Category Archives: Human gut

April 28, 2016

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A special issue of Science with 2 papers on lifestyle factors that determine composition of the stool microbiome in large human cohorts, variation in microbiome LPS immunogenicity contributes to autoimmunity, SEM analysis of cave speleothem microbial communities, and saliva bacteria in Chicha (Ecuadorian beer).

Jobs and Events

Early Career Microbiome Meal, during European Respiratory Society Meeting 2016 London, September 2016

Caporaso Lab is hiring a software engineer to work on QIIME and scikit-bio – Greg Caporaso – MicroBEnet

General microbiome

A special Science Issue called The Microbiota At Work: Screen Shot 2016-04-28 at 12.42PM, Apr 28 1.jpg

Introduction: Manipulating the Microbiota – Caroline Ash, Kristen Mueller  – Science

Review: Cross-species comparisons of host genetic associations with the microbiome – Julia K. Goodrich – Science

Review: How colonization by microbiota in early life shapes the immune system – Thomas Gensollen – Science

Review: Antibiotic use and its consequences for the normal microbiome – Martin J. Blaser – Science

Review: The healthy human microbiome – Jason Lloyd-Price – Genome Medicine

Pregnancy and birth

Infant formula with galacto-oligosaccharides (OM55N) stimulates the growth of indigenous bifidobacteria in healthy term infants – T. Matsuki – Beneficial Microbes

Human oral microbiome

Comparison of Boiling and Robotics Automation Method in DNA Extraction for Metagenomic Sequencing of Human Oral Microbes – Junya Yamagishi – PLOS ONE

Human respiratory microbiome

[PDF] The impact of different methods of DNA extraction on microbial community measures of BALF samples based on metagenomic data – Yan Wen – Am J Transl Res

Human reproductive tract microbiome

[PDF] Barcoded sequencing reveals diverse intrauterine microbiomes in patients suffering with endometrial polyps – Rui-Li Fang – Am J Transl Res

Opinion: Cervicovaginal Microbiomes–Threats and Possibilities – Gregor Reid – Trends in Endocrinology & Metabolism

Review: Foodomics as part of the host-microbiota-exposome interplay – Lorenza Putignani – Journal of Proteomics

Human gut microbiome

Population-level analysis of gut microbiome variation – Gwen Falony – Science

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity – Alexandra Zhernakova – Science

Durable coexistence of donor and recipient strains after fecal microbiota transplantation – Simone S. Li – Science

Review: Resurrecting the intestinal microbiota to combat antibiotic-resistant pathogens – Eric G. Pamer – Science

Associations between dietary flavonoid intake and gut microbiota in a group of adults with cystic fibrosis (CF) – L. Li – Journal of Nutrition & Intermediary Metabolism

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans – Tommi Vatanen – Cell

Gut Bacteria Metabolism Impacts Immune Recovery in HIV-infected Individuals – Sergio Serrano-Villar – EBioMedicine

Serologic microbial associated markers can predict Crohn’s disease behaviour years before disease diagnosis – R. S. Choung – Alimentary Pharmacology & Therapeutics

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: Human gut microbiota and healthy aging: Recent developments and future prospective – Manish Kumar – Nutrition an Healthy Aging

Animal and other models

Soluble and Insoluble Fiber Differentially Impact Canine Fecal Microbiome and Circulating Metabolome – Matthew Irick Jackson – The FASEB Journal

Germ-free and antibiotic-treated mice are highly susceptible to epithelial injury in DSS colitis – Cristina Hernández-Chirlaque – Journal of Crohn’s and Colitis

High intensity exercise training increases the diversity and metabolic capacity of the mouse distal gut microbiota during diet-induced obesity – Emmanuel Denou – American Journal of Physiology

Induction of Subacute Ruminal Acidosis Affects the Ruminal Microbiome and Epithelium – Joshua C. Mccann – Frontiers in Microbiology

Review: Oral microbial biofilm models and their application to the testing of anticariogenic agents – Christina P.C. Sim – Journal of Dentistry

Animal microbiome

Patterns of bacteria-host associations suggest different ecological strategies between two reef building cold-water coral species – Anne-Leila Meistertzheim – Deep Sea Research Part I: Oceanographic Research Papers

Plant, root, and soil microbiome

Characterizing and handling different kinds of AM fungal spores in the rhizosphere – Xueguang Sun – World Journal of Microbiology and Biotechnology

Illumina-based analysis of the rhizosphere microbial communities associated with healthy and wilted Lanzhou lily (Lilium davidii var. unicolor) plants grown in the field – Qianhan Shang – World Journal of Microbiology and Biotechnology

Microbial community structures and metabolic profiles response differently to physiochemical properties between three landfill cover soils – Xi-En Long – Environmental Science and Pollution Research

The effects of host age and spatial location on bacterial community composition in the English Oak tree (Quercus robur) – S. Meaden – Environmental Microbiology Reports

Universal indicators for oil and gas prospecting based on bacterial communities shaped by light-hydrocarbon microseepage in China – Chunping Deng – Journal of Microbiology and Biotechnology

Performance of 16s rRNA primer pairs in the study of rhizosphere and endosphere bacterial microbiomes in metabarcoding studies – Bram Beckers – Frontiers in Microbiology

Water and extremophiles

The unexpected extremophile: Tolerance to fluctuating salinity in the green alga Picochlorum – Fatima Foflonker – Algal Research

Microbial communities in a range of carbon dioxide fluxes from a natural volcanic vent in Campo de Calatrava, Spain – Irena Fernández-Montiel – International Journal of Greenhouse Gas Control

On the use of high-throughput sequencing for the study of cyanobacterial diversity in Antarctic aquatic mats – Igor Stelmach Pessi – Journal of Phycology

Quorum sensing plays a complex role in regulating the enzyme hydrolysis activity of microbes associated with sinking particles in the ocean – Andreas Krupke – Frontier in Marine Science

Succession of bacterial community structure during the early stage of biofilm development in the Antarctic marine environment – Yung Mi Lee – Korean Journal of MIcrobiology

Using scanning electron microscopy to study microbial communities in speleothem samples collected from Iron Curtain Cave – Cohord Mason – The Journal of Experimental Microbiology & Immunology

Large differences in potential denitrification and sediment microbial communities across the Laurentian great lakes – Gaston E. Small – Biogeochemistry

Built environment microbiome

Ecological succession of the microbial communities of an air conditioning cooling coil in the tropics – Enzo Acerbi – Indoor Air

Web Alert: Microbiology in archaeology: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology – Lawrence P. Wackett – Environmental Microbiology

Food microbiology

Bacteria associated with human saliva are major microbial components of Ecuadorian indigenous beers (chicha) – Ana L. Freire – PeerJ

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 and metagenomics

BaitFisher: A Software Package for Multispecies Target DNA Enrichment Probe Design – Christoph Mayer – Molecular Biology and Evolution

Microbial ecology

The Evolution of Quorum Sensing as a Mechanism to Infer Kinship – Jonas Schluter – PLOS Computational Biology

Co-existence facilitates interspecific biofilm formation in complex microbial communities – Jonas S Madsen – Environmental Microbiology

Viruses and phages

Molecular evolution of epizootic hemorrhagic disease viruses in North America based on historical isolates using motif fingerprints – W. C. Wilson – Virus Genes

Techniques

[Video Protocol] Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization – Melis N. Anahtar – Journal of Visualized Experiments

Comparison of Boiling and Robotics Automation Method in DNA Extraction for Metagenomic Sequencing of Human Oral Microbes – Junya Yamagishi – PLOS ONE

The impact of different methods of DNA extraction on microbial community measures of BALF samples based on metagenomic data – Yan Wen – Am J Transl Res

Microbes in the news

Your gut bacteria are more than what you eat – Elizabeth Pennisi – Science

With quotes from me! New research confirms thriving gut bacteria is linked to a healthier body – Russell Brandom – The Verge

Want more good bugs in your gut? Try yogurt. And coffee – Patrick Skerrett – STAT News

This Bacteria Strain Offers a Curious Mix of Hope and Danger. The Elizabethkingia strain could cure malaria, but it’s also sickened dozens in Wisconsin – Lisa Margonelli – Slate

Bacteria beneficial to plants have spread across California – UC Riverside study shows spread of Bradyrhizobium has important implications for biofertilizers – EurekAlert

The Benefits of Slathering Your Newborn Baby with Vaginal Bacteria – Rebecca Schiller – Vice Broadly

A Timely Gut Check. At the American Museum of Natural History, meet your microbiome – Ralph Gardner – The Wall Street Journal

A Comprehensive Survey of Pre-Clinical Microbiology Curricula Among United States Medical Schools – Dora Melber – Clinical Infectious Diseases

Mayo Clinic Ventures Firm Explores Commercialization Of Gut Microbe Treatment – Don Jacobson – Twin City Business

Microbes and art

Quilting with soil: soil microorganisms had “painted” their efforts on the cloth in an unexpected variety of colors. – Martha Pings – Soils

Science, publishing, and career

Is most published research really false? – Jeffrey T Leek, Leah R Jager – bioRxiv

Who’s downloading pirated papers? Everyone. In rich and poor countries, researchers turn to the Sci-Hub website – John Bohannon – Science

The frustrated science student behind Sci-Hub – John Bohannon – Science

Plagiarism: A worm poking holes into the quality of our academic work – Christine Osae – The New Times

Bik’s Picks
Doctor ready to perform first human head transplant – Ross Kenneth Urken – News Week

April 27, 2016

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

Events

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

Pregnancy and birth

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

Human respiratory microbiome

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

Human reproductive tract microbiome

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

Human gut microbiome

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

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

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

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

Animal and bioreactor models

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

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

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

Plant, root, and soil microbiome

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

Water and extremophile microbiome

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

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

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

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

Pollution and waste microbiology

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

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

Microbial ecology

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

Bioinformatics and metagenomics

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

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

Microbes in the news

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

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

Quick mapping of our microbiomes and metabolomes – Science Daily

Viral Skin Infections – Tomislav Meštrović – News Medical

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

Bacterial virulence is stimulated by burns – EurekAlert

Science, publishing, and career

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

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

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

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

Bik’s Picks

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

April 26, 2016

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

Jobs and events

Assistant/Associate Professor in Microbiome Studies – University of Arizona

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

General microbiome

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

Pregnancy and birth

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

Human oral microbiome

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

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

Human blood ‘microbiome’

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

Human gut microbiome

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

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

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

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

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

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

Animal and other models

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

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

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

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

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

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

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

Animal microbiome

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

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

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

Plant, root, and soil microbiome

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

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

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

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

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

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

Water microbiome

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

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

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

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

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

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

Built environment microbiome

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

Food microbiology

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

Waste and pollution microbiology

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

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

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

Viruses and phages

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

Metagenomics, phylogeny, and bioinformatics

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

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

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

Microbes in the news

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

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

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

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

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

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

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

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

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

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

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

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

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

April 25, 2016, back in Cali

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Arrived back at SFO, and enough material for another digest. Longitudinal assessment of sputum microbiome, patient perspectives on FMT,  blue whale feces, and decontamination of amplicon datasets.

Events

Microbiome & Mice 2016, Advancing Microbiome Research Symposium – April 26, New York

Human oral microbiome

Longitudinal assessment of sputum microbiome by sequencing of the 16S rRNA gene in non-CF bronchiectasis patients – Michael J Cox – bioRxiv preprint

The gut and oral microbiome in HIV disease: a workshop report – DL Moyes – Oral Diseases

Modulation of the orodigestive tract microbiome in HIV-infected patients – D Saxena – Oral Diseases

Human vaginal microbiome

Molecular assessment of bacterial vaginosis by Lactobacillus abundance and species diversity – Joke A. M. Dols – BMC Infectious Diseases

Human gut microbiome

Patient Perspectives on Fecal Microbiota Transplantation for Clostridium Difficile Infection – Caroline Zellmer – Infectious Diseases and Therapy

Animal models

Effects of a diet high in resistant starch on fermentation end-products of protein and mucin secretion in the colons of pigs – Liping Zhou – Starch

Extensive Mobilome-Driven Genome Diversification in Mouse Gut-Associated Bacteroides vulgatus mpk – Anna Lange – Genome Biology and Evolution

Animal microbiome

Analysis of the microbial diversity in faecal material of the endangered blue whale, Balaenoptera musculus – Olivia Guass – Antonie van Leeuwenhoek

Water microbiome

Effects of land use on the structure and function of leaf-litter microbial communities in boreal streams – Caroline E. Emilson – Freshwater Biology

Biological responses to environmental heterogeneity under future ocean conditions – Philip W. Boyd – Global Change Biology

Techniques

Decontamination of 16S rRNA gene amplicon sequence datasets based on bacterial load assessment by qPCR – Vladimir Lazarevic – BMC Microbiology

Microbes in the news

“Amazing. If I ever want to know what city I’m in, all I need is a microscope!” Study: Cities Have Unique ‘Bacterial Fingerprints’ – American Voices – The Onion
Cities Are Microbial Wastelands Built On Dead Skin – Laurie Winkless – Forbes

How researchers teach bacteria new behaviors – Science Daily

A Very Precious Free Gift For a Newborn Baby – Toni Harman – Huffington Post

Have exploding cells blown up MV dogma? – Naomi Attar – Nature Reviews Microbiology

Science, publishing and career

BMJ editor Fiona Godlee takes on corruption in science – CBC News

April 25, 2016

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Just a short digest before I hop onto the plane back home at Amsterdam Airport.

Human gut microbiome

Might be DGGE; not sure (no access for me): Gastrointestinal Hormones, Intestinal Microbiota and Metabolic Homeostasis in Obese Patients: Effect of Bariatric Surgery – Alessandro Federico – In Vivo

Hypothesis: Microbes, molecular mimicry and molecules of mood and motivation – J.A. Morris – Medical Hypotheses

Review: The Intestinal Microbiome and Estrogen Receptor–Positive Female Breast Cancer – Maryann Kwa – Journal of the National Cancer Institute

Review: Pathophysiological role of host microbiota in the development of obesity – Nazarii Kobyliak – Nutrition Journal

Animal models

Fistulated dogs, food withheld for 5 days – not sure if the small gain in knowledge justifies the animal experiment here : The effects of feeding and withholding food on the canine small intestinal microbiota – A.C. Kasiraj – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Non-target impact of fungicide tetraconazole on microbial communities in soils with different agricultural management – Sławomir Sułowicz – Ecotoxicology

Air microbiome

Contribution of vegetation to the microbial composition of nearby outdoor air – Despoina S. Lymperopoulou – Applied and Environmental Microbiology

Microbes in the news

Anorexia may be caused by bacterial infection, say scientists – Sarah Knapton – The Telegraph

Chromosomes Have A Lot to Talk About – Here’s How They Do it – Nandita Jayaraj – The Wire

Science, publishing, and career

Has the time come for preprints in biology? – Needhi Bhalla – bioRxiv

April 24, 2016

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

Human oral microbiome

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

Human gut microbiome

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

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

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

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

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

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

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

Animal models

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

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

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

Plant, root, and soil microbiome

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

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

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

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

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

Water and extremophile microbiome

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

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

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

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

Built environment microbiology

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

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

Food microbiology

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

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

Taxonomy, new techniques, bioinformatics

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

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

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

Microbes in the news

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

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

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

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

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

Microbes and art

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

April 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 22, 2016

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General microbiome

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

Human skin and eye microbiome

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

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

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

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

Human gut microbiome

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

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

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

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

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

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

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

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

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

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

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

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

Animal microbiome

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

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

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

Water and extremophile microbiome

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

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

Food microbiology

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

Phages, viruses, and CRISPRs

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

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

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

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

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

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

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

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

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

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

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

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

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

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

April 20, 2016

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Posting from SJC: The reproductive tract microbiome from heterosexual couples, olfactory epithelium changes in GF mice, and life in the twilight zone.

Jobs

Post doc positions in human microbiome research in the Lynch Lab at #UCSF – Jonathan Eisen – MicroBEnet

Human respiratory microbiome

Culture-Independent Identification of Nontuberculous Mycobacteria in Cystic Fibrosis Respiratory Samples – Lindsay J. Caverly – PLOS ONE

Human reproductive tract microbiome

Rationale and Safety Assessment of a Novel Intravaginal Drug-Delivery System with Sustained DL-Lactic Acid Release, Intended for Long-Term Protection of the Vaginal Microbiome – Hans Verstraelen – PLOS ONE

Bacterial communities in penile skin, male urethra, and vaginas of heterosexual couples with and without bacterial vaginosis – Marcela Zozaya – Microbiome

Human gut microbiome

Review: Antibiotics, obesity and the link to microbes – what are we doing to our children? – Olli Turta – BMC Medicine

Review: Microbiome mediation of infections in the cancer setting – Ying Taur – Genome Medicine

Review: Moody microbes or fecal phrenology: what do we know about the microbiota-gut-brain axis? – Paul Forsythe – BMC Medicine

Animal models

Olfactory epithelium changes in germfree mice – Adrien François – Scientific Reports

Association between Polycystic Ovary Syndrome and Gut Microbiota – Yanjie Guo – PLOS ONE

Effect of fidaxomicin versus vancomycin on susceptibility to intestinal colonization with vancomycin-resistant enterococci and Klebsiella pneumoniae in mice – Abhishek Deshpande – Antimicrobial Agents and Chemotherapy

Intestinal microbiota and oral administration of Enterococcus faecium associated with the growth performance of new-born piglets – Y.B. Wang – Beneficial Microbes

Animal microbiome

Impact of the Chromatin Remodeling Factor CHD1 on Gut Microbiome Composition of Drosophila melanogaster – Johanna Sebald – PLOS ONE

Minireview: Lower Termite Associations with Microbes: Synergy, Protection, and Interplay – Brittany F. Peterson – Frontiers in Microbiology

Plant, root, and soil microbiome

Volatile compounds emitted by diverse phytopathogenic microorganisms promote plant growth and flowering through cytokinin action – Ángela María Sánchez-López – Plant, Cell & Environment

Quantifying the associations between fungal endophytes and biocontrol-induced herbivory of invasive purple loosestrife (Lythrum salicaria L.) – Aaron S David – Mycologia

Effect of CaMSRB2-Expressing Transgenic Rice Cultivation on Soil Microbial Community – Soo-In Sohn – Journal of Microbiology and Biotechnology

Water microbiome

Marine protist associations and environmental impacts across trophic levels in the twilight zone and below – VP Edgcomb – Current Opinion in Microbiology

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

Probiotics

Review: Probiotic approach to prevent antibiotic resistance – Arthur C. Ouwehand – Annals of Medicine

Infection microbiology

Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology – Sarah K. Hilton – Frontiers in Microbiology

More microbiology
A Generalized Spatial Measure for Resilience of Microbial Systems – Ryan S. Renslow – Frontiers in Microbiology

Community assembly and coexistence in communities of arbuscular mycorrhizal fungi – Kriszta Vályi – The ISME Journal

Microbes in the news

Exploding bacteria could help in our battle against superbugs: Aussie researchers have discovered that some bacteria explode to share useful resources with others, causing the whole group to become nastier. – Signe Dean – SBS

Phylo.io: interactive viewing and comparison of large phylogenetic trees on the web – Oscar Robinson – Molecular Biology and Evolution

April 19, 2016

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

Pregnancy and birth

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

Human skin microbiome

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

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

Human oral microbiome (also see Animal models, below)

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

Human gastric microbiome

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

Human gut microbiome

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

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

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

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

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

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

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

Animal models of microbiome research

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

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

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

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

Animal microbiome

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

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

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

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

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

Plant, root, and soil microbiome

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

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

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

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

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

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

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

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

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

Water microbiome

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

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

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

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

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

Built environment microbiome

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

Waste and pollution microbiology

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

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

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

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

Phages and viruses

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

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

Bioinformatics and metagenomics

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

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

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

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

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

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

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

More microbiology

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

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

Microbes in the news

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

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

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

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

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

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

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

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

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

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

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

Science, publishing, and career

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

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

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

Bik’s Picks

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