Category Archives: Metabolomics

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 19, 2016

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Two papers on triclosan effects, genome reduction in a common soil bacterium, spatial patterns of ocean microbes, and deep sequencing in unexplained fever cases.

Triclosan and microbiome

Two very different papers about the effect of triclosan on the microbiome:

Crossover Control Study of the Effect of Personal Care Products Containing Triclosan on the Microbiome – Angela C. Poole – mSphere

Antimicrobial in Common Toothpaste Doesn’t Impact Gut, Oral Microbiome – ASM

but:

Triclosan Exposure Is Associated with Rapid Restructuring of the Microbiome in Adult Zebrafish – Christopher A. Gaulke – PLOS ONE

The Case Against Antibacterial Soap Is Getting Stronger – Alexandra Sifferlin – Time

Human oral microbiome

Undergraduate thesis: Exploring a possible correlation between the human oral microbiome and body mass index – Ivy S. McDermot – University of Colorado Boulder

Human gut microbiome

Irritable Bowel Syndrome special in Nature: 
Irritable bowel syndrome – Michelle Grayson
Microbiome: Bacterial broadband – Michael Eisenstein

HIV infection results in metabolic alterations in the gut microbiota different from those induced by other diseases – Sergio Serrano-Villar – Scientific Reports

Review: The intestinal microbiome, barrier function, and immune system in inflammatory bowel disease: a tripartite pathophysiological circuit with implications for new therapeutic directions – Stephen M. Vindigni – Therapeutic Advances in Gastroenterology

Animal experiments

Microbiome-metabolome responses in the cecum and colon of pig to a high resistant starch diet – Yue Sun – Frontiers in Microbiology

Animal microbiome

Characterisation of the bacterial community structures in the intestine of Lampetra morii – Yingying Li – Antonie van Leeuwenhoek

Review: Microbiomes, metagenomics, and primate conservation: New strategies, tools, and applications – R.M. Stumpf – Biological Conservation

Plant, root, and soil microbiome

Genome reduction in an abundant and ubiquitous soil bacterial lineage – Tess Brewer – bioRxiv

Insight into structure dynamics of soil microbiota mediated by the richness of replanted Pseudostellaria heterophylla – Yong-Po Zhao – Scientific Reports

Review: Microbial inoculation of seed for improved crop performance: issues and opportunities – Maureen O’Callaghan – Applied Microbiology and Biotechnology

Water and extremophile microbiome

Distinct Spatial Patterns of SAR11, SAR86, and Actinobacteria Diversity along a Transect in the Ultra-oligotrophic South Pacific Ocean – Nyree J. West – Frontiers in Microbiology

In situ Dynamics of O2, pH, Light, and Photosynthesis in Ikaite Tufa Columns (Ikka Fjord, Greenland)—A Unique Microbial Habitat – Erik C. L. Trampe – Frontiers in Microbiology

Waste and pollution microbiology

Diversity of ammonia-oxidizing bacteria and archaea in response to different aeration rates during cattle manure composting – Lei Yan – Ecological Engineering

Microbes and infection

Deep sequencing approach for investigating infectious agents causing fever – T. N. Susilawati – European Journal of Clinical Microbiology & Infectious Diseases

Metagenomics and bioinformatics

A two-part mixed-effects model for analyzing longitudinal microbiome compositional data – Eric Z. Chen – Bioinformatics

Review: Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis – Vanessa Aguiar-Pulido, Wenrui Huang, Victoria Suarez-Ulloa, Trevor Cickovski, Kalai Mathee and Giri Narasimhan – Evolutionary Bioinformatics

More microbiology

Structure of the T4 baseplate and its function in triggering sheath contraction – Nicholas M. I. Taylor – Nature

How viruses infect bacteria: A tale of a tail – EurekAlert

A platform for the discovery of new macrolide antibiotics – Ian B. Seiple – Nature

Microbes in the news

Darwinolide, a New Diterpene Scaffold That Inhibits Methicillin-Resistant Staphylococcus aureus Biofilm from the Antarctic Sponge Dendrilla membranosa – Jacqueline L. von Salm – Organic Letters
University of South Florida Scientists Discover Antarctic Sponge Extract Can Help Kill MRSA – University of South Florida
Arctic Sponge Extract May Be Potent Against MRSA – Xuan Pham – Lab Roots

These bacteria are all over your wallet and smartphone
“Due to rising temperatures, we will NOT be accepting boob or sock money.” – Maria Lamagna – MarketWatch

Tampa Bay: Bacteria threatens Bay Area palm trees #Phytoplasma

Panda poop study provides insights into microbiome, reproductive troubles – EurekAlert

Indian gut similar to Bangladeshis, omnivorous animals, claims study
We acquire them from our mothers during birth, pass on to us through the breast milk and live with us till we die – Anuradha Mascarehnas – Indian Express

Science, publishing, and career

Ecology: The sea-otter whisperer – Jane Lubchenco – Nature

Bik’s Picks

MinION in space: Virologist Kate Rubins is set to make history as the first person to sequence DNA in space – Frontline Genomics

With lighting by my husband’s company Xicato: Arts: California on camera. The re-opening of the San Francisco Museum of Modern Art – John Gilbey – Nature

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 10, 2016, 2nd edition

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Nitrate and oral microcosms, microbial tryptophan metabolism effects on astrocytes, creating germ free plants, a systematic review of the (lack of) effect of probiotics on the gut microbiome, and a phage/host prediction tool.

Event

Starts today: Food-Microbiome Interaction: Implications for Health & Disease – New York Academy of Sciences and the Quadram Institute at The Royal Society in London

Pregnancy and birth

Prenatal and post-natal exposure to antibiotics and risk of asthma in childhood – J. Metsälä – Clinical & Experimental Allergy

Review: Obesity and overweight: Impact on maternal and milk microbiome and their role for infant health and nutrition – Izaskun Garcia-Mantrana – Molecular Nutrition and Food Research

Human respiratory microbiome

Comparison of two commercial DNA extraction kits for the analysis of nasopharyngeal bacterial communities – Marcos Pérez-Losada – AIMS Microbiology

Human oral microbiome

Nitrate and the Origin of Saliva Influence Composition and Short Chain Fatty Acid Production of Oral Microcosms – Jessica E. Koopman – Microbial Ecology

Human skin microbiome

A systematic review and meta-analysis on Staphylococcus aureus carriage in psoriasis, acne and rosacea – J. E. E. Totté – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

Global investigation of composition and interaction networks in gut microbiomes of individuals belonging to diverse geographies and age-groups – Deepak Yadav – Gut Pathogens

Alterations in fecal microbiota composition by probiotic supplementation in healthy adults: a systematic review of randomized controlled trials – Nadja B. Kristensen – Genome Medicine

Tissue Microbiome Profiling Identifies An Enrichment of Specific Enteric Bacteria In Opisthorchis viverrini Associated Cholangiocarcinoma – Kern Rei Chng – EBioMedicine

Editorial: Transkingdom interactions: Liver flukes and the microbiota in cancer – Lisa Osborne – EBioMedicine

Review: Could physical exercise help modulate the gut microbiota in chronic kidney disease? – Marta Esgalhado – Future Microbiology

Review: The Gut Microbiota and Immune System Relationship in Human Graft-versus-Host Disease – Lucrezia Laterza – Mediterranean Journal of Hematology and Infectious Diseases

Review: Gut Immunity and Type 1 Diabetes: a Mélange of Microbes, Diet, and Host Interactions? – David Endesfelder – Current Diabetes Reports

Animal experiments

Rumen and Cecum Microbiomes in Reindeer (Rangifer tarandus tarandus) Are Changed in Response to a Lichen Diet and May Affect Enteric Methane Emissions – Alejandro Salgado-Flores – PLOS ONE

Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants – Sheerli Kruger Ben Shabat – The ISME Journal

Book Chapter: Germ-Free Mice Model for Studying Host–Microbial Interactions – Yogesh Bhattarai – Mouse Models for Drug Discovery – Springer

Animal microbiome

Review: Bioprospecting Sponge-Associated Microbes for Antimicrobial Compounds – Anak Agung Gede Indraningrat – Marine Drugs

Plant, root, and soil microbiome

Wheat seed embryo excision enables the creation of axenic seedlings and Koch’s postulates testing of putative bacterial endophytes – Rebekah J. Robinson – Scientific Reports

Evidence of novel plant-species specific ammonia oxidizing bacterial clades in acidic South African fynbos soils – Jean-Baptiste Ramond – Journal of Basic Microbiology

Plants of the Fynbos biome harbour host species-specific bacterial communities – Tsakani Miyambo – FEMS Microbiology Letters

Extremophile microbiome

In situ hydrogen dynamics in a hot spring microbial mat during a diel cycle – Niels Peter Revsbech – Applied and Environmental Microbiology

Metabolomics

Type I interferons and microbial metabolites of tryptophan modulate astrocyte activity and central nervous system inflammation via the aryl hydrocarbon receptor – Veit Rothhammer – Nature Medicine

CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands – Bruno Lamas – Nature Medicine

Review: Urolithins, the rescue of ‘old’ metabolites to understand a ‘new’ concept: metabotypes as a nexus between phenolic metabolism, microbiota dysbiosis and host health status – Francisco A. Tomás-Barberán – Molecular Nutrition & Food Research

Metagenomics and bioinformatics –

Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data – J. A. Frank – Scientific Reports

OrfM: A fast open reading frame predictor for metagenomic data – Ben J. Woodcroft – Bioinformatics

Phages and viruses

HostPhinder: A Phage Host Prediction Tool – Julia Villarroel – MDPI Viruses

More microbiology

Nonclinical Safety Assessment of SYN-004: An Oral β-lactamase for the Protection of the Gut Microbiome From Disruption by Biliary-Excreted, Intravenously Administered Antibiotics – John F. Kokai-Kun – International Journal of Toxicology

Rapid identification of health care–associated infections with an integrated fluorescence anisotropy system – Ki Soo Park – Science Advances

In situ real-time evaluation of radiation-responsive promoters in the extremely radioresistant microbe Deinococcus radiodurans – Narasimha Anaganti – Journal of Biosciences

Microbes in the news

Stool Bank OpenBiome Is Expanding to Somerville. The bank wants more Boston-area residents to donate – Jamie Ducharme

Do probiotics have an effect on healthy adults? It’s too early to tell – EurekAlert

The Microbiome in Pediatric Rheumatic Diseases – Matthew Stoll – The Rheumatologist

May 10, 2016

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A very selective antibiotic that does not disturb the microbiota, metabolic pathways of the Deepwater Horizon spill, and GI microbiome role in acute myeloid leukemia.

Jobs and events

Postdoc funding opportunity “Microbiology of the built environment”, Alfred P. Sloan Foundation

The 4th Microbiome R&D and Business Collaboration Forum: USA – 3-4 October 2016, La Jolla, San Diego, USA

Human gut microbiome

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

Animal experiments

The native microbiome of the nematode Caenorhabditis elegans: gateway to a new host-microbiome model – Philipp Dirksen – BMC Biology

Editorial: Caenorhabditis microbiota: worm guts get populated – Laura C. Clark – BMC Biology

A Pathogen-Selective Antibiotic Minimizes Disturbance to the Microbiome – Jiangwei Yao – Antimicrobial Agents and Chemotherapy

Waste, pollution, and water treatment microbiology

Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill – Nina Dombrowski – Nature Microbiology

The effects of sodium hypochlorite against selected drinking water-isolated bacteria in planktonic and sessile states – I.B. Gomes – Science of the Total Environment

Microbes in the news

Gut Microbiome Startup CeMeT Aims to Build Reference Database from 10K Volunteers in Germany – Julia Karow – Genome Web

Microbiome linked to infectious complications in AML – Medical Xpress

Narrow-Spectrum Antibiotic Could Spare the Microbiome. A drug that singles out Staphylococcus aureus leaves gut-dwelling microbiota largely intact, a mouse study shows – Amanda B. Keener – The Scientist

Genetic potential of oil-eating bacteria from the BP oil spill decoded – University of Texas at Austin

Fooling the test: Antibiotic-resistant bacteria that look susceptible – Phys.org

A new industry that uses bacteria to remediate old mines? – Jonathan Migneault – Sudbury

The Mighty Microbes of Yellowstone – Scalding water is home to what microbiologists call extremophiles, heat-loving creatures that have figured in many scientific breakthroughs – David Quammen – National Geographic

Science, publishing, and career

John Oliver exposes how the media turns scientific studies into “morning show gossip”
– German Lopez – Vox

Tracking Career Outcomes for Postdoctoral Scholars: A Call to Action – Elizabeth A. Silva – PLOS Biology

With quotes from me: Image manipulation in biomedical papers is commonplace – Maria Burke – Chemistry World

Open-access index delists thousands of journals. Many publications did not reapply after leading directory tightened its quality criteria – Monya Baker

April 29, 2016

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After Science’s Microbiome Issue yesterday, today’s digest features Genome Biology’s special Translational Microbiome issue. Papers on detecting colon cancer, Clostridium difficile infection, high-fat diets in mice. Also check out papers on H2 metabolism in the colon, no effects of temperature rise on soil microbiome of wet tropical forests, and ultra-basic springs.

Jobs and events

Nice speaker line-up: May 16-18, Michigan Meeting on Microbial Communities: a deep dive into the world of microbes – University of Michigan

Job opening in our lab: Life Science Research Professional  – Stanford

Pregnancy and birth

Gestational age, mode of birth and breastmilk feeding all influence acute early childhood gastroenteritis: a record-linkage cohort study – Jason P. Bentley – BMC Pediatrics

Human gut microbiome

Special issue Genome Medicine: Translating the microbiome: health and disease, Guest Editor: Curtis Huttenhower

Editorial: A roadmap to translating the microbiome – Rabia Begum – Genome Medicine

Detecting colon cancer using microbiota:  Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions – Nielson T. Baxter – Genome Medicine

Dynamics of the fecal microbiome in patients with recurrent and nonrecurrent Clostridium difficile infection – Anna Maria Seekatz – Genome Medicine

Use of Shotgun Metagenome Sequencing to Detect Fecal Colonization with Multi-Drug Resistant Bacteria in Children – Heidi Andersen – Journal of Clinical Microbiology

Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection – Emmanuel Montassier – Genome Medicine

Impact of Helminth Infection on the Clinical and Microbiological Presentation of Chagas Diseases in Chronically Infected Patients – Fernando Salvador – PLOS Neglected Tropical Diseases

Malaria, helminths and malnutrition: a cross-sectional survey of school children in the South-Tongu district of Ghana – Patrick Ferdinand Ayeh-Kumi – BMC Research Notes

Review: The Microbiome and Mental Health: Looking Back, Moving Forward with Lessons from Allergic Diseases – Alan C. Logan – Clinical Psychopharmacology and Neuroscience

Review: Mechanistic and Technical Challenges in Studying the Human Microbiome and Cancer Epidemiology – Mukesh Verma – Technology in Cancer Research & Treatment

Animal models
Effects of Isoflavone-Enriched Feed on the Rumen Microbiota in Dairy Cows – Jitka Kasparovska – PLOS ONE

Deep-fried oil consumption in rats impairs glycerolipid metabolism, gut histology and microbiota structure – Zhongkai Zhou – Lipids in Health and Disease

Dietary supplementation of Rosmarinus officinalis L. leaves in sheep affects the abundance of rumen methanogens and other microbial populations – Gabriella Cobellis – Journal of Animal Science and Biotechnology

Microorganisms in the rumen and reticulum of buffalo (Bubalus bubalis) fed two different feeding systems – Raul Franzolin – BMC Research Notes

Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet – Douglas Mahana – Genome Medicine

A fish, not the bird: Combined effects of dietary mannan- and fructo-oligosaccharide on growth indices, body composition, intestinal bacterial flora and digestive enzymes activity of regal peacock (Aulonocara stuartgranti) – S. S. Mirzapour-Rezaee – Aquaculture Nutrition

Plant, root, and soil microbiome

The composition, localization and function of low-temperature adapted microbial communities involved in methanogenic degradations of cellulose and chitin from Qinghai-Tibetan Plateau wetland soils – Yumei Dai – Journal of Applied Microbiology

Effect of different levels of nitrogen on rhizosphere bacterial community structure in intensive monoculture of greenhouse lettuce – Jian-Gang Li – Scientific Reports

Pichia kudriavzevii as a representative yeast of North Patagonian winemaking terroir – Silvana M. del Mónaco – International Journal of Food Microbiology

Increases in mean annual temperature do not alter soil bacterial community structure in tropical montane wet forests – Paul C. Selmants – Ecosphere

Water and extremophile microbiome

A role for fungi as parasites in the black box of marine trophic interactions – Thomas A. Richards – Environmental Microbiology Reports

Exploring the metabolic potential of microbial communities in ultra-basic, reducing springs at The Cedars, CA, USA: Experimental evidence of microbial methanogenesis and heterotrophic acetogenesis – Lukas Kohl – Journal of Geophysical Research

Viruses and phages

Minireview: Virus-host interplay in high salt environments – Nina S. Atanasova – Environmental Microbiology Reports

Metagenomics and bioinformatics

Inferring Intra-Community Microbial Interaction Patterns from Metagenomic Datasets Using Associative Rule Mining Techniques – Disha Tandon – PLOS ONE

Metabolomics

H2 metabolism is widespread and diverse among human colonic microbes – Patricia G. Wolf – Gut Microbes

Localizing metabolic synthesis in microbial cultures with kinetic mass spectrometry imaging (kMSI) – Katherine Louie – bioRxiv

Viruses and phages

The virome: a missing component of biological interaction networks in health and disease – Scott A. Handley – Genome Medicine

Microbial ecology

Commentary: Bacteriophages or bacteriovores – that is the question: variations on the theme of eating Stenotrophomonas maltophilia – Harald Brüssow – Environmental Microbiology Reports

Microbes in the news

Lots of press coverage for the Science and Genome Medicine special issues today!

Scientists think they’ve found the secret to better poop transplants – Rachel Feltman – The Washington Post

Why Are Your Gut Microbes Different From Mine? To find out, scientists collected poop from thousands of people—but they ended up with more questions than answers – Ed Yong – The Atlantic

Food you eat and medicines you take can alter your gut bacteria in both good and bad ways – Emma Tiller – NH Voice

Special microbiome issue – Science Codex

Gut Microbiome Makeup Influenced by Medication Use, Other Factors – Genome Web

In Dutch: Zijn koffie, rode wijn en chocola nou wel of niet goed voor je? – Sander Voormolen – NRC

Title fail: World’s first microbiome study reveals links between lifestyle and gut flora – EurekAlert

Lifestyle has a strong impact on intestinal bacteria – Medical Xpress

The “Friendly” Bacteria In Your Gut Isn’t As Set At Birth As We Thought – Tom Chivers – BuzzFeed

Gut bacteria may predict risk of life-threatening infections following chemotherapy – Science Daily

What Can Happen When You’re Way Too Clean – Alice Park – Time

10 Bizarre (and Wonderful) Facts About Microbes:truly amazing facts about the human microbiome – Dawn Field – TopTenz

Vancouver couple develops slime-free water dishes for dogs – Eric MacKenzie – Vancouver 24h

Podcast: Microbe Talk, April 2016, Can parasitic worms treat inflammatory diseases?

Some superbugs literally explode when they die, making them even more deadly
Ticking time bomb – Jacinta Bowler – Science Alert

Science, publishing, and career

Unconditional data sharing, plus peer review transparency, is key to research reproducibility – Leonid Schneider – The Winnower

Featuring our paper: Seeing double: Duplicated images plague research papers – Ivan Oransky and Adam Marcus – STAT News

Paper linking fecal transplants to obesity in rats retracted for faked data – Dalmeet Singh Chawla – Retraction Watch

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 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 5, 2016

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Differences in myelination and gene expression in prefrontal cortex between GF and conventional mice, migratory passerines, metagenomics of probiotics, and megaviromes.

Events

NAS Meeting: Microbiomes of the Built Environment: From Research to Application – David Coil – MicroBEnet

Human oral microbiome

Impact of age and sex on the composition and abundance of the intestinal microbiota in individuals with and without enteric infections – Pallavi Singh – Annals of Epidemiology

Review [PDF]: Oral Microbial Shift: Factors affecting the Microbiome and Prevention of Oral Disease – Namrata Dagli – Journal of Contemporary Dental Practice

Human reproductive tract microbiome

Review: Incorporating microbiota data into epidemiological models: Examples from vaginal microbiota research – Janneke van de Wijgert – Annals of Epidemiology

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

Human gut microbiome

Diversified mcr-1-Harbouring Plasmid Reservoirs Confer Resistance to Colistin in Human Gut Microbiota – Huiyan Ye – mBio

Animal models

Regulation of prefrontal cortex myelination by the microbiota – AE Hoban – Translational Psychiatry

Responses of fecal bacterial communities to resistant starch intervention in diabetic rats – Zhongkai Zhou – Starch

Resveratrol Attenuates Trimethylamine-N-Oxide (TMAO)-Induced Atherosclerosis by Regulating TMAO Synthesis and Bile Acid Metabolism via Remodeling of the Gut Microbiota – Ming-liang Chen – mBio

Commentary: Policing of gut microbiota by the adaptive immune system – Laurent Dollé – BMC Medicine

Animal microbiome

Sample processing impacts the viability and cultivability of the sponge microbiome – Ana I. Esteves – Frontiers in Microbiology

Characterization of the gut microbiota of migratory passerines during stopover along the northern coast of the Gulf of Mexico – William B. Lewis – Journal of Avian Biology

Highlight: Microbes matter: herbivore gut endosymbionts play a role in breakdown of host plant toxins – Franziska Beran – Environmental Microbiology

Selective feeding by the giant barrel sponge enhances foraging efficiency – Steven E. McMurray – Limnology and Oceanography

PhD Thesis: Molecular investigation of Australian termites and their gut symbionts – Nurdyana Abdul Rahman – University of Queensland

Plant, root, and soil microbiome

Distance-dependent effects of pathogenic fungi on seedlings of a legume tree: impaired nodule formation and identification of antagonistic rhizosphere bacteria –  Lan Liu – Journal of Ecology

Bacterial community dynamics during ensiling of perennial ryegrass at two compaction levels monitored by terminal restriction fragment length polymorphism – K. Graf – Journal of Applied Microbiology

Microsite differentiation drives the abundance of soil ammonia oxidizing bacteria along aridity gradients – Manuel Delgado-Baquerizo – Frontiers in Microbiology

Not exactly microbes but sounded interesting: Do tropical rain forest soils have greater nematode diversity than High Arctic tundra? A metagenetic comparison of Malaysia and Svalbard – Dorsaf Kerfahi – Global Ecology and Biogeography

Use of two spatially separated plant species alters microbial community function in horizontal subsurface flow constructed wetlands – Mark Button – Ecological Engineering

Water microbiome

Spatio-temporal interdependence of bacteria and phytoplankton during a Baltic Sea spring bloom – Carina Bunse – Frontiers in Microbiology

Protist-bacteria associations: Gammaproteobacteria and Alphaproteobacteria are prevalent as digestion-resistant bacteria in ciliated protozoa – Jun Gong – Frontiers in Microbiology

Particulate matter stoichiometry driven by microplankton community structure in summer in the Indian sector of the Southern Ocean – M. Rembauville – Limnology and Oceanography

Waste and pollution microbiome

Functional Metagenomics of a Biostimulated Petroleum-Contaminated Soil Reveals an Extraordinary Diversity of Extradiol Dioxygenases – Laura Terrón-González – Applied and Environmental Microbiology

Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community – Christopher L. Hemme – mBio

Built environment microbiome

A novel, optical, on-line bacteria sensor for monitoring drinking water quality – Bo Højris – Scientific Reports

Food and probiotics microbiology

Culture-Independent Metagenomic Surveillance of Commercially Available Probiotics with High-Throughput Next-Generation Sequencing – Jennifer N. Patro – mSphere

Unravelling the effect of clostridia spores and lysozyme on microbiota dynamics in Grana Padano cheese: A metaproteomics approach – Alessio Soggiu – Journal of Proteomics

Viruses and phages / metagenomics

VIP: an integrated pipeline for metagenomics of virus identification and discovery – Yang Li – Scientific Reports

Antibiotic Resistome: Improving Detection and Quantification Accuracy for Comparative Metagenomics – Ali H. A. Elbehery – OMICS

Themed Issue of Current Opinion in Microbiology: Environmental microbiology/Megaviromes
Review: Giants among larges: how gigantism impacts giant virus entry into amoebae – Rodrigo Araújo Lima Rodrigues – Current Opinion in Microbiology
Review: Updating strategies for isolating and discovering giant viruses – Jacques Yaacoub Bou Khalil
Review, but not sure about what: Persistent virus and addiction modules: an engine of symbiosis – Luis P Villarreal

Metabolomics

In silico methods for linking genes and secondary metabolites: The way forward – Shradha Khater – Synthetic and Systems Biotechnology

Techniques and bioinformatics

It’s all relative: analyzing microbiome data as compositions – Gregory B. Gloor – Annals of Epidemiology

Not metagenomics but about a not-clearly defined 16S rRNA gene amplification pipeline. Not a good paper: Snapshot on a pilot metagenomic study for the appraisal of gut microbial diversity in mice, cat and men – Coline Plé – Gastroenterology Research and Practice

More microbiology

Expression of arsenic resistance genes in the obligate anaerobe Bacteroides vulgatus ATCC 8482, a gut microbiome bacterium – Jiajiao Li – Anaerobe

Cholesterol Analogs with Degradation-resistant Alkyl Side Chains Are Effective Mycobacterium tuberculosis Growth Inhibitors – Daniel J. Frank – The Journal of Biological Chemistry

Microbiology and art

This Artist Paints With Bacteria, And It’s Strangely Beautiful – Jacqueline Howard – Huffington Post

Microbes in the news

With a quote from me! Gut bacteria regulate nerve fibre insulation – Mo Costandi – The Guardian

Europe’s Microbiology Society’s Annual Conference 2016: the Twitter story – Microbepost

Antibiotic soap can alter a baby’s gut bacteria – Tim Sandle – Digital Journal

The fridge that detects bacteria in your food – NZ Herald

About COPD: Take a deep breath – your lung microbiome will appreciate it – GSK

Microbiome and the modern environment: a global drift toward dysbiosis? – Susan Prescott and Alan Logan – BioMed Central blog

Biofilm researcher: New Faces: Boo Shan Tseng: This Life Sciences professor is all about communities – University of Nevada, Las Vegas

Study by the University of Kaiserslautern: Viruses cause bacteria to produce pink pigments – AlphaGalileo

Promising new method inhibits TB–causing bacteria – Phys.org

Bacteria Hysteria

Do you know how clean your lean workout is? The DEADLY bacteria found in your gym mat – Kat Romero – Express

Bik’s Picks

Cellular telephone use during free-living walking significantly reduces average walking speed – Jacob E. Barkley – BMC Research Notes

So cool: The Cemetery as Archive: A 177-year-old cemetery is preparing to digitize millions of records that shed light on New York City’s shifting demographics – Jessica Leigh Hester