Category Archives: Human skin

February 10, 2017

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Today’s digest features fascinating  research articles on the potential of glycomacropeptide in modulating human gut microbiota of elderly, identifying IBD-like microbiome in at-risk healthy relatives of IBD patients with no clinical signs of inflammation,  long-term climate change affects soil microbial communities and  a reviews on the potential role of transglutaminases in autoimmunity.

General microbiome

Comparative study of the gut microbiome potentially related to milk protein in Murrah buffaloes (Bubalus bubalis) and Chinese Holstein cattle – Jiachao Zhang – Scientific Reports

The microbiome of the octocoral Lobophytum pauciflorum: minor differences between sexes and resilience to short-term stress – Wiebke Wessels – FEMS Microbiol Ecology

Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas – Hannah Wang- Genome Medicine

Microbiota composition of simultaneously colonized mice housed under either a gnotobiotic isolator or individually ventilated cage regime – Randi Lundberg – Scientific Reports

Microbial strain-level population structure and genetic diversity from metagenomes – Duy Tin Truong – Genome Research

*Review: Transglutaminases in Dysbiosis As Potential Environmental Drivers of Autoimmunity – Aaron Lerner- Frontiers in Microbiology

Pregnancy and early life

Perspective: The maternal microbiome: Cause or consequence of obesity risk in the next generation? – Jacob E. Friedman – Obesity

Review: Charting the Maternal and Infant Microbiome: What Is the Role of Diabetes and Obesity in Pregnancy? – Sirtaj Singh – Current Diabetes Reports

Human skin microbiome

Skin Microbiome in Small- and Large-plaque Parapsoriasis – Alexander Salava – Acta Dermato-Venereologica

Human gut microbiome

*Glycomacropeptide sustains microbiota diversity and promotes specific taxa in an artificial colon model of elderly gut microbiota – Alexandra Ntemiri – Journal of Agricultural and Food Chemistry

A Disease-Associated Microbial and Metabolomics State in Relatives of Pediatric Inflammatory Bowel Disease Patients – Jonathan P. Jacobs – Cellular and Molecular Gastroenterology and Hepatology

Comparative study on the in vitro effects of Pseudomonas aeruginosa and seaweed alginates on human gut microbiota – Shaofeng Bai – PLOS ONE

Review: Gut microbiota modulation and anti-inflammatory properties of dietary polyphenols in IBD: new and consolidated perspectives.  – Angelo Santino – Current Pharmaceutical Design

Animal experiments 

Changes in Microbiota in Rumen Digesta and Feces Due to a Grain-Based Subacute Ruminal Acidosis (SARA) Challenge – Jan C. Plaizier – Microbial Ecology

A maternal Western diet during gestation and lactation modifies offspring’s microbiota activity, blood lipid levels, cognitive responses, and hippocampal neurogenesis in Yucatan pigs – David Val-Laillet – FASEB Journal

Animal microbiome 

Bacterial community composition and fermentation in the rumen of Xinjiang brown cattle (Bos taurus), Tarim red deer (Cervus elaphus yarkandensis), and Karakul sheep (Ovis aries) – Wenxi Qian – Canadian Journal of Microbiology

Plant, root, and soil microbiome

Plants Assemble Species Specific Bacterial Communities from Common Core Taxa in Three Arcto-Alpine Climate Zones – Manoj Kumar – Frontiers in Microbiology

*Links between soil microbial communities and plant traits in a species-rich grassland under long-term climate change – Emma J. Sayer – Ecology and Evolution

Specificity of root microbiomes in native-grown Nicotiana attenuata and plant responses to UVB increase Deinococcus colonization – Rakesh Santhanam – Molecular Ecology

Water and extremophile microbiome 

Metagenomic survey of the taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic – Etienne Yergeau – Scientific Reports

Phages and viruses

Things Are Getting Hairy: Enterobacteria Bacteriophage vB_PcaM_CBB – Colin Buttimer – Frontiers in Microbiology

Techniques

Successive DNA extractions improve characterization of soil microbial communities – Mauricio R. Dimitrov – PeerJ

Microbes in the news

Bacteria fed synthetic iron-containing molecules turn into electrical generators

Method to identify bacteria in blood samples works in hours instead of days

Characterizing Cervical Cancer by HPV Strain, Mutations, and Molecular Features

Phage In The Time Of Cholera

An Innovative New Cancer Therapy Hijacks Bacteria to Fight Tumors

Microbes on the market

Chan Zuckerberg Biohub funds first crop of 47 investigators

Anitha’s non-microbiology picks 

Could this pollinating drone replace butterflies and bees?

The physics of why valve amps sound better

Circuits survive on Venus, electronics powered by stomach acid

February 9, 2017

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Metabolomic analysis to determine affects of antibiotic treatment on the microbiome, capsular polysaccharide structure from marine bacterium, altering soil bacterial communities from use of organic-inorganic fertilization, new CRISPR-Cas systems discovered in uncultivated microbes.

General microbiome

Metabolic effects of Lactobacillus reuteri DSM 17938 in people with type 2 diabetes: A randomized controlled trial – Reza Mobini – Diabetes, Obesity and Metabolism

Pregnancy and early life

Diversity and composition of vaginal microbiota of pregnant women at risk for transmitting Group B Streptococcus treated with intrapartum penicillin – Luiz Fernando Wurdig Roesch – PLOS ONE

Human oral microbiome

Isolation and identification methods of Rothia species in oral cavities – Osamu Tsuzukibashi – Journal of Microbiological Methods

Association of oral microbiome with type 2 diabetes risk – J Long – Journal of Periodontal Research

Human skin microbiome

Microbiome precision editing: Using PEG as a selective fermentation initiator against methicillin-resistant Staphylococcus aureus – Ming-Shan Kao – Biotechnology Journal

Human gut microbiome

Comparative study on the in vitro effects of Pseudomonas aeruginosa and seaweed alginates on human gut microbiota – Shaofeng Bai – PLOS ONE

Rett Syndrome: A Focus on Gut Microbiota – Elisa Borghi – International Journal of Molecular Sciences

Colonization with enterotoxigenic Bacteroides fragilis is associated with early-stage colorectal neoplasia – Rachel V Purcell – PLOS ONE

Gut dysbiosis is associated with metabolism and systemic inflammation in patients with ischemic stroke – Kazuo Yamashiro – PLOS ONE

Glycomacropeptide sustains microbiota diversity and promotes specific taxa in an artificial colon model of elderly gut microbiota – Alexandra Ntemiri – Journal of Agricultural and Food Chemistry

Animal experiments

* Early life antibiotic exposure affects pancreatic islet development and metabolic regulation – Jiaying Li – Scientific Reports

Reduction of Abeta amyloid pathology in APPPS1 transgenic mice in the absence of gut microbiota – T Harach – Scientific Reports

Animal microbiome

Comparative study of the gut microbiome potentially related to milk protein in Murrah buffaloes (Bubalus bubalis) and Chinese Holstein cattle – Jiachao Zhang – Scientific Reports

Fish Intestinal Microbiome: Diversity and Symbiosis Unraveled by Metagenomics – AM Tarnecki – Journal of Applied Microbiology

Plant, root, and soil microbiome

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

Community-level physiological profiling analyses show potential to identify the copiotrophic bacteria present in soil environments – Salvador Lladó – PLOS ONE

Arbuscular mycorrhiza enhance the rate of litter decomposition while inhibiting soil microbial community development – Heng Gui – Scientific Reports

Bacterial Community Structure after Long-term Organic and Inorganic Fertilization Reveals Important Associations between Soil Nutrients and Specific Taxa Involved in Nutrient Transformations – Fang Li – Frontiers in Microbiology

The effects of fluoride based fire-fighting foams on soil microbiota activity and plant growth during natural attenuation of perfluorinated compounds – Renato Nallin Montagnolli – Environmental Toxicology and Pharmacology

Chapter: Phytostimulation and Biocontrol by the Plant-Associated Bacillus amyloliquefaciens FZB42: An Update – Rainer Borriss – Bacilli and Agrobiotechnology

Chapter: New Insights in Plant-Associated Paenibacillus Species: Biocontrol and Plant Growth-Promoting Activity – Sadhana Lal – Bacilli and Agrobiotechnology

Variations of soil microbial community structures beneath broadleaved forest trees in temperate and subtropical climate zones – Sihang Yang – Frontiers in Microbiology

Water and extremophile microbiome

The effects of elevated seawater temperatures on Caribbean gorgonian corals and their algal symbionts, Symbiodinium spp. – Tamar L. Goulet – PLOS ONE

* Structural characterization of an all-aminosugar-containing capsular polysaccharide from Colwellia psychrerythraea 34H – Angela Casillo – Antonie van Leeuwenhoek

Illumina sequencing-based analysis of sediment bacteria community in different trophic status freshwater lakes – Yu Wan – Microbiology Open

Bacterial communities in sediment of a Mediterranean Marine Protected Area – Valentina Catania – Canadian Journal of Microbiology

Metagenomic survey of the taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic – Etienne Yergeau – Scientific Reports

The effect of top-predator presence and phenotype on aquatic microbial communities – Karen E. Sullam – Ecology and Evolution

Metabolomics

Divergent Relationships between Fecal Microbiota and Metabolome following Distinct Antibiotic-Induced Disruptions – Jocelyn M. Choo – mSphere

Techniques

A novel LCMSMS method for quantitative measurement of short-chain fatty acids in human stool derivatized with 12C- and 13C-labelled aniline – James Chun Yip Chan – Journal of Pharmaceutical and Biomedical Analysis

More microbes

* New CRISPR–Cas systems from uncultivated microbes – David Burstein – Nature

Adaptation of genetically monomorphic bacteria: evolution of copper resistance through multiple horizontal gene transfers of complex and versatile mobile genetic elements – D Richard – Molecular Ecology

Microbes in the news

Microbial Molecules from the Multitudes within Us – Matthew R. Redondo – Cell Metabolism

Boston Children’s Hospital and uBiome to Investigate Premature Births – PRWeb

Cholera bacteria stab and poison enemies at predictable rates – Georgia Institute of Technology – ScienceDaily

ADA funds Kostic Lab to create model linking the microbiome to type 1 diabetes – EurekAlert

February 8, 2017

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A dense Digest today, a lot of reviews on the human gut microbiome, a plethora of papers on plant, soil and water microbiomes, and an alarmingly high rate of multi-drug resistant bacteria from human fecal samples in China

Jobs

Teaching and Learning Fellow in Microbiome Data Analysis – University of British Columbia

Microbiology Quality Technician II – CR Bard

Postdoctoral Research Assistant on the Social Dimensions of the Microbiome – University of Oxford

General microbiology

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

Effect of antibiotics on bacterial populations: a multi-hierachical selection process – José Luis Martínez – F1000 Research

Plant growth promoting potential and phylogenetic characteristics of a lichenized nitrogen fixing bacterium, Enterobacter cloacae – Chidanandamurthy Thippeswamy Swamy – Journal of Basic Microbiology

*High rates of human faecal carriage of mcr-1-positive multi-drug resistant isolates emerge in China in association with successful plasmid families – Lan-Lan Zhong – bioRxiv

Assessing the genome level diversity of Listeria monocytogenes from contaminated ice cream and environmental samples linked to a listeriosis outbreak in the United States – Yi Chen – PLoS One

Human skin microbiome

Significant disparities in allergy prevalence and microbiota between the young people in Finnish and Russian Karelia – Lasse Ruokolainen – Clinical & Experimental Allergy

Beyond Cell Division: the Ecological Roles of Autolysins in Oral Biofilm Communities – Nyssa Cullin – Current Oral Health Reports

Human lung microbiome

Longitudinal assessment of sputum microbiome by sequencing of the 16S rRNA gene in non-cystic fibrosis bronchiectasis patients – Michael J. Cox – PLoS One

Human gut microbiome

Review: Intestinal Microbiota: Facts and Fiction – M Kverka – Digestive Diseases

Review: Evolutionary and ecological forces that shape the bacterial communities of the human gut – J S Messer – Mucosal Immunology

Review: Dietary Fiber and Prebiotics and the Gastrointestinal Microbiota – Hannah D. Holscher – Gut Microbes

Review: The Fungal Mycobiome and Its Interaction with Gut Bacteria in the Host – Qi Hui Sam – International Journal of Molecular Sciences

Review: The Gut Microbiome in Irritable Bowel Syndrome and Other Functional Bowel Disorders – Yehuda Ringel – Gastroenterology Clinics of North America

Many more human gut microbiome reviews available from the March Issue of the Gastroenterology Clinics of North America

Human gut-microbiome-brain axis

Editorial: Tightening the Case for Gut Microbiota in Autism-Spectrum Disorder – Jonathan Braun – CMGH Cellular and Molecular Gastroenterology and Hepatology

Review: The Microbiome-Gut-Brain Axis in Health and Disease – Timothy G. Dinan – Gastroenterology Clinics of North America

Metabolomics

Review: Mixing omics: combining genetics and metabolomics to study rheumatic diseases – Cristina Menni – Nature Reviews Rheumatology

Review: Emerging Approaches to Tuberculosis Drug Development: At Home in the Metabolome – Robert S. Jansen – Trends in Pharmacological Sciences

Rats Urinary Metabolome Reveals for the Potential Role of Functional Foods and Exercise in Obesity Management – Mohammed Farag – Food and Function

Untargeted metabolomics approach for unraveling robust biomarkers of nutritional status in fasted gilthead sea bream (Sparus aurata) – Ruben Gil-Solsona – PeerJ

Animal experiments

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

Metagenomics approach to the study of the gut microbiome structure and function in zebrafish Danio rerio fed with gluten formulated diet – Hyunmin Koo – Journal of Microbiological Methods

Commentary: Zebrafish screens for new colitis treatments – a bottom-up approach – Jou A. Lee – The FEBS Journal

Mouse: Resistant starch can improve insulin sensitivity independently of the gut microbiota – Laure B. Bindels – Microbiome

Animal microbiome

Invited review: Large-scale indirect measurements for enteric methane emissions in dairy cattle: A review of proxies and their potential for use in management and breeding decisions – E. Negussie – Journal of Dairy Science

Variation of the microbiota and metabolome along the canine gastrointestinal tract – Julia B. Honneffer – Metabolomics

Effects of Organic Amendments on Microbiota Associated with the Culex nigripalpus Mosquito Vector of the Saint Louis Encephalitis and West Nile Viruses – Dagne Duguma – mSphere

Review: Progress in fish gastrointestinal microbiota research – An R. Wang – Reviews in Aquaculture

Diversity and functions of the sheep faecal microbiota: a multi-omic characterization – Alessandro Tanca – Microbial Biotechnology

Microbial shifts in the porcine distal gut in response to diets supplemented with Enterococcus Faecalis as alternatives to antibiotics – Pinghua Li – Scientific Reports

Plant, root and soil microbiome

Fungi from Brazilian Savannah and Atlantic rainforest show high antibacterial and antifungal activity – Paula de Paula Menezes Barbosa – Biocatalysis and Agricultural Biotechnology

Impact of Elevated CO2 and/or Temperature on the AM Fungal Diversity in Groundnut Rhizosphere under Open Top Chamber facility – HN Asha – International Journal of Current Microbiology and Applied Sciences

Seed-coating fenugreek with Burkholderia rhizobacteria enhances yield in field trials and can combat Fusarium wilt – Harish Kuma – Rhizosphere

Changes at the Rhizosphere Microbiota of the Sunflower–Orobanche cumana Wallr Pathosystem – TH Hristev – International Journal of Current Microbiology and Applied Sciences

Review: Phosphate Solubilizing Microbes: An Overview – KP Ingle – International Journal of Current Microbiology and Applied Sciences

Draft Genome Sequence of Plant Growth-Promoting Drought-Tolerant Bacillus sp. Strain CMAA 1363 Isolated from the Brazilian Caatinga Biome – Vanessa Nessner Kavamura – Genome Announcements

Effects of Garlic/Cucumber Relay Intercropping on Soil Enzyme Activities and the Microbial Environment in Continuous Cropping – Lantian Du – HortScience

Characterization of bacterial communities from Masseiras, a unique Portuguese greenhouse agricultural system – Cristina Becerra-Castro – Antonie van Leeuwenhoek

Soil microbial community responses to long-term land use intensification in subtropical grazing lands – Sutie Xu – Geoderma

The impact of salinity on the microbial response to drying and rewetting in soil – Kristin M. Rath

The influence of different concentrations of bio-organic fertilizer on cucumber Fusarium wilt and soil microflora alterations – Nan Huang – PLoS One

Cowpea Nodules Harbor Non-rhizobial Bacterial Communities that Are Shaped by Soil Type Rather than Plant Genotype – Jakson Leite – Frontiers in Plant Science

Microbial Interactions in the Phyllosphere Increase Plant Performance under Herbivore Biotic Stress – Muhammad Saleem – Frontiers in Microbiology

Water and extremophile microbiome

Complete Genome Sequence of Thermus thermophilus TMY, Isolated from a Geothermal Power Plant – Yasuhiro Fujino – Genome Announcements

Marine Microbes as a Potential Source of Cellulolytic Enzymes – N. Trivedi – Chapter 2 of Advances in Food and Nutrition Research, Vol. 79

Genetic toolbox for controlled expression of functional proteins in Geobacillus spp. – Ivan Pogrebnyakov – PLoS One

Coupled Effects of Electrical Stimulation and Antibiotics on Microbial Community in Three-Dimensional Biofilm-Electrode Reactors – Hai-Liang Song – Water, Air, & Soil Pollution

Do biofilm communities respond to the chemical signatures of fracking? A test involving streams in North-central Arkansas – Wilson H. Johnson – BMC Microbiology

Effects of chemical cleaning on RO membrane inorganic, organic and microbial foulant removal in a full-scale plant for municipal wastewater reclamation – Tong Yu – Water Research

Microbial nitrification, denitrification and respiration in the leached cinnamon soil of the upper basin of Miyun Reservoir – Wen Xu – Scientific Reports

Microbes in space

The Effects of HZE Particles, γ and X-ray Radiation on the Survival and Genetic Integrity of Halobacterium salinarum NRC-1, Halococcus hamelinensis, and Halococcus morrhuae – Leuko Stefan – Astrobiology

Survival, DNA Integrity, and Ultrastructural Damage in Antarctic Cryptoendolithic Eukaryotic Microorganisms Exposed to Ionizing Radiation – Pacelli Claudia – Astrobiology

Phages and viruses

Genomic sequence of ‘Candidatus Liberibacter solanacearum’ haplotype C and its comparison with haplotype A and B genomes – Jinhui Wang – PLoS One

Technology

Microbial Typing by Machine Learned DNA Melt Signatures – Nadya Andini – Scientific Reports

Bioinformatics

From Culture to High-Throughput Sequencing and Beyond: A Layperson’s Guide to the “Omics” and Diagnostic Potential of the Microbiome – Paul W. O’Toole – Gastroenterology Clinics of North America

Microbes in the news

2017 sneak peek: What the new year holds for science – Elizabeth Gibney – Nature

Is It the “Terrible Twos”? Or Is It a Disrupted Gut Microbiome? – Chris Kresser

Microbes on the market

Human Microbiome Market : Global Market Snapshot by 2020 – Persistence Market Research

January 26, 2017

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Environmental ecology review presents how microbial life strategy concepts are applied in complex microbial communities.   Two interesting model systems are described in the techniques section, plus potentially scalable workflow for the preparation of high potency Akkermansia muciniphila cells for therapeutic interventions.  The importance of understanding the role of the microbiome in preventing complications after organ transplant and surgeries are discussed in two reviews.   Another study shows that proton pump inhibitors used to prevent gastric ulcers were associated with distinct gut microbiota signatures.  For faster wound healing, try some saliva. A study shows the beneficial effects of saliva on wound healing in human epidermal keratinocytes and on the attenuation of intracellular Staph. aureus infection.

Pregnancy and early life

Assessment of the synbiotic properties of human milk oligosaccharides and Bifidobacterium longum subsp. infantis in vitro and in humanised mice – S Musilova- Beneficial Microbes

Multi-site human microbiome

Review: Infection in Organ Transplantation – Jay A. Fishman – American Journal of Transplantation

Review: The gut microbiome and the mechanism of surgical infection – J.C. Alverdy – The British Journal of Surgery

Human Oral Microbiome

Salivary mucins promote the coexistence of competing oral bacterial species – Erica Shapiro Frenke- The ISME Journal

Human skin microbiome

Saliva induces expression of antimicrobial peptides and promotes intracellular killing of bacteria in keratinocytes by epidermal growth factor receptor transactivation – T. Mohanty – British Journal of Dermatology

Human gut microbiome

The influence of proton pump inhibitors and other commonly used medication on the gut microbiota – Floris Imhann – Gut Microbes

Animal experiments

Review: Understanding host-microbial interactions in rumen: searching the best opportunity for microbiota manipulation – Nilusha Malmuthuge  – Journal of Animal Science and Technology

Plant, root, and soil microbiome

Review: Revisiting life strategy concepts in environmental microbial ecology – Adrian Ho- FEMS Microbiology Ecology

Diclofop-methyl affects microbial rhizosphere community and induces systemic acquired resistance in rice – Si Chen – Journal of Environmental Sciences

Food microbiology

Review: Human pathogens in plant biofilms: Formation, physiology, and detection – Eduardo Ximenes – Biotechnology and Bioengineering

Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork -Koji Yahara – Environmental Microbiology

Digestive fate of dietary carrageenan: Evidence of interference with digestive proteolysis and disruption of gut epithelial function – Lulu Fahoum – Molecular Nutrition Food Research

Bioinformatics

It’s a big data problem: researchers from the University of California, San Diego and the J.C. Venter Institute used machine learning to teach a computer to learn to distinguish between healthy and unhealthy gut microbiomes. The new approach shows promise for predicting related health issues and providing guidance for therapy development. More from the press

Techniques

Preparation and preservation of viable Akkermansia muciniphila cells for therapeutic interventions – JP Ouwerkerk  -Beneficial Microbes

Evaluation of colonization resistance in stool of human donors using ex vivo, in vitro and in vivo assays – MF Galvão  – Beneficial Microbes

Improving metabolite production in microbial co-cultures using a spatially constrained hydrogel – Matthew J. Smith – Biotechnology and Bioengineering

Microbes in the news

CRISPR research institute expands into agriculture, microbiology

Dog obesity, a growing problem, may be managed through diet and exercise and- microbiology

Every surfer knows you should stay out of the water for 72 hours after it rains. Public health officials issued an advisory for all Los Angeles County beaches, cautioning swimmers and surfers to stay away from areas near storm drains, creeks and rivers. But when the waves show – some surfers just can’t help themselves.

January 22, 2017

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Events and Jobs

PhD scholarship in Molecular Microbiology– University of Copenhagen-Last Date: February 8, 2017

Quality Control Associate-Microbiology–US-CA-Del Mar

General Microbiome

Impacts of chemical gradients on microbial community structure-Jianwei Chen-The ISME Journal

Human Skin

Proteomic and peptidomic analysis of human sweat with emphasis on proteolysis-Yijing Yu-Journal of Proteomics

Human Respiratory Microbiome

Nasopharyngeal Microbiome Diversity Changes over Time in Children with Asthma–Marcos Pérez-Losada-PLOS One

Adherence of Pseudomonas aeruginosa to cystic fibrosis buccal epithelial cells–Meike Lingner-ERJ

Human Vaginal Microbiome

The interaction between vaginal microbiota, cervical length, and vaginal progesterone treatment for preterm birth risk-Lindsay M. Kindinger-Microbiome

Human Gut Microbiome

Role of Gastrointestinal Microbiota on Kidney Injury and the Obese Condition-Keerati Wanchai-The American Journal of the Medical Sciences

Review-Altered Molecular Signature of Intestinal Microbiota in Irritable Bowel Syndrome Patients Compared with Healthy Controls: a Systematic Review and Meta-analysis-Hai Ning Liu-Digestive and Liver Disease

Animal Microbiome

Bacterial community composition and fermentation in the rumen of Xinjiang brown cattle (Bos taurus), Tarim red deer (Cervus elaphus yarkandensis), and Karakul sheep (Ovis aries)-Wenxi Qian-Canadian Journal of Microbiology

The Gut Microbiome of the Vector Lutzomyia longipalpis Is Essential for Survival of Leishmania infantum–Stephen M. Beverley-mBio

The normal vaginal and uterine bacterial microbiome in giant pandas (Ailuropoda melanoleuca)-Xin Yang-Microbiological Research

Pathogen-mediated manipulation of arthropod microbiota to promote infection–Nabil M. Abraham-PNAS

The gastrointestinal tract of farmed mink (Neovison vison) maintains a diverse mucosa-associated microbiota following a 3-day fasting period-Martin I. Bahl-Microbiology Open

Ovarian cycling and reproductive state shape the vaginal microbiota in wild baboons–Elizabeth A. Miller-BMC Microbiome

Plant, root, and soil microbiome

A decade of irrigation transforms the soil microbiome of a semi-arid pine forest-Martin Hartmann-Molecular Ecology

Methane Emissions and Microbial Communities as Influenced by Dual Cropping of Azolla along with Early Rice-Jingna Liu-Scientific Reports

Differential responses of soil bacterial communities to long-term N and P inputs in a semi-arid steppe-Ning Ling-Geoderma

Mineralization of “non-metabolizable” glucose analogues in soil: potential chemosensory mimics of glucose-Kyle Mason-Jones-Journal of Plant Nutrition and Soil Science

Deciphering composition and function of the root microbiome of a legume plant-Kyle Hartman-BMC Microbiome

Isolation and characterization of Rhizobium sp. strain YS-1r that degrades lignin in plant biomass-Colin A. Jackson-Journal of Applied Microbiology

Metagenomic insights into effects of spent engine oil perturbation on the microbial community composition and function in a tropical agricultural soil–Lateef B. Salam-Environmental Science and Pollution Research

Biocontrol effects of Brevibacillus laterosporus AMCC100017 on potato common scab and its impact on rhizosphere bacterial communities-Shengfu Chen-Biological Control

Co-inoculation with Enterobacter and Rhizobacteria on Yield and Nutrient Uptake by Wheat (Triticum aestivum L.) in the Alluvial Soil Under Indo-Gangetic Plain of India-Ashok Kumar-Journal of Plant Growth Regulation

 Ornamental flowers in new light: Artificial lighting shapes the microbial phyllosphere community structure of greenhouse grown sunflowers (Helianthus annuus L.)–Beatrix W. Alsanius–Scientia Horticulturae

Extremophiles

Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats-Meinhard Simon-ISME

Review: Marine Bacterioplankton Seasonal Succession Dynamics-Carina Bunse-Trends in Microbiology

Review: Stress response physiology of thermophiles–Preeti Ranawat-Archives of Microbiology

The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights-Emanuele Bosi-BMC Genomics

Sulfur compound oxidation and carbon co-assimilation in the haloalkaliphilic sulfur oxidizers Thioalkalivibrio versutus and Thioalkalimicrobium aerophilum-Wee Kiong Ang-Research in Microbiology

Geological and Geochemical Controls on Subsurface Microbial Life in the Samail Ophiolite, Oman–Kaitlin R. Rempfert-Extreme Microbiology

Microbial character related sulfur cycle under dynamic environmental factors based on the microbial population analysis in sewerage system-Qian Dong-Aquatic Microbiology

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

Unraveling the microbial processes of black band disease in corals through integrated genomics-Yui Sato-Scientific Reports

Preliminary Phylogenetic Analysis of Thermophilic Bacteria Producing Protease isolated from Kuantan Malaysia -Essam A. Makky-JBSR

Identification of a novel fatty acid in the cell membrane of Chryseobacterium frigidisoli PB4T isolated from an East Antarctic glacier forefield-Kai Mangelsdorf-Organic Geochemistry

Phosphorus removal by marine bacterium enhanced with iron in the presence of silicon–Yanru Wang-Journal of Chemical Technology and Biotechnology

 Built Environment Microbiology

Developing Evidence-based Tools for Designing and Evaluating Hospital Inpatient Rooms–Xiaobo Quan-Journal of Interior Design

Building-related symptoms are linked to the in vitro toxicity of indoor dust and airborne microbial propagules in schools: A cross-sectional study-J T Salin-Environmental Research

Techniques

Review:  Application of meta-omics techniques to understand greenhouse gas emissions originating from ruminal metabolism-Robert J. Wallace-Genetics Selection Evolution

Balance Trees Reveal Microbial Niche Differentiation–James T. Morton-Ecological and Evolutionary Science

Virus

Review: Virus–host interactions and their roles in coral reef health and disease–Rebecca Vega Thurber-Nature Reviews Microbiology

Virome of US bovine calf serum-Mohammadreza Sadeghi-Biologicals

More Microbes

Bacillus zeae sp. nov. isolated from the rhizosphere of Zea mays– Peter Kämpfer-International Journal of Systematic and Evolutionary Microbiology

Microbes in News

Capnophilic Enterobacteriaceae-JM. Sahuquillo Arce-Diagnostic Microbiology and Infectious Disease

January 20, 2017

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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 16, 2017

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Environmental pollutants have become an increasingly common health hazard. The possible effects of environmental pollutants on gut microbiota and their subsequent effects on health is discussed in highlighted review.

Pregnancy and early life

Antibiotics in Pregnancy Increase Children’s Risk of Otitis Media and Ventilation Tubes – Tine Marie Pedersen – The journal of Pediatrics

Human skin microbiome

Insights into the mast cell–microbiome connection in the skin – Alon Y. Hershko – Journal of Allergy and Clinical Immunology

Microbiota fingerprints lose individually identifying features over time – David Wilkins – Microbiome

Human vaginal microbiome

Association between preterm labor and genitourinary tract infections caused by Trichomonas vaginalis, Mycoplasma hominis, Gram-negative bacilli, and coryneforms – Alaa El-Dien M.S. Hosny – Journal of the Chinese Medical Association

The Vaginal Microbiota and Urinary Tract Infection – Ann E. Stapleton – Microbiol Spectrum

Human nearly-sterile sites 

Metabolic profiles of exudates from chronic leg ulcerations – Adam Junka – Journal of Pharmaceutical and Biomedical Analysis

Human oral microbiome

Review: Ecology of the Oral Microbiome: Beyond Bacteria – Jonathon L. Baker – Trends in Microbiology

On-going Mechanical Damage from Mastication Drives Homeostatic Th17 Cell Responses at the Oral Barrier – Nicolas Dutzan – Immunity

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

Human gut microbiome

Expert review: Management of Clostridium difficile Infection in Inflammatory Bowel Disease: Expert Review from the Clinical Practice Updates Committee of the AGA Institute – Sahil Khanna – Clinical Gastroenterology and Hepatology

Review: Effects of environmental pollutants on gut microbiota – Yuanxiang Jin – Environmental Pollution

Impact of dietary pattern of the fecal donor on in vitro fermentation properties of whole grains and brans – Sandrayee Brahma – Journal of Functional Foods

Review: The role of the gut microbiota in sepsis – Bastiaan W Haak – The Lancet Gastroenterology & Hepatology

Gut microbiota interactions with the immunomodulatory role of vitamin D in normal individuals – Renata V. Luthold – Metabolism

“Angelakisella massiliensis” gen. nov., sp. nov., a new bacterial species isolated from human ileum – Morgane Mailhe – New Microbes and New Infections

Helicobacter pylori–related metabolic syndrome as predictor of progression to esophageal carcinoma in a subpopulation-based Barrett’s esophagus cohort – Jannis Kountouras – Gastrointestinal Endoscopy

Impact of dietary pattern of the fecal donor on in vitro fermentation properties of whole grains and brans – Sandrayee Brahma – Journal of Functional Foods

Absence of intestinal microbiota increases ß-cyclodextrin stimulated reverse cholesterol transport – Rima H. Mistry – Molecular Nutrition & Food Research

European consensus conference on faecal microbiota transplantation in clinical practice – Giovanni Cammarota – Gut
Animal experiments

Gd-DTPA-induced dynamic metabonomic changes in rat biofluids – Chuanling Wan – Magnetic Resonance Imaging

Increasing dietary nitrate has no effect on cancellous bone loss or fecal microbiome in ovariectomized rats – Melissa N. Conley – Molecular Nutrition & Food Research

Animal microbiome

Improved growth rate and disease resistance in olive flounder, Paralichthys olivaceus, by probiotic Lactococcus lactis WFLU12 isolated from wild marine fish – Thanh Luan Nguyen – Aquaculture

Plant, root, and soil microbiome

The effects of tree species and substrate on carbon sequestration and chemical and biological properties in reforested post-mining soils – Agnieszka Józefowska – Geoderma

Impacts of inorganic and organic fertilization treatments on bacterial and fungal communities in a paddy soil – Jichen Wang – Applied Soil Ecology

Water and extremophile microbiome

Effects of the halophilic fungi Cladosporium sphaerospermum, Wallemia sebi, Aureobasidium pullulans and Aspergillus nidulans on halite formed on sandstone surface – Maisa M.A. Mansour – International Biodeterioration & Biodegradation

Epiphytic Planctomycetes communities associated with three main groups of macroalgae – Joana Bondoso – FEMS Microbiology Ecology

Floc formation reduces the pH stress experienced by microorganisms living in alkaline environments -C.J. Charles – Applied and Environmental Microbiology

Capturing compositional variation in denitrifying communities: A multiple primer approach that includes autotrophic denitrifying Epsilonproteobacteria – S.A. Murdock  – Applied and Environmental Microbiology

Waste and pollution microbiology

Review: Aerobic and anaerobic fungal metabolism and Omics insights for increasing polycyclic aromatic hydrocarbons biodegradation – Sevcan Aydin – Fungal Biology Reviews

Built environment 

Biological invasion in the indoor environment: the spread of Eurotium halophilicum on library materials – Andrea Polo – International Biodeterioration & Biodegradation

Review: Integrated management of the risks of stored grain spoilage by seedborne fungi and contamination by storage mould mycotoxins – An update – Francis Fleurat-Lessard – Journal of Stored Products Research

Food microbiology

Impact of environmental conditions and process modifications on microbial diversity, fermentation efficiency and chemical profile during the fermentation of mezcal in Oaxaca – Manuel R. Kirchmayr – LWT – Food Science and Technology

Anti-aging and redox state regulation effects of A-type proanthocyanidins-rich cranberry concentrate and its comparison with grape seed extract in mice – Jingjing Jiao – Journal of Functional Foods

Probiotics / prebiotics

Probiotic mixture improves fatty liver disease by virtue of its action on lipid profiles, leptin, and inflammatory biomarkers – Hessah Mohammed Al-muzafar – BMC Complementary and Alternative Medicine

January 10, 2017

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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

Review: An 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 8, 2017

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Human mouth microbiome

Comparison of sputum microbiome of legionellosis-associated patients and other pneumonia patients: indications for polybacterial infections – Hila Mizrahi – Scientific Reports

Human reproductive tract microbiome

Investigation of the microbiota of the reproductive tract in women undergoing a total hysterectomy and bilateral salpingo-oopherectomy – Shana M. Miles – Fertility and Sterility

Human skin microbiome

Review: Performing Skin Microbiome Research: A Method to the Madness – Heidi H. Kong – Journal of Investigative Dermatology

Human gut microbiome

Sleeve gastrectomy drives persistent shifts in the gut microbiome – Cyrus Jahansouz – Surgery for Obesity and Related Diseases

Review: Gut microbiota in vascular disease: Therapeutic target? – Anbazhagan AN – Current Vascular Pharmacology

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

Reviews in Gastroenterology Clinics of North America
Diet and the Microbiome – Nida Murtaza
The Gut Microbiota in Inflammatory Bowel Disease – Donal Sheehan
The Microbiome-Gut-Brain Axis in Health and Disease – Timothy G. Dinan
Biology of the Microbiome : Interactions with the Host Immune Response – Sylwia Smolinska
Biology of the Microbiome 2: Metabolic Role – Jia V. Li

Animal experiments

Structural and functional alterations in the colonic microbiome of the rat in a model of stress induced irritable bowel syndrome – Nicolaas H Fourie – Gut Microbes

Animal microbiome

Greater Species Richness of Bacterial Skin Symbionts Better Suppresses the Amphibian Fungal Pathogen Batrachochytrium Dendrobatidis – Jonah Piovia-Scott – Microbial Ecology

Plant, root, and soil microbiome

Namib Desert edaphic bacterial, fungal and archaeal communities assemble through deterministic processes but are influenced by different abiotic parameters – Riegardt M. Johnson – Extremophiles

Plant Community Richness Mediates Inhibitory Interactions and Resource Competition between Streptomyces and Fusarium Populations in the Rhizosphere – Adil Essarioui – Microbial Ecology

Changes in Soil Fungal Community Structure with Increasing Disturbance Frequency – Hyunjun Cho – Microbial Ecology

Water and extremophile microbiome

Effect of salinity on mercury methylating benthic microbes and their activities in Great Salt Lake, Utah – Eric S. Boyd – Science of the Total Environment

Waste and pollution microbiology

Low temperature MBBR nitrification: Microbiome analysis – Bradley Young – Water Research

Microbes in space

MELiSSA the minimal biosphere: Human life, waste and refuge in deep space – Jeremy Walker – Future

Metabolomics

Bacterial Signaling to the Nervous System via Toxins and Metabolites – Nicole J. Yang – Journal of Molecular Biology

Bioinformatics

An Informative Approach on Differential Abundance Analysis for Time-course Metagenomic Sequencing Data – Dan Luo – Bioinformatics

Microbial ecology

Cheating fosters species co-existence in well-mixed bacterial communities – Anne Leinweber – ISME Journal

Microbes in the news

Life after death: the science of human decomposition – Mo Costandi

Japan’s fantastic emerald green algae. These great balls of fuzz, look lovely, are zero maintenance and keep water clean – James Wong

Cavities Are Contagious: Kissing And 3 Other Ways Harmful Bacteria Spreads And Causes Tooth Decay – Lizette Borreli – Medical Daily

Same bacteria found in Indian River Lagoon killed 10 in Florida in 2016 | Map – Tyler Treadway – TC Palm

Wake up, wipe out: How oxygen can help take down antiobiotic-resistant bacteria – Cordis

Your child’s microbiome, and why its health matters – Jennifer Graham – The Washington Times

December 29, 2016

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A foundational coral, bacteria in tree hollows, mining and visualizing microbiome data with Calypso, viral metagenomics in aquaculture.

General microbiome

Editorial: You are not alone – M. Ludwig – Acta Physiologica

Human ear microbiome

The Relationship of the Middle Ear Effusion Microbiome to Secretory Mucin Production in Pediatric Patients with Chronic Otitis Media – Krueger, Anna – The Pediatric Infectious Disease Journal

Animal experiments

Improvement of Intestinal Immune Cell Function by Lactic Acid Bacteria for Dairy Products – Tomonori Kamiya – Microorganisms

In poultry: Zeolite food supplementation reduces abundance of enterobacteria – Tanka P. Prasai – Microbiological Research

Animal microbiome

* Effects of predation and nutrient enrichment on the success and microbiome of a foundational coral – Elizabeth C. Shaver – Ecology

By their own devices: invasive Argentine ants have shifted diet without clear aid from symbiotic microbes – Yi Hu – Molecular Ecology

Gut content microbiota of introduced bigheaded carps (Hypophthalmichthys spp.) inhabiting the largest shallow lake in Central Europe – Andrea K. Borsodi – Microbiological Research

Plant, root, and soil microbiome

Ericoid Roots and Mycospheres Govern Plant-Specific Bacterial Communities in Boreal Forest Humus – Sari Timonen – Microbial Ecology

Benzo(a)pyrene degradation and microbial community responses in composted soil – Fengxiao Zhu – Environmental Science and Pollution Research

* Bacteria and Hoverflies (Diptera: Syrphidae) in Tree Hollows From the Iberian Mediterranean Forest – I. R. Sánchez-Galván – Environmental Entomology

Cd immobilization and reduced tissue Cd accumulation of rice (Oryza sativa wuyun-23) in the presence of heavy metal-resistant bacteria – Ya Li – Ecotoxicology and Environmental Safety

Water microbiome

* Environmental Viral Metagenomics Analyses in Aquaculture: Applications in Epidemiology and Disease Control – Hetron M. Munang’andu – Frontiers in Microbiology

Food microbiology

Microbial Ecology Dynamics in Portuguese Broa Sourdough – João M. Rocha – Journal of Food Quality

Bioinformatics and metagenomics

* Calypso: a user-friendly web-server for mining and visualizing microbiome–environment interactions – Martha Zakrzewski – Bioinformatics

DACE: A Scalable DP-means Algorithm for Clustering Extremely Large Sequence Data – Linhao Jiang – Bioinformatics

A novel approach based on KATZ measure to predict associations of human microbiota with non-infectious diseases – Xing Chen – Bioinformatics

Measuring the diversity of the human microbiota with targeted next-generation sequencing – Francesca Finotello – Briefings in Bioinformatics

More microbiology

Collective Resistance in Microbial Communities by Intracellular Antibiotic Deactivation – Robin A. Sorg – PLOS Biology
Microbes in the news

Circadian rhythms and the microbiome – Cosmos Magazine

You Don’t Even Want To Know About Bacteria On The Space Station – Trace Dominguez – Seeker

Rabbits, Bacteria and Calcium – Carl Palazzolo – Long Beach Post

Bacteria evolving more sophisticated antibiotic resistance – Brooks Hays – UPI