoodanan – The Scientist

Capturing the vast diversity of bacteria in our bodies – Megan Thielking – STAT News

A bitter pill. Josiah Zayner’s gut was making his life hell — so he embarked on an extreme DIY fecal transplant – Arielle Duhaime-Ross – The Verge

Article with video: Your mouth is full of bacteria blooming. And it’s beautiful – Hyacinth Empinado – STAT news

Explore this interactive map of the Gowanus Canal’s slightly scary microbiology – Jason Sayer – Architects Newspaper

The Friendly Viruses, and how they can help with the looming antimicrobial resistance crisis – Peter Speck and Anthony Smithyman – OUP blog

How the Gut Microbiome May be Key in Post-Surgery Organ Failure after Heart Surgery in Children – University of Arizona

Bugs as drugs: Harnessing novel gut bacteria for human health – Medical Xpress

Bacteria carrying bug threatens wine industry – John Bartell – ABC

Autonomous Super Mario-Themed Sewer Robots Live-Stream Neighborhood Microbiome Data – The answer to our health is in our excrement – Nickolaus Hines – Inverse

Bay Area Scientists Join Forces To Help Contain Zika Virus – CBS San Francisco

Breast milk hormones found to impact bacterial development in infants’ guts
Intestinal microbiome of children born to obese mothers significantly different from those born to mothers of healthy weight, CU Anschutz researchers find – EurekAlert

Science, publishing, and career

Dealing with retractions – Paul van der Vet – BioMed Central blog

Propagation of errors in citation networks: a study involving the entire citation network of a widely cited paper published in, and later retracted from, the journal Nature – Paul E. van der Vet and Harm Nijveen – Research Integrity and Peer Review