Gut microbiota in stunted children in India, Chinese children with diabetes, Tibetan and Han populations at different altitudes, and searching for Darwin’s Warm Little Pond.

Human skin microbiome

Review: The influence of skin microorganisms on cutaneous immunity – Yasmine Belkaid – Nature Reviews Immunology

Human oral microbiome

Study recruitment: Reducing oral bacteria in those with mild dementia – Shelley Allen – ISRCTN Registry

Human gut microbiome

Weight gain in anorexia nervosa does not ameliorate the faecal microbiota, branched chain fatty acid profiles, and gastrointestinal complaints – Isabelle Mack – Scientific Reports

Longitudinal Analysis of the Intestinal Microbiota in Persistently Stunted Young Children in South India – Duy M. Dinh – PLOS ONE

Effects of Rifaximin on Transit, Permeability, Fecal Microbiome, and Organic Acid Excretion in Irritable Bowel Syndrome – Andrés Acosta – Clinical and Translational Gastroenterology

Imbalance of Fecal Microbiota at Newly Diagnosed Type 1 Diabetes in Chinese Children – Cui-Juan Qi – Chinese Medical Journal

Comparative Analysis of Gut Microbiota of Native Tibetan and Han Populations Living at Different Altitudes – Kang Li – PLOS ONE

Intestinal Microbiota Is Influenced by Gender and Body Mass Index – Carmen Haro – PLOS ONE

Associations between common intestinal parasites and bacteria in humans as revealed by qPCR – L. O’Brien Andersen – European Journal of Clinical Microbiology & Infectious Diseases
Review: Gut microbiota, metabolites and host immunity – Michelle G. Rooks – Nature Reviews Immunology

Review: The behaviour of dietary fibre in the gastrointestinal tract determines its physiological effect – Edoardo Capuano – Critical Reviews in Food Science and Nutrition

Animal experiments

Effects of dietary fibre source on microbiota composition in the large intestine of suckling piglets – Lingli Zhang – FEMS Microbiology Letters

Investigations on the possible impact of a glyphosate-containing herbicide on ruminal metabolism and bacteria in vitro by means of the “Rumen Simulation Technique” – Susanne Riede – Journal of Applied Microbiology

Piglet nasal microbiota at weaning may influence the development of Glässer’s disease during the rearing period – Florencia Correa-Fiz – BMC Genomics

Effects of a Broad-Spectrum Antibiotic on the Siberian Hamster (Phodopus sungorus) Gut Microbiome – Emma A. St. John – The FASEB Journal

Animal microbiome

Comparison of archaeal and bacterial communities in two sponge species and seawater from an Indonesian coral reef environment – Ana Rita Moura Polónia – Marine Genomics

Baboons: Vaginal Dysbiosis from an Evolutionary Perspective – Natalia Schlabritz-Loutsevitch – Scientific Reports

Review: Longevity-modulating effects of symbiosis: insights from Drosophila–Wolbachia interaction – Oleksandr M. Maistrenko – Biogerontology

Water and extremophile microbiome

Essay: A Field Trip to the Archaean in Search of Darwin’s Warm Little Pond – Bruce Damer- MDPI Life

Identification and characterization of yeasts isolated from sedimentary rocks of Union Glacier at the Antarctica – Salvador Barahona – Extremophiles

Ionic Strength Is a Barrier to the Habitability of Mars – Mark G. Fox-Powell – Astrobiology

Built environment microbiology

Urban Dust Microbiome: Impact on Later Atopy and Wheezing – Christina Tischer – Environmental Health Perspectives

Review: Pediatric Asthma and the Indoor Microbial Environment – Lidia Casas – Current Environmental Health Reports

Waste and pollution microbiology

Enhanced methane production via repeated batch bioaugmentation pattern of enriched microbial consortia – Zhiman Yang – Bioresource Technology

Techniques

Effect of short-term room temperature storage on the microbial community in infant fecal samples – Yong Guo – Scientific Reports

Microbial Ecology

Review: Microbial interactions and community assembly at microscales – Otto X Cordero – Current Opinion in Microbiology

Microbes in the news

How to feed a happy, healthy gut – Carrie Dennett – The Washington Post

Development of Gut Microbes and Gut Immunity Linked – Julia Evangelou Strait – Washington University School of Medicine

Newly Discovered Phages Can Target Antibiotic Resistance – Interview with Paul E. Turner PhD – Medical Research

Specter of Oyster Bacteria Brings Suit Against FDA – Lorraine Bailey – Courthouse News

Xenex Germ-Zapping Robot Kills CRE; Robot Destroys Nightmare Bacteria Like CRE, Ebola & C.Diff before They Make People Sick – Business Wire

Science, publishing and career

Excellent podcast for all genders: Sexism in biotech, from scantily clad models to how gender affects this podcast – Meg Tirrell and Luke Timmerman – STAT News

Another unexpected international trip because of sad family circumstances, so blogging from SJC. Bifidobacteria in babies and adults, the human nasal passage, dysbiosis in PSC, giant pandas, and Fairy Circles.And celebrating Microbiome Digest’s 2nd birthday!

Pregnancy and birth

A comparative study of bifidobacteria in human babies and adults – Azra Pachenari  – Bioscience of Microbiota, Food and Health

Human respiratory microbiome

Exploring the bacterial assemblages along the human nasal passage – Melissa L. Wos-Oxley – Environmental Microbiology

Characterisation of Candida within the Mycobiome/Microbiome of the Lower Respiratory Tract of ICU Patients – Robert Krause – PLOS ONE

Human gut microbiome

Fermented milk containing Lactobacillus casei strain Shirota preserves the diversity of the gut microbiota and relieves abdominal dysfunction in healthy medical students exposed to academic stress – Akito Kato-Kataoka – Applied and Environmental Microbiology

Bile Acids and Dysbiosis in Non-Alcoholic Fatty Liver Disease – Marialena Mouzaki – PLOS ONE

Primary sclerosing cholangitis is characterised by intestinal dysbiosis independent from IBD – João Sabino – Gut

Review: Paneth cell α-defensins and enteric microbiota in health and disease
Kiminori Nakamura – Bioscience of Microbiota, Food and Health

Animal experiments

Development of Ruminal and Fecal Microbiomes Are Affected by Weaning But Not Weaning Strategy in Dairy Calves – Sarah J. Meale – Frontiers in Microbiology

Gender-Specific Effects of Organophosphate Diazinon on the Gut Microbiome and Its Metabolic Functions – Bei Gao – Environmental Health Perspectives

Animal microbiome

Dietary Shifts May Trigger Dysbiosis and Mucous Stools in Giant Pandas (Ailuropoda melanoleuca) – Candace L. Williams – Frontiers in Microbiology

The transcriptomic response of the coral Acropora digitifera to a competent Symbiodinium strain: the symbiosome as an arrested early phagosome – A. R. Mohamed – Molecular Ecology

The gut microbiota of the pine weevil is similar across Europe and resembles that of other conifer-feeding beetles – Aileen Berasategui – Molecular Ecology

Plant, root, and soil microbiome

Unique microbial phylotypes in Namib Desert dune and gravel plain Fairy Circle soils – Andries J. Van der Walt – Applied and Environmental Microbiology

Effects Due to Rhizospheric Soil Application of an Antagonistic Bacterial Endophyte on Native Bacterial Community and Its Survival in Soil: A Case Study with Pseudomonas aeruginosa from Banana – Pious Thomas – Frontiers in Microbiology

Commentary: Agroforestry leads to shifts within the gammaproteobacterial microbiome of banana plants cultivated in Central America – Anna Maria Pirttilä – Frontiers in Microbiology

Two Poplar-Associated Bacterial Isolates Induce Additive Favorable Responses in a Constructed Plant-Microbiome System – Collin M. Timm – Frontiers in Plant Science

Warming Alters Expressions of Microbial Functional Genes Important to Ecosystem Functioning – Kai Xue – Frontiers in Microbiology

Water microbiome

Seasonal Succession Leads to Habitat-Dependent Differentiation in Ribosomal RNA:DNA Ratios among Freshwater Lake Bacteria – Vincent J. Denef – Frontiers in Microbiology

Waste and pollution microbiology

Community shifts within anaerobic digestion microbiota facing phenol inhibition: Towards early warning microbial indicators? – Simon Poirier – Water Research

Food microbiology

Review: The Microbiota and Health Promoting Characteristics of the Fermented Beverage Kefir – Benjamin C. T. Bourrie – Frontiers in Microbiology

Bioinformatics

RiboDB Database: A Comprehensive Resource for Prokaryotic Systematics – Frédéric Jauffrit – Molecular Biology and Evolution

Microbes in the news

The Microbiomes of Indigenous Peoples Are Different–Does It Matter? – By Kevin Bonham – Scientific American

The laser that can spot dangerous bacteria in food – Scientists in South Korea develop early warning system that could be used in homes, restaurants and grocery shops – Shane Hickey – The Guardian

The viral and bacterial links to the brain’s decline – Ed Cara – Newsweek

Antimicrobial resistance in soil: Potential impact on the food chain: New research at the University of Southampton is to investigate if large amounts of antibiotic resistant bacteria are present in agricultural soil which may spread into the food chain. – Science Daily

New study suggests digging in the dirt could reduce stress, inflammation – Mycobacterium vaccae is a common bacterium present in soil – CBC News Manitoba

The Michigan Microbe Meeting, fungi in asthma exhaled breath, and fungi recovered after the California Rim Fire.

Events

Ongoing now: Michigan Meeting on Microbial Communities,  May 16-18. Follow on Twitter via #MiMicrobe

Functional Metagenomics 2016: 25-28 September 2016, Jægtvolden fjordhotell, Inderøy, Norway

Human respiratory microbiome

Analysis of the fungal microbiome in exhaled breath condensate of patients with asthma – Giovanna E. Carpagnano – Allergy and Asthma Proceedings

Human gut microbiome

Review: Antibiotic-Induced Changes in the Intestinal Microbiota and Disease – Simone Becattini- Trends in Molecular Medicine

Animal experiments

Stable host gene expression in the gut of adult Drosophila melanogaster with different bacterial mono-associations – Carolyn Elya – BioRxiv

Animal microbiome

Comparative analysis of the fecal bacterial community of five harbor seals (Phoca vitulina) – Daniela Numberger – Microbiology Open

Plant, root, and soil microbiome

Ectomycorrhizal fungal spore bank recovery after a severe forest fire: some like it hot – Sydney I Glassman – The ISME Journal

Soil metaproteomics reveals an inter-kingdom stress response to the presence of black truffles – Elisa Zampieri – Scientific Reports

The effect of different land uses on arbuscular mycorrhizal fungi in the northwestern Black Sea Region – Şahin Palta – Environmental Monitoring and Assessment

Plant powder teabags: A novel and practical approach to resolve culturability and diversity of rhizobacteria – Mohamed S. Sarhan – Physiologia Plantarum

Water and extremophile microbiome

Ecophysiological Distinctions of Haloarchaea from a Hypersaline Antarctic Lake as Determined by Metaproteomics – Bernhard Tschitschko – Applied and Environmental Microbiology

Waste and pollution microbiology

Effect of copper on the performance and bacterial communities of activated sludge using Illumina MiSeq platforms – Fu-Lin Sun – Chemospere

Microbes in the news

African scientists make headway in grasping persistent TB bacteria, offer hope for the future – Jomien Mouton – Mail & Guardian Africa

Bacteria are killing rainbow smelt in upper Lake Sakakawea, North Dakota – KFGO

The innovators: Irish lab develops coating to ward off superbug – Shane Hickey – The Guardian

Doctors are fist-bumping one another – here’s why – Richard Hartley-Parkinson – Metro UK
Doctors and nurses encouraged to swap handshakes for fist-bumps to reduce spread of bugs – John Paul Breslin – Sunday Post

Bacterium Blocks Zika’s Spread. Infecting mosquitoes with Wolbachia greatly reduces the insects’ abilities to transmit the virus – Tanya Lewis – The Scientist

Video: A National Poo Museum opened at the Isle of Wight Zoo in the UK

Satire: “Microbiome of Wounds” to be renamed “Infection” – The Allium

Science, publishing, and career

Opinion: Reimagining the Paper. Breaking down lengthy, narrative-driven biomedical articles into brief reports on singular observations or experiments could increase reproducibility and accessibility in the literature – Ahmed Alkhateeb – The Scientist

Reanalysis of plaque microbiome using Minimum Entropy Decomposition, decomposing cow dung, antimicrobial peptides in Drosophila, and distinct microbiomes in US landfills.

Human oral microbiome

Individuality, Stability, and Variability of the Plaque Microbiome – Daniel R. Utter – Frontiers in Microbiology

Human gut microbiome

Long-term changes of bacterial and viral compositions in the intestine of a recovered Clostridium difficile patient after fecal microbiota transplantation – Felix Broecker – Cold Spring Harbor Molecular Case Studies

Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human gut bacterial microbiota – Christophe Audebert – Scientific Reports

Not sure what is novel here: Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics – Juan Jovel – Frontiers in Microbiology

Review: Local and Long-Distance Calling: Conversations between the Gut Microbiota and Intra- and Extra-Gastrointestinal Tract Infections – Joshua E. Denny – Frontiers in Cellular and Infection Microbiology

Animal and in vitro experiments

Selection of Lactobacillus strains as potential probiotics for vaginitis treatment
– Carolina M. A. Santos – Microbiology

Nod2 deficiency leads to a specific and transmissible mucosa-associated microbial dysbiosis which is independent of the mucosal barrier defect – Ziad Al Nabhani – Journal of Crohn’s and Colitis

The bacteriocin bactofencin A subtly modulates gut microbial populations – Caitriona M. Guinane – Anaerobe

Intestinal microecology associated with fluoride resistance capability of the silkworm (Bombyx mori L.) – Guan-Nan Li – Applied Microbiology and Biotechnology

Animal microbiome

Rapid Microbiome Changes in Freshly Deposited Cow Feces under Field Conditions –
Kelvin Wong – Frontiers in Microbiology

Microbial Diversity in the Gut of Cashew Stem Girdler, Analeptes trifasciata Fabricius (Coleoptera: Cerambycidae), in Ibadan, Nigeria – A.V. Oyedokun – International Journal of Insect Science

Includes eukaryotic microbes: Please mind the gap – Visual census and cryptic biodiversity assessment at central Red Sea coral reefs – John K. Pearman – Marine Environmental Research

Review: Friend, foe or food? Recognition and the role of antimicrobial peptides in gut immunity and Drosophila–microbe interactions – Nichole A. Broderick – Philosophical Transactions of the Royal Society B

Plant, root, and soil microbiome

Deciphering the Pathobiome: Intra- and Interkingdom Interactions Involving the Pathogen Erysiphe alphitoides – Boris Jakuschkin – Microbial Ecology

Distribution of bacterial communities across plateau freshwater lake and upslope soils – Yihui Chen – Journal of Environmental Sciences

Water microbiome

What causes the inverse relationship between primary production and export efficiency in the Southern Ocean? – Frédéric A. C. Le Moigne – Geophysical Research Letters

Waste and pollution microbiology

Municipal Solid Waste Landfills Harbor Distinct Microbiomes – Blake W. Stamps – Frontiers in Microbiology

Yeasts and fungi

Review: Invasive candidiasis: from mycobiome to infection, therapy, and prevention – L. Lagunes – European Journal of Clinical Microbiology & Infectious Diseases

Viruses and phages

Pseudo-nitzschia Challenged with Co-occurring Viral Communities Display Diverse Infection Phenotypes – Michael C. G. Carlson – Frontiers in Microbiology

Techniques

Single cell stable isotope probing in microbiology using Raman microspectroscopy – Yun Wang – Current Opinion in Biotechnology

Microbes in the news

Is Obesity Infectious? Study Suggests Our Gut Microbes Can ‘Spread’ To Others – Alyssa Navarro – Tech Times

Bik’s Picks

If Dung Beetles (Scarabaeidae: Scarabaeinae) Arose in Association with Dinosaurs, Did They Also Suffer a Mass Co-Extinction at the K-Pg Boundary? – Nicole L. Gunter – PLOS ONE

A quiet day, this Friday. The main stories of today are about Bacteroides vesicles that interact with certain genes implicated in Crohn’s disease (in a mouse model), and duplications in Pseudomonas genomes associated with novel traits.

Human respiratory microbiome

Evaluation of Malassezia and Common Fungal Pathogens in Subtypes of Chronic Rhinosinusitis – Jonathan T. Gelber – International Forum of Allergy & Rhinology

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

Influenza Virus Affects Intestinal Microbiota and Secondary Salmonella Infection in the Gut through Type I Interferons – Elisa Deriu – PLOS Pathogens

Techniques

A Novel Computerized Cell Count Algorithm for Biofilm Analysis – Mareike Klinger-Strobel – PLOS ONE

Other microbiology

Fungal Genomics Challenges the Dogma of Name-Based Biosecurity – Alistair R. McTaggart – PLOS Pathogens

Duplication drives novelty: The Genomic Basis of Evolutionary Innovation in Pseudomonas aeruginosa – Macarena Toll-Riera – PLOS Genetics

Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe – David M. Aanensen – mBio

Microbes in the news

Get cozy with your skin bacteria — they’re not going anywhere – Rachel Feltman – Washington Post

Breast Milk Primes Gut for Microbes. Maternal antibodies engender a receptive gut environment for beneficial bacteria in newborn mice – Ruth Williams – The Scientist

Genetic variants in patients with Crohn’s disease prevent ‘good’ gut bacteria from working – Science Daily

How did birds get their wings? Bacteria may provide a clue, say scientists – University of Oxford

Leonardo da Vinci’s DNA: Experts unite to shine modern light on a Renaissance genius – Phys.org

Leptin and insulin levels in breast milk influence infant gut microbiome, temporal stability of the human skin microbiome, gut microbiota in children with CF, and the cocobiota (for the chocolate lovers).

Thank you all for your support! It means a lot to me, and I hope that I will be able to continue the work I put into this blog.
Jobs and events

Postdoctoral Fellow – Senior Bioinformatician : Cambridge, United Kingdom – Nature Jobs

General microbiome
Review: Microbiome Therapeutics – Advances and Challenges – Mark Mimee – Advanced Drug Delivery Reviews

Pregnancy and birth

Alterations in human milk leptin and insulin are associated with early changes in the infant intestinal microbiome – Dominick J Lemas – The American Journal of Clinical Nutrition

Human skin microbiome
Weird illustration (worth another blog post?) Editorial: Microbial Skin Inhabitants: Friends Forever – Pieter C. Dorrestein – Cell

Temporal Stability of the Human Skin Microbiome – Julia Oh – Cell

Human respiratory microbiome

Community dynamics and the lower airway microbiota in stable chronic obstructive pulmonary disease, smokers and healthy non-smokers – G G Einarsson – Thorax

Human reproductive tract microbiome

Review: The vaginal microbiota, host defence and reproductive physiology – Steven B Smith, Jacques Ravel

Human gut microbiome
Disrupted progression of the intestinal microbiota with age in children with cystic fibrosis – Shaun Nielsen – Scientific Reports

Molecular characterization and meta-analysis of gut microbial communities illustrate enrichment of Prevotella and Megasphaera in Indian Subjects – Shrikant Bhute – Frontiers in Microbiology

“Actinomyces ihumii”, a new bacterial species isolated from the digestive microbiota of a HIV-infected patient – Sokhna Ndongo – New Microbes and New Infections

Conference abstract that looks promising: Assessing Relationships Between Dietary Intake, Gut Microbiota and Weight Among a Diverse Cohort of College Freshmen – Elizabeth Journey – The FASEB Journal

Editorial: The Mucosal Microbiome and Recurrence After Surgery for Crohn’s Disease – Alastair J.M. Watson – Gastroenterology

Review: Microbiome in Brain Function and Mental Health – Paul J. Kennedy – Trends in Food Science & Technology

Review: Can exercise affect the course of inflammatory bowel disease? Experimental and clinical evidence – Jan Bilski – Pharmacological Reports

Review: Emerging Concepts on the Gut Microbiome and Multiple Sclerosis – Justin D. Glenn – Journal of Interferon & Cytokine Research

Review: The Intestinal Microenvironment and Functional Gastrointestinal Disorders – Giovanni Barbara – Gastroenterology

Editorial: Frozen faecal matter works as well as fresh for transplantation in C difficile patients – Jacqui Wise – The BMJ

Animal experiments

Comparison of microbial communities isolated from feces of asymptomatic Salmonella-shedding and non-Salmonella shedding dairy cows – Bradd J. Haley – Frontiers in Microbiology

Food microbiology

Review about chocolate production: Cocobiota: Implications for Human Health
Ivan M. Petyaev – Journal of Nutrition and Metabolism

Metagenomics and bioinformatics

Bracken: Estimating species abundance in metagenomics data – Jennifer Lu – bioRxiv preprint

Techniques

Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies – Se Jin Song – mSystems

Microbes in the news

Review on Techniques for Protecting Cultural Heritage Materials from Microbes – Alex Alexiev – MicroBEnet

Bacteria Block Mosquitoes from Transmitting Zika, Brazilian Study Says
Wolbachia bacteria have already been used to control dengue – Julie Steenhuysen – Scientific American

Bacteria-Infected Mosquitoes Could Slow Spread of Zika Virus – Carl Zimmer – New York Times

Vancouver students win more awards for discovering bacteria that destroys polluting plastics – Jeff Lee – Vancouver Sun

Our personal skin microbiome is surprisingly stable – EurekAlert

Disparities in Gut Microbiome Could Lead to Biomarkers for Estrogen-driven Breast Cancer – Kathy Boltz – Oncology Nurse Advisor

Breast milk hormones found to impact bacterial development in infants’ guts
Intestinal microbiome of children born to obese mothers significantly different from those born to mothers of healthy weight – Science Daily

Stephen O’Hara, chief executive of OptiBiotix talks to TPL, develops compounds to modulate the human microbiome – The Pharma Letter

Gut check: Study may shed new light on sleep deprivation: team received $7.5 million grant from DoD – University of Colorado Boulder