March 24, 2017

Complex glycan degradation in the gut; role of LPS-binding protein in NAFLD; contribution of environmental factors to arbuscular mycorrhizal fungi community composition and structure; and ResistoMap, a new web-based bioinformatic tool for visualizing the human gut resistome.

 

Events and jobs
Visiting Professor (Part Time) Microbiology – Chamberlain College of Nursing – Arlington, VA

Scientific Officer (Full Time) Microbiology – Australian Clinical Labs – Sydney, AU

Human respiratory microbiome
Understanding the Lung Abscess Microbiome: Outcomes of Percutaneous Lung Parenchymal Abscess Drainage with Microbiologic Correlation – Christopher Duncan – Cardiovascular and Interventional Radiology

Human oral microbiome
Subgingival microbiota dysbiosis in systemic lupus erythematosus: association with periodontal status – Joice Dias Correa – Microbiome

Candida albicans alters the bacterial microbiome of early in vitro oral biofilms – M. M. Janus – Journal of Oral Microbiology

Human skin microbiome
Injections through skin colonized with Staphylococcus aureus biofilm introduce contamination despite standard antimicrobial preparation procedures – Yi Wang – Scientific Reports

Compartmentalized Control of Skin Immunity by Resident Commensals – Shruti Naik – Science

Human gut microbiome
Complex pectin metabolism by gut bacteria reveals novel catalytic functions – Didier Ndeh – Nature

Protective Factors in the Intestinal Microbiome Against Clostridium difficile infection in Recipients of Allogeneic Hematopoietic Stem Cell Transplantation – Yeon Joo Lee – The Journal of Infectious Diseases

Dysbiosis and compositional alterations with aging in the gut microbiota of patients with heart failure – Takehiro Kamo – PLoS One

Alterations in Gastric Microbiota After H. Pylori Eradication and in Different Histological Stages of Gastric Carcinogenesis – Tung Hiu Li – Scientific Reports

Dietary emulsifiers directly alter human microbiota composition and gene expression ex vivo potentiating intestinal inflammation – Benoit Chassaing – Gut

Review: Gut microbiota: Neonatal gut microbiota induces lung immunity against pneumonia – Sabrina Tamburini & Jose C. Clemente – Nature Reviews Gastroenterology & Hepatology

Proteobacteria explain significant functional variability in the human gut microbiome – Patrick S. Bradley & Katherine S. Pollard – Microbiome

Antigen-Presenting Human γδ T Cells Promote Intestinal CD4+ T Cell Expression of IL-22 and Mucosal Release of Calprotectin – Christopher J. Tyler – Journal of Immunology

Odd Chain Fatty Acids; New Insights of the Relationship Between the Gut Microbiota, Dietary Intake, Biosynthesis and Glucose Intolerance – Benjamin J. Jenkins – Scientific Reports

Review: The gut microbiome in human neurological disease: A review – Helen Tremlett – Annals of Neurology

Animal experiments
Loss of lipopolysaccharide-binding protein attenuates the development of diet-induced non-alcoholic fatty liver disease in mice – Cheng Jun Jin – Journal of Gastroenterology and Hepatology

Animal microbiome
Transcriptional characterization of Vibrio fischeri during colonization of juvenile Euprymna scolopes – Luke R. Thompson – Environmental Microbiology

Plant, root, and soil microbiome
The influence of environmental factors on communities of arbuscular mycorrhizal fungi associated with Chenopodium ambrosioides revealed by MiSeq sequencing investigation – Xihui Xu – Scientific Reports

Intercropping maize and common bean enhances microbial carbon and nitrogen availability in low phosphorus soil under Mediterranean conditions – Mourad Latati – European Journal of Soil Biology

The effects of plant nutritional strategy on soil microbial denitrification activity through rhizosphere primary metabolites – Julien P. Guyonnet – FEMS Microbiology Ecology

Water and extremophile microbiome
Geographic distribution of cadmium and its interaction with the microbial community in the Longjiang River: risk evaluation after a shocking pollution accident – Ming Jiang Zhang – Scientific Reports

Beneficial Microorganisms for Corals (BMC): Proposed Mechanisms for Coral Health and Resilience – Raquel S. Peixoto – Frontiers in Microbiology

Small Molecules Belowground: The Role of Specialized Metabolites in the Rhizosphere – Massalha H – The Plant Journal

Food microbiology
Rice- or pork-based diets with similar calorie and content result in different rat gut microbiota – Xiaozhe Qi – International Journal of Food Sciences and Nutrition

Bioinformatics
ResistoMap – online visualization of human gut microbiota antibiotic resistome – Konstantin Yarygin – bioRxiv

March 10, 2017

Ancient microbial DNA in Neanderthal dental calculus; the role of fungus in inflammatory bowel disease; symbiotic bacteria in the Hawaiian bobtail squid reproductive system; and a colorimetric/electrochemical device for detection of food and waterborne bacteria.

Events and jobs
Microbiology/Immunology Faculty – West Virginia School of Osteopathic Medicine – Lewisburg, West Virginia

Pregnancy and early life
Association of Maternal Gestational Weight Gain With the Infant Fecal Microbiota – Alyssa Robinson – Journal of Pediatric Gastroenterology and Nutrition

Review: Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis – Mohan Pammi – Microbiome

Human oral microbiome
New approach for studying mobile genes using metagenomic analysis – K. Ishihara – Oral Diseases

Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus – Laura S. Weyrich – Nature

In the News: Prehistoric ‘Aspirin’ Found in Sick Neanderthal’s Teeth – National Geographic

Human skin microbiome
Using Shotgun Metagenomics to Examine the Use of Hand Microbiome as a Forensic Tool – Ning Chin – ProQuest Dissertations Publishing

Human vaginal microbiome
Review: The role of the vaginal microbiome in gynecological cancer: a review – Champer M. – BJOG

Human gut microbiome
A translational investigation into the role of dietary fatty acids in modulating endotoxemia and associated inflammation – Joshua Mark Lyte – ProQuest Dissertations Publishing

Orai1-Mediated Antimicrobial Secretion from Pancreatic Acini Shapes the Gut Microbiome and Regulates Gut Innate Immunity – Malini Ahuja – Cell Metabolism

Beyond Digestion: The Pancreas Shapes Intestinal Microbiota and Immunity – Herbert Tilg – Cell Metabolism

Low-dose penicillin exposure in early life decreases Th17 and the susceptibility to DSS colitis in mice through gut microbiota modification – Shuang Jin – Scientific Reports

Gut microbiota modulation of chemotherapy efficacy and toxicity – James. L. Alexander – Nature Reviews Gastroenterology & Hepatology

CD40-signalling abrogates induction of RORγt+ Treg cells by intestinal CD103+ DCs and causes fatal colitis – Christian Barthels – Nature Communications

Faecal microbiota transplantation in clinical practice – E M Terveer – Gut

Distinct Microbiome-Neuroimmune Signatures Correlate With Functional Abdominal Pain in Children With Autism Spectrum Disorder – Ruth Ann Luna – Cellular and Molecular Gastroenterology and Hepatology
Animal experiments
A gut reaction: The combined influence of exercise and diet on gastrointestinal microbiota in rats – Romeo Batacan – Journal of Applied Microbiology

A member of the gut mycobiota modulates host purine metabolism exacerbating colitis in mice – Chiaro TR – Science Translational Medicine

Animal microbiome
Diurnal dynamics of gaseous and dissolved metabolites and microbiota composition in the bovine rumen – Henk J. Van Lingen – Frontiers in Microbiology

Symbiotic bacteria associated with a bobtail squid reproductive system are detectable in the environment, and stable in the host and developing eggs – Allison H. Kerwin – Environmental Microbiology

Plant, root, and soil microbiome
Arsenic Transport in Rice and Biological Solutions to Reduce Arsenic Risk from Rice – Yanshan Chen – Frontiers in Plant Science

Pseudomonas fluorescens Transportome is Linked to Strain-Specific Plant Growth Promotion in Aspen Seedlings Under Nutrient Stress – Shalaka Shinde – Frontiers in Plant Science

Short-term exposure of paddy soil microbial communities to salt stress triggers different transcriptional responses of key taxonomic groups – Jingjing Peng – Frontiers in Microbiology

Fertilization of Phaseolus vulgaris with the Tunisian rock phosphate affects richness and structure of rhizosphere bacterial communities – Darin Trabelsi – Applied Soil Ecology

Bioprospecting plant-associated microbiomes – Christina A. Muller – Journal of Biotechnology

Water and extremophile microbiome
Isolation and identification of indigenous prokaryotic bacteria from arsenic-contaminated water resources and their impact on arsenic transformation – MA Jebelli – Ecotoxicology and Environmental Safety

Performance and kinetics of membrane and hybrid moving bed biofilm-membrane bioreactors treating salinity wastewater – Alejandro Rodriguez-Sanchez – AlChE Journal

Metabolomics
Technological development of high-performance MALDI mass spectrometry imaging for the study of metabolic biology – Adam D. Feenstra – ProQuest Dissertations Publishing

Food microbiology
The Biodiversity of the Microbiota Producing Heat-Resistant Enzymes Responsible for Spoilage in Processed Bovine Milk and Dairy Products – Solimar G. Machado – Frontiers in Microbiology

Culturable microorganisms during fermentation of Veltlínske zelené (Grüner Veltliner) ice wine – K. Ženišová – Journal of Food and Nutrition Research

Metabolomics for empirical delineation of the traditional Korean fermented foods and beverages – Digar Singh – Trends in Food Science & Technology

Probiotics/prebiotics
Case Study: Integrate genome-based assessment of safety for probiotic strains: Bacillus coagulans GBI-30, 6086 as a case study – Elisa Salvetti – Applied Microbiology and Biotechnology

Techniques
Colorimetric and Electrochemical Bacteria Detection Using Printed Paper- and Transparency-Based Analytic Devices – Jaclyn A. Adkins – Analytical Chemistry

Microbes in the news
Exciting Microbe Research? Temper That Giddy Feeling in Your Gut – The New York Times

Garrett’s non-microbiology picks
‘Plan bee’ drone artificially pollinates flowers on behalf of bees – Design Boom

March 8th, 2017

Today is the International Women’s Day! This is a day for awareness about the importance of support equality in rights and opportunities for women.

About International Women’s Day

Gender at Nature Ecology & Evolution

Helping women progress in traditionally male dominated fields

Rosalind Franklin: Navigating workplace politics to gain recognition in science

International Women’s Day 2017: pursuing a career in science

BMC Series Blog: International Women’s Day

Events and Webinars

3rd Annual Translational Microbiome Conference, April 12-13, 2017 in Boston, MA

Webinar: Nomadic nanopore sequencing of metagenomes with the MinION

Microbiome research

Salivary Gluten Degradation and Oral Microbial Profiles in Healthy Individuals and Celiac Disease Patients – Na Tian – Applied and Environmental Microbiology

Impact of Westernized Diet on Gut Microbiota in Children on Leyte Island – Jiro Nakayama – Frontiers in Microbiology

Comparison of culture-dependent and culture-independent molecular methods for characterization of vaginal microflora – Shirali Pandya – Journal of Medical Microbiology

Effect of predatory bacteria on the gut bacterial microbiota in rats – Kenneth Shatzkes – Scientific Reports

Methods article: Critical Issues in Mycobiota Analysis – Bettina Halwachs – Frontiers in Microbiology

Microbiota alteration is associated with the development of stress-induced despair behavior – Ioana A. Marin – Scientific Reports

Review: Beyond Hygiene: Commensal Microbiota and Allergic Diseases – Sung-Wook Hong – Immune Network

Fecal Bacterial Communities in treated HIV infected individuals on two antiretroviral regimens – Sandra Pinto-Cardoso – Scientific Reports

Editorial: How can the gut microbiota affect immune recovery in HIV-infected individuals? – Sergio Serrano-Villar – Future Microbiology

Unexplored Archaeal Diversity in the Great Ape Gut Microbiome – Kasie Raymann – mSphere

Probiotics

Lactobacillus rhamnosus GG supernatant enhance neonatal resistance to systemic Escherichia coli K1 infection by accelerating development of intestinal defense – Xiaolong He – Scientific Reports

Bifidobacterium breve with α-linolenic acid alters the composition, distribution and transcription factor activity associated with metabolism and absorption of fat  – Elaine Patterson – Scientific Reports

Timely use of Probiotics in Hospitalized Adults Prevents Clostridium difficile Infection: a Systematic Review with Meta-Regression Analysis – Nicole T. Shen – Gastroenterology

Metagenomics

Review: Beneficial Microorganisms for Corals (BMC): Proposed Mechanisms for Coral Health and Resilience – Raquel S. Peixoto – Frontiers in Microbiology

Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples – Feiqiao Yu – bioRxiv

Untangling Genomes of Novel Planctomycetal and Verrucomicrobial Species from Monterey Bay Kelp Forest Metagenomes by Refined Binning – John Vollmers – Frontiers in Microbiology

Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean – Yosuke Nishimura – mSphere

Pathogens

Metabolic activity, urease production, antibiotic resistance and virulence in dual species biofilms of Staphylococcus epidermidis and Staphylococcus aureus – Ilse Vandecandelaere – PLoS ONE

Review: Mollicutes in vaginal microbiology: Mycoplasma hominis, Ureaplasma urealyticum, Ureaplasma parvum and Mycoplasma genitalium – David Taylor-Robinson – Research in Microbiology

Case report: Contribution of Ultra Deep Sequencing in the Clinical Diagnosis of a New Fungal Pathogen Species: Basidiobolus meristosporus – Emilie Sitterlé – Frontiers in Microbiology

The Chlamydia suis genome exhibits high levels of diversity, plasticity and mobile antibiotic resistance: comparative genomics of a recent livestock cohort shows influence of treatment regimes – Helena M.B. Seth-Smith – Genome Biology and Evolution

Extremophiles

Reducing salinity by flooding an extremely alkaline and saline soil changes the bacterial community but its effect on the archaeal community is limited – Arit S de León-Lorenzana – Frontiers in Microbiology

Early life

Paleoproterozoic sterol biosynthesis and the rise of oxygen – David A. Gold – Nature

March 6, 2017

Interesting articles on the how the interactions between bacteria and fungi influence N cycling in soils. Also, fecal sample collection methods influence microbial community structure.

General microbiome

The National Biome Initiative: An Allergy Perspective. Furuta GT. Journal of Allergy and Clinical Immunology

The Microbiome in Allergic Disease: Current Understanding and Future Opportunities – 2017 PRACTALL Document of the American Academy of Allergy, Asthma & Immunology and the European Academy of Allergy and Clinical Immunology. Huang YJ. Journal of Allergy and Clinical Immunology

Oral and nasal microbiome

Community analysis of dental plaque and endotracheal tube biofilms from mechanically ventilated patients.      Marino PJ. Journal of Critical Care

Oral and nasal microbiota in Parkinson’s disease. Pereira PA. Parkinsonism and Related Disorders

Gut microbiome

The effect of omeprazole treatment on the gut microflora and neutrophil function. Kostrzewska M. Clinics and Research in Hepatology and Gastroenterology

Water and extremophile microbiome

Bacterial interactions and implications for oil biodegradation process in mangrove sediments. Grativol AD. Marine Pollution Bulletin

Quantifying the importance of the rare biosphere for microbial community response to organic pollutants in a freshwater ecosystem. Wang Y. Applied and Environmental Microbiology

Probiotics

Probiotic treatment reduces depressive-like behaviour in rats independently of diet. Abildgaard A. Psychoneuroendocrinology

Techniques

Comparison of fecal collection methods for microbiota studies in Bangladesh. Vogtmann E. Applied and Environmental Microbiology

Plant, root, and soil microbiome

How interacting fungal species and mineral nitrogen inputs affect transfer of nitrogen from litter via arbuscular mycorrhizal mycelium. He Y. Environmental Science and Pollution Research

Salmonella Senftenberg adaptation to linalool and its association with antibiotic resistance and environmental persistence. Hollander K. Applied and Environmental Microbiology

Fungal and bacterial contributions to nitrogen cycling in cheatgrass-invaded and uninvaded native sagebrush soils of the western USA.  DeCrappeo NM. Plant and Soil

Native soil organic matter as a decisive factor to determine the arbuscular mycorrhizal fungal community structure in contaminated soils. Montiel-Rozas. Biology and Fertility of Soils

January 29, 2017

A post on fecal transplats, the gut microbiome of cranes, fungal diversity of soils, and much more.

Events and Jobs

Assistant Professor of Microbiology, Immunology & Tropical Medicine at George Washington University

General microbiome

The Stromal Intervention: Regulation of Immunity and Inflammation at the Epithelial-Mesenchymal Barrier – Roni Nowarski – Cell

Effect of adsorbants on in vitro biohydrogenation of 22:6n-3 by mixed cultures of rumen microorganisms – Marlene Escobar – Animal

Pregnancy and early life

Airway Microbial Community Turnover Differs by BPD Severity in Ventilated Preterm Infants – Brandie D. Wagner – PLoS One

Mode of Delivery and Its Influence on the Acquisition of Streptococcus mutans in Infants – Ritu G. Ubeja – International Journal of Clinical Pediatric Dentistry

Human gut microbiome

Blood Trimethylamine-N-Oxide Originates from Microbiota Mediated Breakdown of Phosphatidylcholine and Absorption from Small Intestine – Wolfgang Stremmel – PLoS One

Challenges in Fecal Donor Selection and Screening for Fecal Microbiota Transplantation: A Review – Michael H. Woodworth – Gut Microbes

Animal experiments

Peptostreptococcus anaerobius Induces Intracellular Cholesterol Biosynthesis in Colon Cells to Induce Proliferation and Causes Dysplasia in Mice – Ho Tsoi – Journal of AGA Institute: Gastroenterology Special Issure

Animal microbiome

The gut microbiome of hooded cranes (Grus monacha) wintering at Shengjin Lake, China – Guanghong Zhao – Wiley

Linking Peripartal Dynamics of Ruminal Microbiota to Dietary Changes and Production Parameters – Hooman Derakhashani – Frontiers in Microbiology

Effect of antibiotic on survival and development of Spodoptera litura (Lepidoptera: Noctuidae) and its gut microbial diversity – Abhinay Thakur – Bullitin of Entomological Research

Plant, root, and soil microbiome

Fungal diversity in soils across a gradient of preserved Brazilian Cerrado – Ademir Sergio Ferreira de Araujo – Journal of Microbiology

Synthetic photosynthetic consortia define interactions leading to robustness and photoproduction – Stephanie G. Hays – Journal of Biomedical Engineering

Translocation of Bacillus thuringiensis in Phaseolus vulgaris tissues and vertical transmission in Arabidopsis thaliana – Rosalina García-Suárez – Journal of Applied Microbiology

Transport Capabilities of Environmental Pseudomonads for Sulfur Compounds – Sarah Zerbs – Protein Science

Water and extremophile microbiome

Molecular-biological sensing in aquatic environments: recent developments and emerging capabilities – Jonathan S McQuillan – Current Opinion in Biotechnology

Probiotics / prebiotics

Nutritional stimulation of commensal oral bacteria suppresses pathogens: the prebiotic concept – Vera Slomka – Wiley

Microbes in the news

Rebalancing gut microbiome lengthens survival in mouse model of ALS

What We’ve Learned From Studying Microbiomes

Microbiota Transfer Therapy Could Help Children With Autism

Bacteria’s sneaky way to spread by getting you to eat more

Studies show prevalence of multi-drug resistant bacteria in China

Researchers discover molecule that could fight ‘superbug’ bacteria

Microbes on the market

New Market Analysis: The global clinical microbiology market is projected to reach USD 5.77 Billion by 2021

Bacteria Hysteria

SHOCKING: You won’t BELIEVE how many GERMS are on your hands

January 20, 2017

Infant formula with prebiotics and probiotics, acne vulgaris and staphylococcus, IBD and anti-CTLA-4 connected to the flora, protein kinase C δ and prebiotic required to strengthen intestinal epithelial barrier function. 

Events and jobs

Postdoctoral position in immunology to study host-gut microbiota interactions– University of Arizona

Research Engineer in Microbiology– l’Oréal

MICROBIOLOGY SUPERVISOR– via a Large US Medical Device company in Limerick

General microbiome

*A Review: The human microbiome and cancer-Seesandra V Rajagopala-AARC Publications

Pregnancy and early life

Oral Microbiota in Infants Fed a Formula Supplemented with Bovine Milk Fat Globule Membranes – A Randomized Controlled Trial– Niklas Timby- PLoS One

Acquisition and adaptation of the airway microbiota in the early life of cystic fibrosis patients– Sebastien Boutin- Molecular and Cellular Pediatrics

Early Benefits of a Starter Formula Enriched in Prebiotics and Probiotics on the Gut Microbiota of Healthy Infants Born to HIV+ Mothers: A Randomized Double-Blind Controlled Trial-Peter Cooper- Clinical Medicine Insights: Pediatrics

Growth and Morbidity of Gambian Infants are Influenced by Maternal Milk Oligosaccharides and Infant Gut Microbiota– Jasmine C. Davis- Scientific Reports

Oral Microbiota

Evaluating the Impact of DNA Extraction Method on the Representation of Human Oral Bacterial and Fungal Communities-Anna Vesty- PLuS One

Salivary Gluten Degradation and Oral Microbial Profiles in Health and Celiac Disease– Na Tian- Applied Environmental Microbiology

Human respiratory microbiome

*Review: Microbiomes in respiratory health and disease: An Asia-Pacific perspective– Sanjay H. Chotirmall- Official Journal of the Asian Pacific Society of Respirology

Human skin microbiome

The Role of Cutaneous Microbiota Harmony in Maintaining a Functional Skin Barrier-Hilary Baldwin- Journal of Drugs in Dermatology

Skin microbiome and acne vulgaris: staphylococcus, a new actor in acne– Brigitte Dreno- Experimental Dermatology

Human vaginal microbiome

Subclinical Alteration of the Cervical-Vaginal Microbiome in Women with Idiopathic Infertility– Giuseppina Campisciano- Journal of Cellular Physiology

Human gut microbiome

Intestinal Bacteria Composition and Translocation of Bacteria in Inflammatory Bowel Disease– Spyros Vrakas- PLoS One

*Review- The Gastrointestinal Tract as a Key Target Organ for the Health-Promoting Effects of Dietary Proanthocyanidins– Maria Jose Cires- frontiers in Nutrition

Association of the Intestinal Microbiome with the Development of Neovascular Age-Related Macular Degeneration– Martin S. Zinkernagel- Scientific Reports

*Review: Inflammatory bowel disease and cancer response due to anti-CTLA-4: is it in the flora?-Franck Carbonnel- Seminars in immunopathology

Animal experiments

ZiBuPiYin recipe improves cognitive decline by regulating gut microbiota in Zucker diabetic fatty rats– Gu Chunyan – Oncotarget

Animal microbiome

Unique Bacteria Community Composition and Co-occurrence in the Milk of Different Ruminants– Li Zhipeng- Scientific Reports

Plant, root, and soil microbiome

Mycorrhizal specificity does not limit the distribution of an endangered orchid species- Michael Waud – Molecular Ecology

Exploring the symbiont diversity of ancient western redcedars: arbuscular mycorrhizal fungi of long-lived hosts– Monika A. Gorzelak- Molecular Ecology

Probiotics / prebiotics

Protein kinase C δ signaling is required for dietary prebiotic-induced strengthening of intestinal epithelial barrier function– Richard Y. Wu- Scientific Reports

Antioxidant properties and global metabolite screening of the probiotic yeast Saccharomyces cerevisiae var. boulardii– Suprama Datta- Journal of the Science of Food and Agriculture

Bioinformatics

Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons– Illias Lagkouvardos- PeerJ

Microbes on the market

FishTaco: Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome– Ohad Manor

January 18, 2017

Biogeographical patterns and assembly processes of bacterial on glaciers. And, a critical review of interactions between central nervous system and microbiota during health and neurological disease.

● Hospital microbiome

Microbiota-targeted therapies on the intensive care unit. Haak, BW . Current opinions in Critical Care

● Human microbiome and nervous system

Review: Interactions between the microbiota, immune and nervous systems in health and disease. Thomas C Fung.Nature Neuroscience

● Human gut microbiome

A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic. Patrascu O. Scientific Report

Fecal microbiota transplantation to fight Clostridium difficile infections and other intestinal diseases. Moelling, K. Bacteriophage

● Animal experiments 

Pepsin egg white hydrolysate modulates gut microbiota in Zucker obese rats. Requena T. Food & Function

Effect of early antibiotic administration on cecal bacterial communities and their metabolic profiles in pigs fed diets with different protein levels. Zhang C. Anaerobe

● Animal microbiome 

Fiber degradation potential of natural co-cultures of Neocallimastix frontalis and Methanobrevibacter ruminantium isolated from yaks (Bos grunniens) grazing on the Qinghai Tibetan Plateau. Wei YQ. Anaerobe

Gut microbiota isolated from the European pond turtle (Emys orbicularis) and its antimicrobial resistance. Ruzauskas M. Polish Journal of Veterinary Sciences

● Plant, root, and soil microbiome

Restoration using Azolla imbricata increases nitrogen functional bacterial groups and genes in soil. Xiao-Ming Lu. Applied Microbiology and Biotechnology

Ectomycorrhizal fungal diversity associated with endemic Tristaniopsis spp. (Myrtaceae) in ultramafic and volcano-sedimentary soils in New Caledonia. Waseem M. Mycorrhiza

Diversity and Assembling Processes of Bacterial Communities in Cryoconite Holes of a Karakoram Glacier.Ambrosini, R.Microbial Ecology

● Water and extremophile microbiome 

Bacterial community structure and prevalence of Pusillimonas-like bacteria in aged landfill leachate. Remmas, N. Environmental Science and Pollution Research

January 14, 2017

So it is technically already January 15 most countries, but I have been busy today preparing to transfer Microbiome Digest to an eager group of 20 new contributors. It takes a lot of time to hopefully be able to safe some time – if that makes sense.

My inbox is still full of new alerts, but here is what I have been able to “digest” so far. It’s already a lot!

General human microbiome

Navigating social and ethical challenges of biobanking for human microbiome research –
Kim H. Chuong – BMC Medical Ethics

Editorial: Influence of the microbiota on host physiology – moving beyond the gut
– Kim E. Barrett – The Journal of Physiology

Pregnancy and early life

* Pregnant women carrying microcephaly foetuses and Zika virus contain potentially pathogenic microbes and parasites in their amniotic fluid – Diogo Antonio Tschoeke – BMC Medical Genomics

Growth and Morbidity of Gambian Infants are Influenced by Maternal Milk Oligosaccharides and Infant Gut Microbiota – Jasmine C. C. Davis – Scientific Reports

Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates – Matthew R Olm – Genome Research

The Microbiome and Complement Activation A Mechanistic Model for Preterm Birth – Alexis B. Dunn – Biological Research for Nursing

Review: Asthma and the microbiome: defining the critical window in early life – Leah T. Stiemsma – Allergy, Asthma & Clinical Immunology

Human gut microbiome

Alcohol, microbiome, life style influence alcohol and non-alcoholic organ damage – Manuela G. Neuman – Experimental and Molecular Pathology

Serum Trimethylamine N-oxide, Carnitine, Choline and Betaine in Relation to Colorectal Cancer Risk in the Alpha Tocopherol and Beta Carotene Study – Kristin A. Guertin – Cancer Epidemiology, Biomarkers & Prevention

Laboratory Testing of Donors and Stool for Fecal Microbiota Transplantation for Recurrent C. difficile Infection – Michael H. Woodwort – Journal of Clinical Microbiology

Editorial: Gut microbiota: implications for sports and exercise medicine – Owen Cronin – British Journal of Sports Medicine

Review/Addendum: Pathogen control at the intestinal mucosa – H2O2 to the rescue
Ulla G. Knaus – Gut Microbes

Editorial: Tune into the rhythm of your bugs – Purna Kashyap – Science Translational Medicine

Preview: Are Gut Microbes Responsible for Post-dieting Weight Rebound? – Julien Chilloux – Cell Metabolism

Review: Involvement of Reduced Microbial Diversity in Inflammatory Bowel Disease – Dawei Gong – Gastroenterology Research and Practice

Year in Review: Gut microbiota in 2016: A banner year for gut microbiota research – Wendy S. Garrett – Nature Reviews Gastroenterology & Hepatology

Review: Gut microbiota disturbance during helminth infection: can it affect cognition and behaviour of children? – Vanina Guernier – BMC Infectious Diseases

Review: An expanding stage for commensal microbes in host immune regulation – Yan Shi – Cellular & Molecular Immunology

Perspective: Decoding host–microbiota communication in the gut – now we’re flying!
– Stephen J. Keely – The Journal of Physiology

Just based on the abstract, this appears a wild hypothesis potentially ignoring economic status, fiber consumption etc:  Latitude as a co-driver of human gut microbial diversity? – Emma Dikongué – Ideas that Push the Boundaries

Book: Gut Microbiome and Behavior, Volume 131 – John F. Cryan, Gerard Clarke – Elsevier

Animal experiments

Intestinal microbiota as a tetrahydrobiopterin exogenous source in hph-1 mice – Jaques Belik – Scientific Reports

Oral treatment with Lactobacillus rhamnosus attenuates behavioural deficits and immune changes in chronic social stress – Aadil Bharwani – BMC Medicine

Year in review: Microbiome in 2016: T follicular helper cells and the gut microbiome in arthritis – Veena Taneja – Nature Reviews Rheumatology

Animal microbiome

Bacterial Communities Associated with Houseflies (Musca domestica L.) Sampled within and between Farms – Simon Bahrndorff – PLOS ONE

Microbiome variation in corals with distinct depth distribution ranges across a shallow–mesophotic gradient (15–85 m) – Bettina Glasl – Coral Reefs

Symbiont-induced odorant binding proteins mediate insect host hematopoiesis – Joshua B Benoit – eLIFE

Drivers of variation in species impacts for a multi-host fungal disease of bats  –
Kate E. Langwig – Philosophical Transactions of the Royal Society B

Sponges: Evaluating the core microbiota in complex communities: A systematic investigation – Carmen Astudillo-Garcia – Environmental Microbiology

Plant, root, and soil microbiome

Bacterial community composition in costal dunes of the Mediterranean along a gradient from the sea shore to the inland – Haggai Wasserstrom – Scientific Reports

Phylogenetic relatedness, phenotypic similarity and plant–soil feedbacks – Connor R. Fitzpatrick

Review: Microbiome and the future for food and nutrient security – Brajesh K. Singh – Microbial Biotechnology

Water microbiome

Similar community assembly mechanisms underlie similar biogeography of rare and abundant bacteria in lakes on Yungui Plateau, China – Jingqiu Liao – Limnology and Oceanography

Built environment microbiome

Microbial diversity in different compartments of an aquaponics system – Zala Schmautz – Archives of Microbiology

Food microbiology

The influence of thiamine and riboflavin on various spoilage microorganisms commonly found in beer – Barry Hucker – The Journal of The Institue of Brewing

Waste and pollution microbiology

Microbial flora analysis for the degradation of beta-cypermethrin – Zhang Qi – Environmental Science and Pollution Research

Fungi (also see Animal Microbiome)

Medical mycology and fungal immunology: new research perspectives addressing a major world health challenge – Neil A. R. Gow – Philosophical Transactions of the Royal Society B

Proteomics and metabolomics

MAHMI database: a comprehensive MetaHit-based resource for the study of the mechanism of action of the human microbiota – Aitor Blanco-Míguez – Database

PerspectiveProgress in the biology and analysis of short chain fatty acids – Roel J. Vonk – The Journal of Physiology

Bioinformatics and biostatistics

Using Machine Learning to Identify Major Shifts in Human Gut Microbiome Protein Family Abundance in Disease – Mehrdad Yazdani – IEEE

Microscale Insight into Microbial Seed Banks – Kenneth J. Locey – Frontiers in Microbiology

* EMPeror: Bringing the Dynamic Microbiome to Life with Animations – Yoshiki Vázquez-Baeza – Cell Host & Microbe

Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities – Gongchao Jing – Scientific Reports

Identifying Host Genetic Variants Associated with Microbiome Composition by Testing Multiple Beta Diversity Matrices – Hua X. – Human Heredity

MetaDP: a comprehensive web server for disease prediction of 16S rRNA metagenomic datasets – Xilin Xu – Biophysics Reports

Techniques

Methodological flaws introduce strong bias into molecular analysis of microbial populations – N. Krakat – Journal of Applied Microbiology

Editorial: Microbial Nanoscopy: Breakthroughs, Challenges, and Opportunities – Yves F. Dufrêne – ACS Nano

More microbes

Asgard archaea illuminate the origin of eukaryotic cellular complexity – Katarzyna Zaremba-Niedzwiedzka – Nature

* Species-Independent Attraction to Biofilms through Electrical Signaling – Jacqueline Humphries – Cell

A bacterial global regulator forms a prion – Andy H. Yuan – Science

A periplasmic polymer curves Vibrio cholerae and promotes pathogenesis – Thomas M. Bartlett – Cell

Assembly of a nucleus-like structure during viral replication in bacteria – Vorrapon Chaikeeratisak – Science

Microbes in the news

Man’s best friend, bacteria’s worst enemy: dog sniffs out superbug in Canadian hospital – Ashifa Kassam – The Guardian

This article is not as bad as the title suggests but with photoshopped images:
Revealed: The millions of stomach-churning bacteria lurking in YOUR hair, skin, lungs, gut and mouth – and why – Mary Kekatos – Daily Mail

Video: Career profiles: Program Director at National Science Foundation Matthew Kane – American Society for Microbiology

A clear picture of bacteria: A new study has frozen bacteria extremely fast to gain a true-to-nature image of the internal and external structure – Science Daily

January 10, 2017

A culture-based study of 2000 nasal microbiomes, eye metabolites, cardiorespiratory fitness in breast cancer survivors, Akkermansia from a python, chickpea rhizosphere, tobacco wilt suppression, plant rhizosphere mass spectrometry, phyloSkeleton.

Human nasal microbiome

Epidemiological and ecological modelling reveal diversity in microbial population structures from a cross-sectional community swabbing study – Abigail L Coughtrie – bioRxiv

Human eye microbiome

LC-MS-Based Metabolic Fingerprinting of Aqueous Humor – Karolina Pietrowska – Journal of Analytical Methods in Chemistry

Human vaginal microbiome

MS thesis: Metagenomic characterization of the vaginal microbiome – Keshini Devakandan – University of British Columbia

Human gut microbiome

Gut microbiota composition associated with alterations in cardiorespiratory fitness and psychosocial outcomes among breast cancer survivors – Jesseca A. Paulsen – Supportive Care in Cancer

SYN-004 (ribaxamase), an oral β-lactamase designed to protect the gut microbiome from the deleterious effects of certain intravenously administered β-lactam antibiotics, degrades ceftriaxone excreted into the intestine in Phase 2a clinical studies – John F. Kokai-Kun – Antimicrobial Agents Chemotherapy

Animal experiments

Respiration of Microbiota-Derived 1,2-propanediol Drives Salmonella Expansion during Colitis – Franziska Faber – PLOS Pathogens

Animal microbiome

Complete Genome Sequence of Akkermansia glycaniphila Strain PytT, a Mucin-Degrading Specialist of the Reticulated Python Gut – Janneke P. Ouwerkerk – Genome Announcements

Symbiotic bacteria associated with a bobtail squid reproductive system are detectable in the environment, and stable in the host and in eggs throughout development – Allison H. Kerwin – Environmental Microbiology

Plant, root, and soil microbiome

Competition between rhizobia under different environmental conditions affects the nodulation of a legume – Zhao Jun Ji – Systematic and Applied Microbiology

Combined pre-seed treatment with microbial inoculants and Mo nanoparticles changes composition of root exudates and rhizosphere microbiome structure of chickpea (Cicer arietinum L.) plants – E. N. Shcherbakova – Symbiosis

Interactions of soil particulate organic matter chemistry and microbial community composition mediating carbon mineralization in karst soils – Wei Xiao – Soil Biology and Biochemistry

Metabolic profiling of root exudates from two ecotypes of Sedum alfredii treated with Pb based on GC-MS – Qing Luo – Scientific Reports

Effects of Wetland Vegetation on Soil Microbial Composition: A Case Study in Tumen River Basin, Northeast China– Qin Lei – Chin. Geogra. Sci

Microbial communities in pyrene amended soil–compost mixture and fertilized soil – Iris K. U. Adam – AMB Express

Competition assays and physiological experiments of soil and phyllosphere yeasts identify Candida subhashii as a novel antagonist of filamentous fungi – Maja Hilber-Bodmer – BMC Microbiology

Tobacco bacterial wilt suppression with biochar soil addition associates to improved soil physiochemical properties and increased rhizosphere bacteria abundance – Chengsheng Zhang – Applied Soil Ecology

Editorial: Microbial community ecology: Function over phylogeny – Sean M. Gibbons – Nature Ecology & Evolution

Review: Elucidating rhizosphere processes by mass spectrometry – A review – Ariana Rugova – Analytica Chimica Acta

Water and extremophile microbiome

Genomic repertoire of the Woeseiaceae/JTB255, cosmopolitan and abundant core members of microbial communities in marine sediments – Marc Mußmann – The ISME Journal

Food microbiology

ReviewAn Integrated View of the Effects of Wine Polyphenols and Their Relevant Metabolites on Gut and Host Health – Carolina Cueva – Molecules

Microbiological quality of Brazilian UHT milk: Identification and spoilage potential of spore-forming bacteria – Claudia L O Pinto – International Journal of Dairy Technology

Metabolomics for empirical delineation of the traditional Korean fermented foods and beverages – Digar Singh – Trends in Food Science & Technology

Source tracking of prokaryotic communities in fermented grain of Chinese strong-flavor liquor – Xueshan Wang – International Journal of Food Microbiology

Bioinformatics

phyloSkeleton: taxon selection, data retrieval and marker identification for phylogenomics – Lionel Guy – Bioinformatics

Microbes in the news

Hyperthermophiles and Cryophiles: The World’s Most Extreme Organisms – Priya Amin – Harvard Science Review

Bik’s non-microbiology picks

Responses of Human Neonates to Highly Diluted Odorants from Sweat – Helene M. Loos – Journal of Chemical Ecology

January 3, 2017

Denture microbiome, insulin resistance and appendix microbiome in obesity, raw milk microbiome, subtropical forest soils, biofilms in drinking water systems, metabolomics of a Mediterranean diet, cell shape and biofilms.

Human oral microbiome

The Denture-Associated Oral Microbiome in Health and Stomatitis – Baochen Shi – mSphere

Commentary: A novel strategy for diagnosing viral versus bacterial infection: implications for oral diseases – Nataly Kravchenko-Balasha – Oral Diseases

Human gut microbiome

*  Insulin resistance is associated with specific gut microbiota in appendix samples from
morbidly obese patients – Isabel Moreno-Indias – American Journal of Translational Research

Microbiology of nearly sterile sites

Improving molecular diagnosis of neonatal septicaemia: Comparative evaluation of different protocols for extraction of bacterial and fungal DNA from blood samples – Gargi Dangre-Mudey – International Journal of Current Research in Medical Sciences

Animal microbiome

Impacts of Seasonal Housing and Teat Preparation on Raw Milk Microbiota: a High-Throughput Sequencing Study – Conor J. Doyle – Applied and Environmental Microbiology

Biogeography and molecular diversity of coral symbionts in the genus Symbiodinium around the Arabian Peninsula – Maren Ziegler – Journal of Biogeography

Plant, root, and soil microbiome

Colonization and community structure of arbuscular mycorrhizal fungi in maize roots at different depths in the soil profile respond differently to phosphorus inputs on a long-term experimental site – Chao Wang – Mycorrhiza

Arbuscular mycorrhizal fungal community composition is altered by long-term litter removal but not litter addition in a lowland tropical forest – Merlin Sheldrake – New Phytologist

Modeling of mineral nutrient uptake of spruce tree roots as affected by the ion dynamics in the rhizosphere: Upscaling of model results to field plot scale – H. Nietfeld – Ecological Modelling

Competition between rhizobia under different environmental conditions affects the nodulation of a legume – Zhao Jun Ji – Systematic and Applied Microbiology

 

Altered precipitation seasonality impacts the dominant fungal but rare bacterial taxa in subtropical forest soils – Qian Zhao – Biology and Fertility of Soils

Cultivable bacterial communities associated with roots of rose-scented geranium (Pelargonium graveolens) with the potential to contribute to plant growth – Thais Freitas da Silva – Applied Soil Ecology

Isolation of Soil and Endophytic Fungi from Rice (Oryza sativa L.) – Thianrat Leewijit – Journal of Agricultural Technology

Effects of Dry and Wet Sieving of Soil on Identification and Interpretation of Microbial Community Composition – A. Blaud – Advances in Agronomy

Book chapter: The Significance of Plant-Associated Microbial Rhizosphere for the Degradation of Xenobiotic Compounds – Durgesh Kumar Jaiswal – Plant Responses to Xenobiotics

Review: Plant Communication With Associated Microbiota in the Spermosphere, Rhizosphere and Phyllosphere – P. Lemanceau – Advances in Botanical Research

Review: Plant growth promoting Rhizobacteria: Biocontrol potential for pathogens – Roomina Mazhar – Pure Appl Biol

Water and extremophile microbiome

* Spatial and temporal analogies in microbial communities in natural drinking water biofilms – I. Douterelo – Science of The Total Environment

Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments – Rituja Saxena – Frontiers in Microbiology

Response of the microbial community to bioturbation by benthic macrofauna on intertidal flats – Hui Shen – Journal of Experimental Marine Biology and Ecology

Review: Biotechnological Applications of Marine Enzymes From Algae, Bacteria, Fungi, and Sponges – S. Parte – Advances in Food and Nutrition Research

Waste and pollution microbiology

Inhibitory effects of sodium azide on microbial growth in experimental resuspension of marine sediment – Cabrol Léa – Journal of Microbiological Methods

Effect of various chemical oxidation agents on soil microbial communities – Eva Kakosová – Chemical Engineering Journal

Shifts in microbial community structure and function in surface waters impacted by unconventional oil and gas wastewater revealed by metagenomics – N.L. Fahrenfeld – Science of the Total Environment

Changes in the microbial community during bioremediation of gasoline-contaminated soil – Aline Jaime Leal – Brazilian Journal of Microbiology

Performance and microbial communities of completely autotrophic denitrification in a bioelectrochemically-assisted constructed wetland system for nitrate removal – Dan Xu – Bioresource Technology

Screening selectively harnessed environmental microbial communities for biodegradation of polycyclic aromatic hydrocarbons in moving bed biofilm reactors – Marc A. Demeter – Bioresource Technology

Review: Resource recovery from wastewater by biological technologies: opportunities, challenges and prospects – Daniel Puyol – Frontiers in Microbiology

Fungi

A Review of the Ubiquity of Ascomycetes Filamentous Fungi in Relation to Their Economic and Medical Importance – Mary Augustina Egbuta – Advances in Microbiology

Phages

Editorial: Filamentous Bacteriophage in Bio/Nano/Technology, Bacterial Pathogenesis and Ecology – Jasna Rakonjac – Frontiers in Microbiology

Metabolomics

Adherence to a Mediterranean diet influences the fecal metabolic profile of microbial-derived phenolics in a Spanish cohort of middle-age and older people – Isabel Gutiérrez-Díaz – Journal of Agricultural and Food Chemistry

MASTR-MS: a web-based collaborative laboratory information management system (LIMS) for metabolomics – Adam Hunter – Metabolomics

More microbiology

* Cell morphology drives spatial patterning in microbial communities – William P. J. Smith – PNAS

Microbes in the news

A Gut Makeover for the New Year – Roni Caryn Rabin – The New York Times

Keys plan field trial for bacteria-infected mosquitoes – Associated Press

Salmonella bacteria threatens Mudumalai: cattle and elephants died – Times of India

How your gut’s circadian rhythm affects your whole body – Richard G. “Bugs” Stevens – The Conversation

Eat Dirt… It’s Good For You (So Are Worms) – Tanya Mead – The Alternative Daily