March 17, 2017

Circadian clocks are ubiquitous timing systems that induce rhythms of biological activities in synchrony with night and day.In the first highlighted paper the authors present the structural basis of the day-night transition in a cyanobacterial circadian clock. The second highlighted paper evaluated the effects of antibiotic treatment on the honeybee gut microbiome. The authors found that exposure to antibiotics significantly alters the honeybee gut microbial community structure and leads to decreased survival.

General microbiome

Biohybrid Microtube Swimmers Driven by Single Captured Bacteria – Morgan M. Stanton – Small

Structural basis of the day-night transition in a bacterial circadian clock – Roger Tseng – Science

Pregnancy and early life

Breast Milk Polyamines and Microbiota Interactions: Impact of Mode of Delivery and Geographical Location – C Gómez-Gallego  – Annals of Nutrition and Metabolism

 
Human respiratory microbiome

Modulation of behaviour and virulence of a high alginate expressing Pseudomonas aeruginosa strain from cystic fibrosis by oral commensal bacterium Streptococcus anginosus – RD Waite  – PLOS One

Human gut microbiome

Transfer of dysbiotic gut microbiota has beneficial effects on host liver metabolism – Simon Nicolas – Molecular Systems Biology

Fecal microbiota transplantation induces hepatitis B virus e-antigen (HBeAg) clearance in patients with positive HBeAg after long-term antiviral therapy – Yan-Dan Ren – Hepatology

The Microbiome and Host Behavior – Vuong HE – Annual Review of Neuroscience

Nonalcoholic Fatty Liver Disease, the Gut Microbiome, and Diet – Zeinab Mokhtari – Advances in Nutrition

Animal experiments

Intestinal transcriptome modulation by functional diets in rainbow trout: A high-throughput sequencing appraisal to highlight GALT immunomodulation – Ana Teresa Gonçalves – Fish & Shellfish Immunology

Effects of Gliadin consumption on the Intestinal Microbiota and Metabolic Homeostasis in Mice Fed a High-fat Diet – Li Zhang – Scientific Reports

Oral administration of synthetic porcine beta-defensin-2 improves growth performance and cecal microbial flora and down-regulates the expression of intestinal toll-like receptor-4 and inflammatory cytokines in weaned piglets challenged with enterotoxigenic Escherichia coli – Zhiru Tang – Animal Science Journal

RNA-Based Stable Isotope Probing Suggests Allobaculum spp. as Particularly Active Glucose Assimilators in a Complex Murine Microbiota Cultured In Vitro – Elena Herrmann – BioMed Research International

Animal microbiome

Antibiotic exposure perturbs the gut microbiota and elevates mortality in honeybees – Kasie Raymann – PLOS Biology

Plant, root, and soil microbiome

Accessing the Carbofuran Degradation Ability of Cultures From Natural River Biofilms in Different Environments – Chien-Jung Tien – CLEAN – Soil, Air, Water

Impact of Agri-Usable Nanocompounds on Soil Microbial Activity: An Indicator of Soil Health – Priyanka Khati – CLEAN – Soil, Air, Water

Complete genome sequence of Pseudomonas citronellolis P3B5, a candidate for microbial phyllo-remediation of hydrocarbon-contaminated sites – Mitja N.P. Remus-Emsermann – SIGS Standards in Genomic Sciences

Is the methanogenic community reflecting the methane emissions of river sediments?—comparison of two study sites – Prem Prashant Chaudhary – Microbiology Open

Water and extremophile microbiome

Characterizing and predicting cyanobacterial blooms in an 8-year amplicon sequencing time-course – Nicolas Tromas – bioRxiv

Effect of pesticides on microbial communities in container aquatic habitats – Ephantus J. Muturi – Scientific Reports

Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH – KI Twing – Frontiers in Microbiology

Dynamic Succession of Groundwater Sulfate-Reducing Communities during Prolonged Reduction of Uranium in a Contaminated Aquifer – Ping Zhang – Environmental Science & Technology

Reactivation of Deep Subsurface Microbial Community in Response to Methane or Methanol Amendment – Pauliina Rajala – Frontiers in Microbiology

Built environment

Nanoscale zero-valent iron/persulfate enhanced upflow anaerobic sludge blanket reactor for dye removal: Insight into microbial metabolism and microbial community – Fei Pan – Scientific reports

Probiotics / prebiotics

Achieving High Yield of Lactic Acid for Antimicrobial Characterization in Cephalosporin-Resistant Lactobacillus by the Co-Expression of the Phosphofructokinase and Glucokinase – Gong Y – Journal of Microbiology and Biotechnology

Phages and viruses

Inflammation boosts bacteriophage transfer between Salmonella spp.– Médéric Diard – Science

Bioinformatics

microclass: an R-package for 16S taxonomy classification – Kristian Hovde Liland – BMC Bioinformatics

Microbes in the news

Team finds new way that bacteria lay siege to neighboring cells by hijacking two factors involved in protein synthesis – Phys.Org

 

March 12, 2017

The first day of daylight saving time in the USA and if your Sunday morning started in a (relative) darkness just read about the viruses in the oceanic basement.  Then find out why yogurt can help your mood.  More interesting papers about the gut-brain connection, a microbiota-centric view of diseases of the upper gastrointestinal tract, microbiome and Type 1 & 2 diabetes, and a new method of detecting bacteria during root canal treatments.

General microbiome

Review: Calling All Hosts: Bacterial Communication In Situ – Jessica L. Cleary – Chem

Gut-Brain connection

The Association Between Temperament and Microbiota in Healthy Individuals: A Pilot Study  – Kim H – Psychosomatic medicine

Gut-brain actions underlying comorbid anxiety and depression associated with inflammatory bowel disease –  Aine Abautret-Daly -Acta Neuropsychiatrica

Human gut microbiome

A microbiota-centric view of diseases of the upper gastrointestinal tract – Gerardo Nardone- Gastroenterology & Hepatology

Review: Systems Biology of Metabolism: A Driver for Developing Personalized and Precision Medicine – Jens Nielsen – Cell Metabolism

Intestinal Microbiota in Type 2 Diabetes and Chronic Kidney Disease – A. Sabatino – Current Diabetes Reports

The intestinal proteome of diabetic and control children is enriched with different microbial and host proteins  – Elsa Pinto – Microbiology

Therapeutic efficacy of oral immunization with a non-genetically modified Lactococcus lactis-based vaccine CUE-GEM induces local immunity against Helicobacter pylori infection – Wei Liu – Applied Microbiology & Biotech

Water and extremophile microbiome

Viruses in the Oceanic Basement – OD Nigro -MBio

Models

A microengineered collagen scaffold for generating a polarized crypt-villus architecture of human small intestinal epithelium -Yuli Wang – Biomaterials

Built environment

Review: Microbiome involved in microbial electrochemical systems (MESs): Rijuta G Saratale- Chemosphere

Microbes in the news

Probiotic found in yogurt can reverse depression symptoms, Researchers at the University of Virginia School of Medicine finds

New method of detecting bacteria during root canal treatments 

March 4th, 2017

Events and jobs

Head, Microbiome Discovery Research – Johnson & Johnson

Multi-site human microbiome

Characterization of oral and gut microbiome temporal variability in hospitalized cancer patients – Jessica R. Galloway-Peña – Genome Medicine

Human gut microbiome

Childhood BMI in relation to microbiota in infancy and lifetime antibiotic use – K. Korpela – Microbiome

Animal experiments

Metaproteogenomics reveals taxonomic and functional changes between cecal and fecal microbiota in mouse – Alessandro Tanca – Frontiers in Microbiology

Animal microbiome

Cultivable gut bacteria provide a pathway for adaptation of Chrysolina herbacea to Mentha aquatica volatiles – Graziano Pizzolante – BMC Plant Biology

Gut bacteria oversee the special relationship between the green mint leaf beetle and watermint – BMC Series Blog

Effects of tussah immunoreactive substances on growth, immunity, disease resistance against Vibrio splendidus and gut microbiota profile of Apostichopus japonicus – Shuhui Ma – Fish & Shellfish Immunology

Community-Level Differences in the Microbiome of Healthy Wild Mallards and Those Infected by Influenza A Viruses – Holly H. Ganz – mSystems

The microbiome of the ant-built home: the microbial communities of a tropical arboreal ant and its nest – Jane Lucas – Ecosphere

*Perspective: Gut microbiome transmission in lizards – Timothy J. Colston – Molecular Ecology

Plant, root, and soil microbiome

Microbial communities in soil chronosequences with distinct parent material: the effect of soil pH and litter quality – Fernando D. Alfaro – Journal of Ecology

Water and extremophile microbiome

Volcanic ash supports a diverse bacterial community in a marine mesocosm – V. Witt – Geobiology

Methylamine as a Nitrogen Source for Microorganisms from a Coastal Marine Environment – Martin Taubert – Environmental Microbiology

Built environment

Response of microbial community structure to pre-acclimation strategies in microbial fuel cells for domestic wastewater treatment – Younghyun Park – Bioresource Technology

Food microbiology

Viable microbial loads on citrus carpoplane during packhouse processing and survival of foodborne pathogens in reconstituted postharvest fungicides – A. Gomba – Journal of Food Safety

Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage – Lysiane Duniere – BMC Microbiology

Probiotics / prebiotics

Microbiome dynamic modulation through functional diets based on pre- and probiotics (mannan-oligosaccharides and Saccharomyces cerevisiae) in juvenile rainbow trout (Oncorhynchus mykiss) – Ana Teresa Gonçalves – Journal of Applied Microbiology

Exploration of the effect of probiotics supplementation on intestinal microbiota of food allergic mice – Bo Yang – American Journal of Translational Research

Phages and viruses

Human norovirus binding to select bacteria representative of the human gut microbiota – Erin A. Almand – PLoS ONE

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

Bioinformatics

REPARATION: Ribosome Profiling Assisted (Re-)Annotation of Bacterial
genomes – Elvis Ndah – BioRxiv

Normalization and microbial differential abundance strategies depend upon data characteristics – Sophie Weiss – Microbiome

How conserved are the conserved 16S-rRNA regions? – Marcel Martinez-Porchas – PeerJ

Microbes in the news

Gut bacteria affect intestines and brain in IBS patients – Medical News Today

Intestinal Bacteria Alter Gut and Brain Function – Neuroscience News

Why Are People Sending Poop Through the Mail? For Their Health – GQ Magazine

Microbes on the market

Next-gen microbiome drugs are now on sale, should you buy them? – New Scientist

 

February 25, 2017

Insight into the role of gut microbiome lipid metabolites in central nervous system diseases. A role of invasive plants in altering the soil microbiome. Evidence that microbiome alterations in Crohn’s disease are not genetically based.

Events and jobs

Post-Doctoral Research Associate in immunology, microbiology, virology, and/or biochemistry – MRIGlobal, Gaithersburg, Maryland, USA

Research Scientist – Department of Microbiology – University of Illinois at Urbana-Champaign, USA

Part-Time Microbiology Instructor – Foothill-De Anza Community College District, California, USA

First Stage Researcher with background in environmental microbiology – Faculty of Biology, University of Warsaw, Poland

General microbiome

Altered antibiotic tolerance in anaerobic digesters acclimated to triclosan or triclocarban – Daniel E. Carey – Chemosphere

Antimicrobial Resistance and Molecular Characterization of Extended-Spectrum β-Lactamases and Other Escherichia coli Isolated from Food of Animal Origin and Human Intestinal Isolates – Krizman M – Journal of Food Protection

Human oral microbiome

Prospective, randomised, controlled study evaluating early modification of oral microbiota following admission to the intensive care unit and oral hygiene with chlorhexidine – Felipe Francisco Tuon – Journal of Global Antimicrobial Resistance

The potential effect of oral microbiota in the prediction of mucositis during radiotherapy for nasopharyngeal carcinoma -Xiao-Xia Zhu – EBioMedicine

Human urinary microbiome

*Special Issue Preface: Preface to the human microbiome in urologic health and disease – Daniel A. Shoskes – Annals of Translational Medicine

*Review: The mycobiome of the human urinary tract: potential roles for fungi in urology – A. Lenore Ackerman – Annals of Translational Medicine

Human vaginal microbiome

Longitudinal analysis of vaginal microbiota in women with recurrent vulvovaginal candidiasis – Ma X – Journal of Southern Medical University (Nan Fang Yi Ke Da Xue Xue Bao)

Human gut microbiome

The distinct features of microbial ‘dysbiosis’ of Crohn’s disease do not occur to the same extent in their unaffected, genetically-linked kindred – Umer Zeeshan Ijaz – PLOS

Randomised clinical trial: faecal microbiota transplantation for recurrent Clostridum difficile infection – fresh, or frozen, or lyophilised microbiota from a small pool of healthy donors delivered by colonoscopy – Z.D Jiang – Alimentary Pharmacology and Therapeutics

Gut-brain axis: Role of lipids in the regulation of inflammation, pain and CNS diseases – Russo R – Current Medicinal Chemistry

What roles do colon stem cells and gap junctions play in the left and right location of origin of colorectal cancers? – James E. Trosko – Journal of Cell Communication and Signaling

Contributions of the Interaction between Dietary Protein and Gut Microbiota to Intestinal Health – Ma N – Current Protein and Peptide Science

*Review: Dietary Fiber Gap and Host Gut Microbiota – Han M – Protein Peptide Letters

Structural Modulation of Gut Microbiota during Alleviation of Antibiotic-Associated Diarrhea with Herbal Formula – Weijie Lv – International Journal of Biological Macromolecules

Association of diverse bacterial communities in human bile samples with biliary tract disorders: a survey using culture and polymerase chain reaction-denaturing gradient gel electrophoresis methods – E. Tajeddin – European Journal of Clinical Microbiology & Infectious Disease

Immunomodulatory Effects of Lactobacillus plantarumLp62 on Intestinal Epithelial and Mononuclear Cells – Thalis Ferreira dos Santos – BioMed Research International

How to modulate gut microbiota: diet, pre-probiotics or antibiotics? – Ponziani FR – Minerva Gastroenterologica E Dietologica

* Review: AISF position paper on nonalcoholic fatty liver disease (NAFLD): Updates and future directions – Italian Association for the Study of the Liver (AISF), Lonardo A – Digestive and Liver Disease

Clostridium difficile infection in acute flares of inflammatory bowel disease: A prospective study -Harry Sokol – Digestive and Liver Disease

 Multi-site human microbiome

Porphyromonas gingivalis lipopolysaccharide induces pro-inflammatory adipokine secretion and oxidative stress by regulating Toll-like receptor-mediated signaling pathways and redox enzymes in adipocytes – Fanny Le Sage – Molecular and Cellular Endocrinology

Animal experiments

Impact of TIGECYCLINE versus other antibiotics on the fecal metabolome and on colonization resistance to CLOSTRIDIUM DIFFICILE in mice – Robin L.P. Jump – Pathological Immunology

Animal microbiome

Temporal Stability and the Effect of Transgenerational Transfer on Fecal Microbiota Structure in a Long Distance Migratory Bird – Jakub Kreisinger – Frontiers in Microbology

Convergent patterns in the evolution of mealybug symbioses involving different intrabacterial symbionts – Gitta Szabó – The ISME Journal

New roles in hemicellulosic sugar fermentation for the uncultivated Bacteroidetes family BS11 – Lindsey M Solden – The ISME Journal

Changes in rumen microbiota composition and in situ degradation kinetics during the dry period and early lactation as affected by rate of increase of concentrate allowance – K. Dieho – Journal of Dairy Science

Plant, root, and soil microbiome

Response of rhizosphere soil microbial to Deyeuxia angustifolia encroaching in two different vegetation communities in alpine tundra – Lin Li – Scientific Reports

Influence of phylogenetic conservatism and trait convergence on the interactions between fungal root endophytes and plants – Sevda Haghi Kia – The ISME Journal

Comparative fibre-degrading capacity in foals at immediate and late post-weaning periods – C. Faubladier – Cambridge Core

The effect of the source of microorganisms on adaptation of hydrolytic consortia dedicated to anaerobic digestion of maize silage – Krzysztof Poszytek – Anaerobe

Water and extremophile microbiome

Diversity of crude oil-degrading bacteria and alkane hydroxylase (alkB) genes from the Qinghai-Tibet Plateau – Haozhi Long – Environmental Monitoring and Assessment

Direct single-cell biomass estimates for marine bacteria via Archimedes’ principle – Nathan Cermak – The ISME Journal

Evidence for a role of viruses in the thermal sensitivity of coral photosymbionts – Rachel Ashley Levin – The ISME Journal

Use of plankton-derived vitamin B1 precursors, especially thiazole-related precursor, by key marine picoeukaryotic phytoplankton – Ryan W Paerl – The ISME Journal

Elevated temperature increases carbon and nitrogen fluxes between phytoplankton and heterotrophic bacteria through physical attachment – Nestor Arandia-Gorostidi – The ISME Journal

Warming and nutrient enrichment in combination increase stochasticity and beta diversity of bacterioplankton assemblages across freshwater mesocosms – Lijuan Ren – The ISME Journal

Integration of Metagenomic and Stable Carbon Isotope Evidence Reveals the Extent and Mechanisms of Carbon Dioxide Fixation in High-Temperature Microbial Communities – Ryan de Montmollin Jennings – Frontiers in Microbiology

Seasonal Variation in Abundance and Diversity of Bacterial Methanotrophs in Five Temperate Lakes – Md Sainur Samad – Frontiers in Microbiology

Predominance of Viable Spore-Forming Piezophilic Bacteria in High-Pressure Enrichment Cultures from ~1.5 to 2.4 km-Deep Coal-Bearing Sediments below the Ocean Floor – Jiasong Fang – Frontiers in Microbiology

Metagenomics and resistome

Co-occurrence of antibiotic and metal resistance genes revealed in complete genome collection – Li-Guan Li – The ISME

Metabolomics

Assessment of the bimodality in the distribution of bacterial genome sizes – Hyun S Gweon – The ISME Journal

Genome of ‘Ca. Desulfovibrio trichonymphae’, an H2-oxidizing bacterium in a tripartite symbiotic system within a protist cell in the termite gut – Hirokazu Kuwahara – The ISME Journal

A family of interaction-adjusted indices of community similarity – Thomas Sebastian Benedikt Schmidt – The ISME Journal

Refined experimental annotation reveals conserved corrinoid autotrophy in chloroform-respiring Dehalobacter isolates – Po-Hsiang Wang – The ISME Journal

Phylogenetic relationships among Staphylococcus aureus isolated from clinical samples in Mashhad, Iran – Farzad Khadem – Journal of Infection and Public Health

Closed-reference metatranscriptomics enables in planta profiling of putative virulence activities in the grapevine trunk-disease complex – Abraham Morales-Cruz – Molecular Plant Pathology

More microbes

Redox potential as a master variable controlling pathways of metal reduction by Geobacter sulfurreducens – Caleb E Levar – The ISME Journal

Coupled molecular and isotopic evidence for denitrifier controls over terrestrial nitrogen availability – Erin F E Lennon – The ISME Journal

Enhanced microbial electrosynthesis by using defined co-cultures – Jörg S Deutzmann – The ISME Journal

Temperature is a key factor in Micromonas–virus interactions – David Demory – The ISME Journal

Evolutionary convergence in experimental Pseudomonas populations – Peter A Lind – The ISME Journal

Microbes in the news

Are There Health Benefits To Exposing Our Immune Systems To Bacteria? – Forbes
Nutrition: Trust your gut instincts — whole grains are good for you – Los Angeles Daily News

There could be a surprising link between how people respond to a new cancer treatment and their microbiome – Lydia Ramsey – Business Insider

February 23, 2017

Today’s selection includes an interesting review on how bacteria keep their time. Long term ceftriaxon sodium usage alters gut microbiota and immune system. Clostridium perfringens toxin genes in the gut microbiota of autistic children. Taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic. Enjoy!

General microbiome

Distinct signatures of dental plaque metabolic byproducts dictated by periodontal inflammatory status. – Akito Sakanaka – Scientific Reports

*Review: Timing the day: what makes bacterial clocks tick? – Carl Hirschie Johnson – Nature Reviews Microbiology

Human urinary microbiome

Review: The female urinary microbiota, urinary health and common urinary disorders. – Linda Brubaker – Annals of Translational Medicine

Review: Questions and challenges associated with studying the microbiome of the urinary tract – Yige Bao – Annals of Translational Medicine

Review: The association between bacteria and urinary stones. – Andrew L. Schwaderer – Annals of Translational Medicine

Human nearly-sterile sites 

The Conserved Phylogeny of Blood Microbiome – Malay Bhattacharyya – Molecular Phylogenetics and Evolution

Human gut microbiome

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

Review: Gut microbiome-based medical methodologies for early-stage disease prevention – Jing-Zhang Wang – Microbial Pathogenesis

Review: Gut microbiome and chronic prostatitis/chronic pelvic pain syndrome. – Hans C. Arora – Annals of Translational Medicine

*Long-term use of ceftriaxone sodium induced changes in gut microbiota and immune system. – Yanjie Guo – Scientific Reports

Note Elies Bik: This study was not performed in humans but in a horrible rat model that can only be qualified as torture. This does not test for depression but for extreme stress. Should not have performed. Proceed with extreme caution. Variations in gut microbiota and fecal metabolic phenotype associated with depression by 16S rRNA gene sequencing and LC/MS-based metabolomics. – Meng Yu – Journal of Pharmaceutical and Biomedical Analysis

Specific inulin-type fructan fibers protect against autoimmune diabetes by modulating gut immunity, barrier function and microbiota homeostasis. – Kang Chen – Molecular Nutrition and Food Research

Gut microbiota and oxalate homeostasis. – Marguerite Hatch – Annals of Translational Medicine

Tryptophan: A gut microbiota-derived metabolites regulating inflammation. – Lucie Etienne-Mesmin –  World Journal of Gastrointestestinal Pharmacology

*Detection of Clostridium perfringens toxin genes in the gut microbiota of autistic children. – Sydney M. Finegold – Anaerobe

Animal experiments

Butyrate restores HFD induced adaptations in brain function and metabolism in mid-adult obese mice – Ilse A. C. Arnoldussen – International Journal of Obesity

Toxin-positive Clostridium difficile latently infect mouse colonies and protect against highly pathogenic C. difficile. – Lucie Etienne-Mesmin – Gut

Animal microbiome

Individual Signatures Define Canine Skin Microbiota Composition and Variability. – Anna Cuscó – Frontiers in Veterinary Science

Plant, root, and soil microbiome

Differential sharing and distinct co-occurrence networks among spatially close bacterial microbiota of bark, mosses and lichens‬‬. – Ines Aline Aschenbrenner – Molecular Ecology

Links between soil microbial communities and plant traits in a species-rich grassland under long-term climate change. – Lin Li – Ecology and Evolution

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

High-resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils. – Adrienne Narrowe – Environmental Microbiology

Food microbiology

Enhanced Control of Listeria monocytogenes by Enterococcus faecium KE82, a Multiple Enterocin–Producing Strain, in Different Milk Environments. – Elpinki Vandera – Journal of food protection

Probiotics / prebiotics

Review: Probiotics for prevention of urinary stones. – John C. Lieske – Annals of Translational Medicine

Review: Review of the mechanisms of probiotic actions in the prevention of colorectal cancer. – Sandra A. dos Reis – Nutrition Research

Phages and viruses

The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses – Lisa Zeigler Allen – mSystems

Microbes in the news 

The Future Of Skin Care: Lotions That Feed Our Microbiome

Collapse of Aztec society linked to catastrophic salmonella outbreak

Smart’ bacteria remodel their genes to infect our intestines

Smallest CRISPR So Far Comes from Food Poisoning Bacteria

Anitha’s non-microbiology picks 

An epigenetics gold rush: new controls for gene expression

Scientists discover 7 ‘Earthlike’ planets orbiting a nearby star

February 10, 2017

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

January 22, 2017

Events and Jobs

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

Quality Control Associate-MicrobiologyUS-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 AsthmaMarcos Pérez-Losada-PLOS One

Adherence of Pseudomonas aeruginosa to cystic fibrosis buccal epithelial cellsMeike 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 infantumStephen 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 infectionNabil 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 baboonsElizabeth 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 soilLateef 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. AlsaniusScientia 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 thermophilesPreeti 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, OmanKaitlin 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 siliconYanru Wang-Journal of Chemical Technology and Biotechnology

 Built Environment Microbiology

Developing Evidence-based Tools for Designing and Evaluating Hospital Inpatient RoomsXiaobo 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 DifferentiationJames T. Morton-Ecological and Evolutionary Science

Virus

Review: Virus–host interactions and their roles in coral reef health and diseaseRebecca 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 maysPeter Kämpfer-International Journal of Systematic and Evolutionary Microbiology

Microbes in News

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