Category Archives: Human oral

May 12, 2017

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Highlighted articles today bring some interesting news about bacteria. in the first one study of Lebreton et al. shed light on the evolutionary history of pathogens, which evolved nearly indestructible properties and have become leading causes of modern antibiotic-resistant infections in hospitals. In the second highlighted article Schnettger et al. discover a natural mechanism by which our cells kill the bacterium responsible for tuberculosis (TB)  – without the use of antibiotics, meaning that even antibiotic-resistant
strains could be eliminated.

Events and jobs

Postdoctoral researcher – nitrogen-fixing bacteria and cereals

Postdoctoral Research Fellowship in Marine Phycology

General microbiome

Global Phylogenetic Analysis Of Escherichia coli And Plasmids Carrying The mcr-1 Gene Indicates Bacterial Diversity But Plasmid Restriction – Sebastien Matamoros – bioRxiv

Predictive compound accumulation rules yield a broad-spectrum antibiotic – Michelle F. Richter – Nature

Tracing the Enterococci from Paleozoic Origins to the Hospital – François Lebreton – Cell

The Threat of Antimicrobial Resistance on the Human Microbiome – Lauren Brinkac- Microbial Ecology

Evolutionary Biology Needs Wild Microbiomes – Sarah M. Hird – Frontiers in Microbiology

Pregnancy and early life

Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome – Pia S. Pannaraj – JAMA Pediatr

Oral microbiome

The Antibacterial Effect of Additional Photodynamic Therapy in Failed Endodontically Treated Teeth: A Pilot Study – Mohammad Asnaashari – Journal of Lasers in Medical Science

Microbiota Analysis of Biofilms on Experimental Abutments Mimicking Dental Implants: An in Vivo Model – Berta Cortés-Acha – Journal of Periodontology

Human vaginal microbiome

Comparison of the vaginal environment in rhesus and cynomolgus macaques pre- and post-lactobacillus colonization – Gregory J. Daggett Jr – Journal of Medical Primatology

Human nearly-sterile sites (blood, organs, brain)

Active Trachoma Cases In The Solomon Islands Have Varied Polymicrobial Community Structures But Do Not Associate With Individual Non-Chlamydial Pathogens Of The Eye – Robert Butcher – bioRxiv

Human gut microbiome

Gut Microbiome Function Predicts Response to Anti-integrin Biologic Therapy in Inflammatory Bowel Diseases – Ashwin N. Ananthakrishnan – Cell Host & Microbiome

Current challenges in the treatment of severe Clostridium difficile infection: early treatment potential of fecal microbiota transplantation – Yvette H. van Beurden –
Therapeutic Advances in Gastroenterology

Review: Food additives, contaminants and other minor components: effects on human gut microbiota—a review – Paula Roca-Saavedra – Journal of Physiology and Biochemistry

Emulating Host-Microbiome Ecosystem of Human Gastrointestinal Tract in Vitro – Gun-Seok Park – Stem Cell Reviews and Reports

Animal experiments 

A Rab20-Dependent Membrane Trafficking Pathway Controls M. tuberculosis Replication by Regulating Phagosome Spaciousness and Integrity – Laura Schnettger – Cell host & Microbiome

Cooperating Commensals Restore Colonization Resistance to Vancomycin-Resistant Enterococcus faecium – Silvia Caballero – Cell Host & Microbe

Animal microbiome

Characterization of the juvenile green turtle (Chelonia mydas) microbiome throughout an ontogenetic shift from pelagic to neritic habitats – James T. Price – PLoS ONE

A Meta-Transcriptomics Survey Reveals Changes in the Microbiota of the Chinese Mitten Crab Eriocheir sinensis Infected with Hepatopancreatic Necrosis Disease – Huaishun Shen – Frontiers in Microbiology

Plant, root, and soil microbiome

Modifying And Reacting To The Environmental pH Drives Bacterial Interactions – Christoph Ratzke – bioRxiv

Differential responses of soil bacteria, fungi, archaea and protists to plant species richness and plant functional group identity – Sigrid Dassen – Molecular Ecology

Analysis of the bacterial strains using Biolog plates in the contaminated soil from Riyadh community – Fahad Abdullah M. Al-Dhabaan – Saudi Journal of Biological Sciences

Biosurfactant-producing microorganism Pseudomonas sp. SB assists the phytoremediation of DDT-contaminated soil by two grass species – Beibei Wang – Chemosphere

Water and extremophile microbiome 

Molecular Diversity of Sea Spray Aerosol Particles: Impact of Ocean Biology on Particle Composition and Hygroscopicity – Richard E. Cochran – Chem, Cell Press

The novel bacterial phylum Calditrichaeota is diverse, widespread and abundant in marine sediments and has the capacity to degrade detrital proteins – Ian P. G. Marshall – Environmental Microbiology Reports

Single-cell genomics reveals pyrrolysine-encoding potential in members of uncultivated archaeal candidate division MSBL1 – Yue Guan – Environmental Microbiology Reports

The Paradox Of Constant Oceanic Plastic Debris: Evidence For Evolved Microbial Biodegradation? – Ricard Sole – bioRxiv

Copper Pollution Increases the Resistance of Soil Archaeal Community to Changes in Water Regime – Jing LiYu-Rong Liu – Microbial Ecology

Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA) – Jessica M. Morrison – PLoS ONE

Nitrotoga is selected over Nitrospira in newly assembled biofilm communities from a tap water source community at increased nitrite loading – Marta Kinnunen – Environmental Microbiology

Unveiling microbial interactions in stratified mat communities from a warm saline shallow pond – Aurélien Saghaï – Environmental Micorbiology

Probiotics / prebiotics

Genotypic and phenotypic diversity of Lactobacillus rhamnosus clinical isolates, their comparison with strain GG and their recognition by complement system – Eija Nissilä – PLoS ONE

Bioinformatics

A Bayesian taxonomic classification method for 16S rRNA gene sequences with improved species-level accuracy – Xiang Gao – BMC Bioinformatics

gCoda: Conditional Dependence Network Inference for Compositional Data – Huaying Fang – Journal of Computational Biology

Effect of Lactobacillus rhamnosus HN001 and Bifidobacterium longum BB536 on the healthy gut microbiota composition at phyla and species level: A preliminary study – Marco Toscano – World Journal of Gastroenterology

Biotechnology

Review:Cyanobacterial metabolites as a source of sunscreens and moisturizers: a comparison with current synthetic compounds – Peyman Derikvand – European Journal of Phycology

Microbes in the news

Dramatic cooperation between two infectious bacteria revealed – Medicalxpress.com

Study finds bacteria in marine sponge produce toxic flame retardant-like compounds – Phys.org

Scientists Find Molecular ‘Key’ to Killing Hearty Bacteria – Extremetech.com

How our gut bacteria affect cancer risk and response to treatment – Theconversation.com

16S sequencing reveals differences between microbiomes in eyes, throat – Healio.com

Cosmetic Companies Now Develop Skin Care Products That Contain Live Bacteria To Treat Several Skin Problems – Sciencetimes.com

 

May 11, 2017

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Gram-negative gut bacteria and Toll-like receptor 4 linked to stimulation of cerebral cavernous malformations, suppression of a single gene by the microbiota promotes T cell survival in mice, quorum sensing negatively regulates toxin production in insect-associated bacteria and may facilitate stable colonization.

General microbiome

Lactobacillus plantarum producing a Chlamydia trachomatis antigen induces a specific IgA response after mucosal booster immunization – Katarzyna Kuczkowska – PLoS ONE

Human oral microbiome

The dental calculus metabolome in modern and historic samples – Irina M Velsko – bioRxiv

Insights of the dental calculi microbiome of pre-Columbian inhabitants from Puerto Rico – Tasha M Santiago-Rodriguez – PeerJ

Arginine Improves pH Homeostasis via Metabolism and Microbiome Modulation – M Angelo – Journal of Dental Research

Human gut microbiome

Faecal Microbiota Transplantation for Inflammatory Bowel Disease: A Systematic Review and Meta-analysis – Sudarshan Paramsothy – Journal of Crohn’s and Colitis

Significantly higher faecal counts of the yeasts candida and saccharomyces identified in people with coeliac disease – Joanna Harnett – Gut Pathogens

Research Highlight: Tooling up for microbiota research – Hugh Thomas – Nature Reviews Gastroenterology & Hepatology

Review: The gut microbiota: a key factor in the therapeutic effects of (poly)phenols – Juan Carlos Espín – Biochemical Pharmacology

Animal experiments

* Endothelial TLR4 and the microbiome drive cerebral cavernous malformations – Alan T Tang – Nature

* Microbiota promotes systemic T-cell survival through suppression of an apoptotic factor – Raymond Soto – PNAS

Bifidobacterium adolescentis IM38 ameliorates high-fat diet-induced colitis in mice by inhibiting NF-κB activation and lipopolysaccharide production by gut microbiota – Su-Min Lim – Nutrition Research

Tyrosine kinase inhibitors of Ripk2 attenuate bacterial cell wall-mediated lipolysis, inflammation and dysglycemia – Brittany M Duggan – Scientific Reports

Total fecal microbiota transplantation alleviates high-fat diet-induced steatohepatitis in mice via beneficial regulation of gut microbiota – Da Zhou – Scientific Reports

Animal microbiome

* Quorum Sensing Attenuates Virulence in Sodalis praecaptivus – Shinichiro Enomoto – Cell Host & Microbe

The digestive and defensive basis of carcass utilization by the burying beetle and its microbiota – Heiko Vogel – Nature Communications

Plant, root, and soil microbiome

Antibacterial producing actinomycetes from Extra Andean Patagonia – M S Vela Gurovic – Journal of Arid Environments

High-throughput sequencing reveals bacterial community composition in the rhizosphere of the invasive plant Flaveria bidentis – Z Song – Weed Research

Microbiomes associated with infective stages of root-knot and lesion nematodes in soil – Ahmed Elhady – PLoS ONE

Review: Plant-insect-pathogen interactions: a naturally complex ménage à trois – Flávia P Franco – Current Opinion in Microbiology

Review: CuO and ZnO Nanoparticles Modify Interkingdom Cell Signaling Processes Relevant to Crop Production: A Review – Anne Anderson – Journal of Agricultural and Food Chemistry

The phosphotransferase system gene ptsi in Bacillus cereus regulates expression of soda2 and contributes to colonization of wheat roots – Tantan Gao – Research in Microbiology

Water and extremophile microbiome

Review: Microbial processes driving coral reef organic carbon flow – Cynthia B Silveira – FEMS Microbiology Reviews

Diversity of biocrust-forming cyanobacteria in a semiarid gypsiferous site from Central Spain – Concha Cano-Díaz – bioRxiv

Probiotics/prebiotics

Probiotic Bifidobacterium longum NCC3001 Reduces Depression Scores and Alters Brain Activity: a Pilot Study in Patients With Irritable Bowel Syndrome – Maria Ines Pinto-Sanchez – Gastroenterology

Bioinformatics

dbOTU3: A new implementation of distribution-based OTU calling – Scott W Olesen – PLoS ONE

MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads – Thomas Nordahl Petersen – PLoS ONE

Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes – Sheng-Yong Niu – Briefings on Bioinformatics

Techniques

Review: Imaging mass spectrometry for metabolites: technical progress, multimodal imaging, and biological interactions – Ying-Ning Ho – WIREs Systems Biology and Medicine

Live-Cell Nanoscopy in Antiadhesion Therapy – Joan A Geoghegan – Trends in Microbiology

Low concentration DNA extraction and recovery using a silica solid phase – Constantinos Katevatis – PLoS ONE

More microbes

When more is less: Emergent suppressive interactions in three-drug combinations – Casey Beppler – BMC Microbiology

Effects of stochasticity and division of labor in toxin production on two-strain bacterial competition in Escherichia coli – Benedikt von Bronk – PLoS Biology

Biosynthesis of the antibiotic nonribosomal peptide penicillin in baker’s yeast – Ali R Awan – Nature Communications

Microbes in the news

Cosmetics: The next microbiome frontier – Marc S Reisch – Chemical and Engineering News

A defence mechanism that can trap and kill TB bacteria – Science Daily

Is IBS All In Your Mind? New Study Hints at Close Ties Between the Brain and the Gut – Jessica Wapner – Newsweek

Bacteria art

Scientists ‘paint’ with bacteria, create microbial masterpieces – Tom Ensey – wistv.com

May 1, 2017

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General microbiome

From Gene Annotation to Function Prediction for Metagenomics – F Sharifi – Protein Function Prediction

*Review: A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: implications for research on the pioneer infant microbiome – ME Perez-Muñoz – Microbiome

Collateral damage during antibiotic treatment of C. difficile infection in the aged host: insights into why recurrent disease happens – JH Shin – Gut Microbes

 

Human oral microbiome

Oral Treponeme Major Surface Protein: Sequence Diversity and Distributions within Periodontal Niches – M You – Molecular Oral Microbiology

 

Human gut microbiome

Reduction in fecal microbiota diversity and short-chain fatty acid producers in Methicillin-resistant Staphylococcus aureus infected individuals as revealed by PacBio single molecule, real-time sequencing technology – J Zhao – European Journal of Clinical Microbiology & Infectious Diseases

Gut Check: The evolution of an educational board game – DA Coil – PLoS Biology

From sensing to shaping microbiota: insights into the role of NOD2 in intestinal homeostasis and progression of Crohn’s Disease – I Balasubramanian – Am. J. Physiol. Gastrointest. Liver Physiol.

Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients – JR Bedorf – Genome Medicine

 

Animal microbiome

Progressive response of large intestinal bacterial community and fermentation to the stepwise decrease of dietary crude protein level in growing pigs – Y Peng – Applied Microbiology and Biotechnology

Repeated inoculation of cattle rumen with bison rumen contents alters the rumen microbiome and improves nitrogen digestibility in cattle – GO Ribeiro – Scientific Reports

Impact and consequences of polyphenols and fructooligosaccharide interplay on gut microbiota in rats – CJ Zheng – Food & Function

 

Plant, root and soil microbiome

Not just browsing: an animal that grazes phyllosphere microbes facilitates community heterogeneity – R O′ Rorke – ISME

Environmental Metabarcoding Reveals Contrasting Belowground and Aboveground Fungal Communities from Poplar at a Hg Phytomanagement Site –  A Durand – Microbial Ecology

Understory Dwarf Bamboo Affects Microbial Community Structures and Soil Properties in a Betula ermanii Forest in Northern Japan – B Kong – Microbes & Environments

Effects of root exudates on denitrifier gene abundance, community structure and activity in a micro-polluted constructed wetland – H Wu – Sci. Total Environ

Contribution of native phosphorous-solubilizing bacteria of acid soils on phosphorous acquisition in peanut (Arachis hypogaea L.) – M Pradhan – Protoplasma

 

Probiotics

Aggregation and Adhesion Activity of Lactobacilli Isolated from Fermented Products In Vitro and In Vivo: a Potential Probiotic Strain – S Grigoryan – Probiotics and Antimicrobial Proteins

 

Built environment microbiology

Three-stage anaerobic co-digestion of food waste and horse manure – J Zhang – Scientific Reports

 

Microbes in news

Undeveloped microbiomes make infants more prone to illness – R Saxena – ARS Technica

Being a guinea pig for science can be a long, slow slog – B Jefferson – SCPR

Pharma pollution fuels resistance to antibiotics, bacteria turns super bug – TNN – The Times of India

Cleaning up Iowa’s beaches – E Jordan – The Gazette

Augusta hospital adopts test to help find treatment for some patients quicker – S Turner – Aiken Standard

Only a superweapon can kill superbacteria, and humanity finally found it – W Nicol – Digital Trends

‘Lab in a cell’ helps crack code on chlamydia – R Shore –  Edmonton Journal

 

 

April 28, 2017

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Quite a few interesting articles and news about microbes: are we colonised with bacteria in utero? What is the relevance of cooperative interactions in microbial biotechnological processes? Microbe colonies  in space? Read more in today’s Microbiome Digest..

General microbiome

Variable habitat conditions drive species covariation in the human microbiota – Charles K. Fisher – PLOS

Pregnancy and early life

*Review: The prenatal gut microbiome: are we colonized with bacteria in utero? – R. W. Walker – Pediatric Obesity

Development of the cutaneous microbiome in the preterm infant: A prospective longitudinal study – Mohan Pammi – PLOS
 Human respiratory microbiome

A commensal streptococcus hijacks a Pseudomonas aeruginosa exopolysaccharide to promote biofilm formation – Jessica A. Scoffield – PLOS
Human oral microbiome

A genome-wide association study identifies nucleotide variants at SIGLEC5 and DEFA1A3 as risk loci for periodontitis – Matthias Munz – Human Molecular Genetics

Human nearly-sterile sites 

A case of polymicrobial anaerobic spondylodiscitis due to Parvimonas micra and Fusobacterium nucleatum – Leanne M Cleaver – JMM Case Reports

Human gut microbiome

Small Molecules from Deep within the Gut – Michael Ehrmann – ChemBioChem

Single Delivery of High-Diversity Fecal Microbiota Preparation by Colonoscopy Is Safe and Effective in Increasing Microbial Diversity in Active Ulcerative Colitis – Jacob Vinita – Inflammatory Bowel Diseases

Fecal Microbiota Transplantation for Refractory Clostridium difficile Colitis in Solid Organ Transplant Recipients – R. J. Friedman-Moraco – American Journal of Transplantation

Abundance profiling of specific gene groups using precomputed gut metagenomes yields novel biological hypotheses – Konstantin Yarygin – PLOS
Animal experiments

Neonatal mono-colonization of germ-free mice with Lactobacillus casei enhances casein immunogenicity after oral sensitization to cow’s milk – Matieny Aicha Maiga – Molecular Nutrition & Food Research

Shifts in the Gut Microbiota Composition Due to Depleted Bone Marrow Beta Adrenergic Signaling Are Associated with Suppressed Inflammatory Transcriptional Networks in the Mouse Colon – Tao Yang – Frontiers in Physiology

Animal microbiome

Viral gut metagenomics of sympatric wild and domestic canids, and monitoring of viruses: Insights from an endangered wolf population – Nádia Conceição-Neto – Ecology and Evolution

The environmental and host-associated bacterial microbiota of Arctic seawater-farmed Atlantic salmon with ulcerative disorders – C Karlsen – Journal of Fish Diseases

Plant, root, and soil microbiome

Soil aggregation and associated microbial communities modify the impact of agricultural management on carbon content – Pankaj Trivedi – Environmental Microbiology

In-depth characterization of bacterial and archaeal communities present in the abandoned Kettara pyrrhotite mine tailings (Morocco) – Odile Bruneel –  Extremophiles

Water and extremophile microbiome 

Geochemistry and microbial diversity of cave waters in the gypsum karst aquifers of Emilia Romagna region, Italy – Ilenia M. D’Angeli – Science of The Total Environment
Probiotics / prebiotics

Characterization, identification and application of lactic acid bacteria isolated from Leymus chinensis silage – Qing Zhang – Grassland Science
Biotechnology

*Review: Cooperation in microbial communities and their biotechnological applications – Matteo Cavaliere – Environmental Microbiology

Techniques

MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data – Achal Dhariwal – Nucleic Acid Research

Microbes in the news

Adaptive Phage Therapeutics – Terminally Ill Patient Successfully Treated With Bacteriophage – BioSpace

Research Links Microbiome Makeup To Remission in Pediatric Crohn’s – Gastroenterology & Endoscopy News

NASA Astronauts Are Close to Identifying Unknown Microbe Colonies That Grow in Space – Sciencealert.com

 

April 27, 2017

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An exploration of fish as an alternative to mice for models of host-microbe interactions, a review on what we can learn from Bacteroides about the gut micriobiome, a news story on successful phage therapy for a multi drug resistant infection.

Human oral microbiome

The human oral microbiome is shaped by shared environment rather than genetics: evidence from a large family of closely-related individuals – Liam Shaw – bioRxiv

Human gut microbiome

* Review: An insider’s perspective: Bacteroides as a window into the microbiome – Aaron G Wexler – Nature Microbiology

Gut Microbiota: Small Molecules Modulate Host Cellular Functions – Jacob M. Luber – Current Biology

Fecal microbial characterization of hospitalized patients with suspected infectious diarrhea shows significant dysbiosis – Tzipi Braun – Scientific Reports

Animal experiments

Supplemental feeding of a gut microbial metabolite of linoleic acid, 10-hydroxy-cis-12-octadecenoic acid, alleviates spontaneous atopic dermatitis and modulates intestinal microbiota in NC/nga mice – Hiroko Kaikiri – International Journal of Food Sciences and Nutrition

Microbiota-activated CD103+ DCs stemming from microbiota adaptation specifically drive γδT17 proliferation and activation – Chris Flemming – Microbiome

Radiation induces proinflammatory dysbiosis: transmission of inflammatory susceptibility by host cytokine induction – Shiran Gerassy-Vainberg – Gut

Animal microbiome

Tick-Pathogen Interactions and Vector Competence: Identification of Molecular Drivers for Tick-Borne Diseases – José de la Fuente – Frontiers in Cellular and Infection Microbiology

Plant, root, and soil microbiome

Review: Managing the plant microbiome for biocontrol fungi: examples from Hypocreales – Ryan M Kepler – Current Opinion in Microbiology

Occurrence of perchlorate in groundwater, paired farmland soil, lettuce, and rhizosphere soil from Chengdu, China – Yulu Tang – Environmental Science: Processes & Impact

Water and extremophile microbiome

The Trichodesmium consortium: conserved heterotrophic co-occurrence and genomic signatures of potential interactions – Michael D Lee – The ISME Journal

Bringing methanotrophy in rivers out of the shadows – Felicity Shelley – Limnology and Oceanography

Rainfall increases the abundance of antibiotic resistance genes within a riverine microbial community – Andrea Di Cesare – Environmental Pollution

Impact of selectively enriched microbial communities on long-term fermentative biohydrogen production – R Kanniah Goud – Bioresource Technology

Probiotics/prebiotics

Perspective: Next-generation probiotics: the spectrum from probiotics to live biotherapeutics – Paul W O’Toole – Nature Microbiology

Molecular assessment of the fecal microbiota in healthy cats and dogs before and during supplementation with fructo-oligosaccharides (FOS) and inulin using high-throughput 454-pyrosequencing – Jose F Garcia-Mazcorro – PeerJ

Bioinformatics

Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments – Arghya Mukherjee – Scientific Reports

Techniques

Faecal volatile organic compounds analysis using field asymmetric ion mobility spectrometry: non-invasive diagnostics in paediatric inflammatory bowel disease – Nora van Gaal – Journal of Breath Research

* Teleosts as Model Organisms to Understand Host-Microbe Interactions – Emily A Lescak – Journal of Bacteriology

Synthetic and analytical strategies for the quantification of phenyl-γ-valerolactone conjugated metabolites in human urine – Nicoletta Brindani – Molecular Nutrition & Food Research

More microbes

Species ecological similarity modulates the importance of colonization history for adaptive radiation – Jiaqi Tan – International Journal of Organic Evolution

Interaction of Bacterial Membrane Vesicles with Specific Species and Their Potential for Delivery to Target Cells – Yosuke Tashiro – Frontiers in Microbiology

Microbes in the news

Phage Therapy Saves Patient from Drug-Resistant Microbes – Genetic Engineering & Biotechnology News

Chronic fatigue syndrome linked to imbalanced microbiome – EurekAlert

Komodo Dragon Blood Could Become Tool in Fight Against Bacteria – Elizabeth Pratt – Healthline

Researchers move closer to preventing frost damage in vineyards by managing bacteria on the vines – Greg Northcutt – Western FarmPress

Underwater volcano eruptions allow new bacteria to take over seafloor – Lisa-Ann Lee – New Atlas

Microbes on the market

Taconic Biosciences Expands Microbiome Product and Service Platform – GlobeNewswire

Bacteria and art

This Art Exhibition Is Made From Bacteria, Live Insects And Human Sweat – Ryan F Mandelbaum – Gizmodo Australia

Art Made with CRISPR Aims to Raise Awareness of Antibiotic Resistance – Clara Rodríguez Fernández – Labiotech.eu

Amy’s non-microbiology picks

Microscopy: A larger palette for biological imaging – Charles H Camp Jr – Nature

April 24, 2017

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General Microbiome

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

Dietary High Zinc Oxide Modulates the Microbiome of Ileum and Colon in Weaned Piglets – Ting Yu – Frontiers in Microbiology

Clostridium difficile colonizes alternative nutrient niches during infection across distinct murine gut environments –  Matthew L Jenior – BioRxiv

Review: Strategies to promote abundance of Akkermansia muciniphila, an emerging probiotics in the gut, evidence from dietary intervention studies – Kequan Zhou – Journal of Functional Foods

Protective effects of milk fermented by Lactobacillus plantarum B7 from Brazilian artisanal cheese on a Salmonella enterica serovar Typhimurium infection in BALB/c mice – Journal of Functional Foods

 

Pathogens

Molecular Demonstration of a Pneumocystis Outbreak in Stem Cell Transplant Patients: Evidence for Transmission in the Daycare Center – Frontiers in Microbiology

A New Rabbit-skin Model to Evaluate Protective Efficacy of Tuberculosis Vaccines – Xun Liu – Frontiers in Microbiology

Molecular epidemiology and antibiotic resistance profiles of methicillin-resistant Staphylococcus aureus strains in a tertiary hospital in China – Haishen Kong – Frontiers in Microbiology

 

Environmental Microbiology

Microbial community assembly differs by mineral type in the rhizosphere – Thea Whitman – BioRxiv

Interaction between DAPG and HCN producing Pseudomonas brassicacearum LBUM300 and Clavibacter michiganensis subsp. michiganensis in the rhizosphere of tomato – Applied Environmental Microbiology

Nitrogen-Fixing Populations Of Planctomycetes And Proteobacteria Are Abundant In The Surface Ocean – Tom O. Delmont – BioRxiv

Bacterial communities in boreal forest mushrooms are shaped both by soil parameters and host identity – Mari Pent – Frontiers in Microbiology

 

Genomics

Isoprenoid Pyrophosphate-Dependent Transcriptional Regulation of Carotenogenesis in Corynebacterium glutamicum – Nadja A. Henke – Frontiers in Microbiology

Whole genome sequencing of 7 strains of Staphylococcus lugdunensis allows identification of mobile genetic elements – Xavier Argemi – Genome Biology and Evolution

Pooled CRISPR interference screens enable high-throughput functional genomics study and elucidate new rules for guide RNA library design in Escherichia coli – Tianmin Wang – BioRxiv

 

Evolution

Tunneling through time: Horizontal gene transfer constrains the timing of methanogen evolution –  Joanna M. Wolfe – BioRxiv

 

Bioinformatics

AliTV-interactive visualization of whole genome comparisons – Markus J. Ankenbrand – PeerJ (not peer-reviewed)

TaxaSE: Exploiting evolutionary conservation within 16S rDNA sequences for enhanced taxonomic annotation – Ali Z Ijaz – PeerJ (not peer-reviewed)

 

Other

Preprinting Microbiology – Patrick D Schloss – BioRxiv

 

Non – Microbiology picks

News: Scientists across the world take to the streets to demand freedom from political interference – The Telegraph (via Yahoo News)

Human umbilical cord plasma proteins revitalize hippocampal function in aged mice – Joseph M. Castellano –  Nature

 

April 14, 2017

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Quite a number of biofilms based reviews for today’s digest. Local adaptation in natural microbial communities. Bacterial community varies along the natural water balance gradient in the Tibetan Plateau.

Events and jobs

Senior Program Officer  – The Paul G. Allen Frontiers Group – Seattle, WA, United States

 

General microbiome

Culturomics: A New Kid on the Block of OMICS to Enable Personalized Medicine – ME Kambouris – Omics

Introduction: microbial local adaptation: insights from natural populations, genomics and experimental evolution – T Giraud – Molecular Ecology

*Review: Central venous catheters and biofilms: where do we stand in 2017? – M Gominet – APMIS

 

Human oral microbiome

*Review: Dental biofilm infections – an update – T Larsen – APMIS

*Review: Microbiological diagnosis of device-related biofilm infections – Y Xu – APMIS

*Review: Biofilms in orthopedic infections: a review of laboratory methods – AC Dibartola – APMIS

 

Human vaginal microbiome

Vaginal lactic acid elicits an anti-inflammatory response from human cervicovaginal epithelial cells and inhibits production of pro-inflammatory mediators associated with HIV acquisition – AC Hearps – Mucosal Immunology

*Review: Chronic urinary tract infections in patients with spinal cord lesions – biofilm infection with need for long-term antibiotic treatment – N Tofte – APMIS

 

Human gut microbiome

Curcuminoid Demethylation as an Alternative Metabolism by Human Intestinal Microbiota – S Burapan – Journal of Agricultural and Food Chemistry

Inflammasomes and intestinal inflammation – N Zmora – Mucosal Immunology

Gut Microbial Diversity in Antibiotic-Naive Children After Systemic Antibiotic Exposure: A Randomized Controlled Trial – T Doan – Clinical Infectious Diseases

 

Animal microbiome

Fish oil, lard and soybean oil differentially shape gut microbiota of middle-aged rats – He Li – Scientific Reports

Co-diversification of gastrointestinal microbiota and phylogeny in passerines is not explained by ecological divergence – L Kropáčková – Molecular Ecology

 

Plant, root and soil microbiome

Responses of denitrifying bacterial communities to short-term waterlogging of soils – Y Wang – Scientific Reports

Distinct Soil Microbial Communities in habitats of differing soil water balance on the Tibetan Plateau – Y Li – Scientific Reports

Convergence and contrast in the community structure of Bacteria, Fungi and Archaea along a tropical elevation-climate gradient – KG Peay – FEMS Microbiology Ecology

Continuous production of indole-3-acetic acid by immobilized cells of Arthrobacter agilis – M Ozdal – 3 Biotech

*Review: Agriculturally important microbial biofilms: Present status and future prospects – K Velmourougane – Journal of Basic Microbiology

 

Water and extremophile

Temporal abundance and activity trends of vinyl chloride (VC)-degrading bacteria in a dilute VC plume at Naval Air Station Oceana – Y Liang – Environmental Science and Pollution Research International

Spatial variation in bacterial community in natural wetland-river-sea ecosystems – H Zhang – Journal of Basic Microbiology

Bioremediation Management Reduces Mass Discharge at a Chlorinated DNAPL Site – BR Baldwin – Groundwater Monitoring & Remediation

 

Techniques

Enhancing Multiplex Genome Editing by Natural Transformation (MuGENT) via inactivation of ssDNA exonucleases – TN Dalia – bioRxiv

An Efficient Moments-Based Inference Method for Within-Host Bacterial Infection Dynamics – D Price – bioRxiv

 

More microbes

Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle – S Mandal De – BMC Microbiology

Microbiome yarns: microbiomology of winter rosy face – K Timmis – Microbial Biotechnology

*Review: In vitro studies evaluating the effects of biofilms on wound-healing cells: a review – KR Kirker – APMIS

Vector competence and innate immune responses to dengue virus infection in selected laboratory and field-collected Stegomyia aegypti (= Aedes aegypti) – IM Serrato – Medical and Veterinary Entomology

*Review: Antibiotic treatment of biofilm infections – O Ciofu – APMIS

Microenvironmental characteristics and physiology of biofilms in chronic infections of CF patients are strongly affected by the host immune response – PØ. Jensen – APMIS

 

Microbes in news

To see the unseen: ‘Microbiomes’ show explores the common ground between arts, science – M McINALLY – Gazette-Times

Unprotected sex may disrupt the microbiome in vagina – J Hamzelou – New Scientist

Sol-gel-based stainless steel surface reduces fouling and biofilm formation during milk pasteurization – J Cornall- Dairy Reporter

Gut Microbes Contribute to Age-Associated Inflammation in Mice – A Olena – The Scientist

Microbiome Plus+ Gastrointestinal: New Probiotic Supplement Proven to Increase Vitamin D Levels While Lowering Cholesterol – Military News – Miltech

OPINION: How probiotics research is taking us to the next level of understanding – M Cunningham – Food Navigator

New synthetic peptide promotes wound healing – T Sandle – Digital Journal

Air Pollution Might Make Dangerous Bacteria Harder to Kill – V Greenwood – The Atlantic

Researchers studying how to disrupt bacteria to better treat infections – Phys.org

Bacteria with a bias – K Zehr – UNM HSC Newsbeat

Glowing bacteria could help in landmine cleanup efforts – D Quick – New Atlas

Trump budget plan could sink Shore beaches bacteria reports – R Zimmer – Asbury Park Press

How genetically-altered E.coli strain can kill dangerous bone-eating superbug Pseudomonas aeruginosa – B Crouch – The Advertiser

Study on lactic acid bacteria from kimchi sheds light on treatment of atopic dermatitis – The Korea Herald

This strain of probiotic bacteria treats and protects against anxiety, stress and inflammation – St. Joseph’s Healthcare

 

April 12, 2017

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A pretty broad Digest today, with a promising phylogenetic marker for fungal community studies, a new issue of the Journal of Microbiological Methods, and several news pieces, including one about brain stimulating for weight loss.

Jobs

Microbiology Technician – Lonza America Inc

BMS Microbiology – South West England

General microbiology

*A new promising phylogenetic marker to study the diversity of fungal communities: the GLYCOSIDE HYDROLASE 63 gene – L. Pérez-Izquierdo – Molecular Ecology Resources

pH-Controlled Cerium Oxide Nanoparticle Inhibition of Both Gram-Positive and Gram-Negative Bacteria Growth – Ece Alpaslan – Scientific Reports

Human oral microbiome

The probiotics in dentistry: a narrative review – A.M. Pujia – European Review for Medical and Pharmacological Sciences

Human ear microbiome

Microbiomes of the normal middle ear and ears with chronic otitis media – Shujiro B. Minami – Laryngoscope

Human gut microbiome

PrePrint: Household triclosan and triclocarban exposure impacts the adult intestinal microbiome but not the infant intestinal microbiome – Jessica V. Ribado – bioRxiv

Corrigendum: Antibiotic treatment at delivery shapes the initial oral microbiome in neonates – Luisa F. Gomez-Arango – Scientific Reports

Seven versus 10 days antibiotic therapy for culture-proven neonatal sepsis: A randomised controlled trial – Smriti Rohatgi – Journal of Paediatrics and Child Health

Animal experiments

Metabolic adaptation to the aqueous leaf extract of Moringa oleifera Lam.-supplemented diet is related to the modulation of gut microbiota in mice – Xiaoyu Gao – Applied Microbiology and Biotechnology

Bioactive Molecule from Streptomyces sp Mitigates MDR Klebsiella pneumoniae in Zebrafish Infection Model – Lalitha Cheepurupalli – Frontiers in Microbiology

Animal microbiome

Cassava foliage affects the microbial diversity of Chinese indigenous geese caecum using 16S rRNA sequencing – Mao Li – Scientific Reports

Plant, root and soil microbiome

Biological Control of Bacterial Fruit Blotch of Watermelon Pathogen (Acidovorax citrulli) with Rhizosphere Associated Bacteria – Mahesh Adhikari – The Plant Pathology Journal

Book Chapter: Ecological Restoration Techniques for Management of Degraded, Mined-Out Areas and the Role Played by Rhizospheric Microbial Communities – Prashant Pant & Pratibha Pant – Green Technologies and Environmental Sustainability

Abstract: Consistently inconsistent drivers of patterns of microbial diversity and abundance at macroecological scales – Hendershot JN – Ecology

Population densities of indigenous Acidobacteria change in the presence of plant growth promoting rhizobacteria (PGPR) in rhizosphere – Sadaf Kalam – Journal of Basic Microbiology

Water and extremophile microbiome

Abstract: Salinity and macrophyte drive the biogeography of the sedimentary bacterial communities in a brackish water tropical coastal lagoon – P. Behera – Science of the Total Environment

PDF: The Effects of Soil Environmental Factors on the Colonization of Marine Biocontrol Bacteria – Zenghai Bao – Journal of Residuals Science & Technology

Book chapter: New Generation DNA Sequencing (NGS): Mining for Genes and the Potential of Extremophiles – Bhagwan Rekadwad & Juan M. Gonzalez – Microbial Applications Vol.1

Effects of short-term warming and altered precipitation on soil microbial communities in alpine grassland of the Tibetan Plateau – Kaoping Zhang – Frontiers in Microbiology

Effects of toxic organic flotation reagent (aniline aerofloat) on an A/O submerged membrane bioreactor (sMBR): Microbial community dynamics and performance – Weixiong Lin – Ecotoxicology and Environmental Safety

Environmental degradation results in contrasting changes in the assembly processes of stream bacterial and fungal communities – Heikki Mykrä – Oikos

Microbes in space

Transcriptomic changes in an animal-bacterial symbiosis under modeled microgravity conditions – Giorgio Casaburi – Scientific Reports

Phages and viruses

iTRAQ-based Proteomic Analysis of Porcine Kidney Epithelial PK15 cells Infected with Pseudorabies virus – Songbai Yang – Scientific Reports

Technology

Release of a new issue of the Journal of Microbiological Methods, with various technical articles of potential interest.

Bioinformatics

The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism – Garrett W. Birkel – BMC Bioinformatics

IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models – Chao Ye – Scientific Reports

Quantifying uncertainty of taxonomic placement in DNA barcoding and metabarcoding – Panu Somervuo – Methods in Ecology and Evolution

Microbes in the news

DIRTY PINTS One in three pints served in pubs use ‘bad’ bacteria-filled beer because landlords aren’t cleaning the pumps properly – Sara Kamouni – The Sun

Melioidosis: More cases of potentially fatal bacterium from NT dirt emerge – Eleni Rousos – ABC News

*Magnetic brain stimulation causes weight loss – Tim Sandle – Digital Journal

5 Ways to Ruin Wine Before It’s Even Bottled – Laura Burgess – Vine Pair

A public health failure – Otago Daily Times

Study to develop faster detection of antibiotic resistance – Scoop

Microbes on the market

Superbugs receive a dual drug attack – Kate Dearling – The Badger Online

Breast Milk Helps In The Growth Of Microbes Beneficial To Human Colon, Best For Babies Too – Jezreel Smith – The Science Times

April 11, 2017

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In today’s Microbiome Digest the first interesting study comes not from bacteria but from virus domain. Examining the genomes within a sample from a wastewater treatment plant in Austria, Schulz et al. assembled a previously undiscovered giant virus genome with more genes encoding components of the protein translation machinery than in other giant viruses. The second highlighted  study introduces new oleaginous microalga as a new potential source of compounds for biotechnological applications.

Events and jobs

QC Microbiology Analyst – Dublin, Ireland

Assistant Lecturer in Microbiology – Sligo, Ireland

General microbiome

The genetics of human longevity: an intricacy of genes, environment, culture and microbiome – Serena Dato – Mechanisms of Ageing and Development

Pregnancy and early life

Correlation between early-life regulation of the immune system by microbiota and allergy development – Thomas Gensollen – Journal of Allergy and Clinical Immunology

Microbial Community Assembly And Metabolite Profile Of The Gut Microbiome In Extremely Low Birthweight Infants – Stephen Wandro – bioRxiv

Molecular Insight into Evolution of Symbiosis between Breast-Fed Infants and a Member of the Human Gut Microbiome Bifidobacterium longum – Chihaya Yamada – Cell Chemical Biology

A Comparative Study of Oral Microbiota in Infants with Complete Cleft Lip and Palate or Cleft Soft Palate – Agnieszka Machorowska-Pieniążek – BioMed Research International

Effect of probiotics on digestibility and immunity in infants: A study protocol for a randomized controlled trial – Lingli Xiao – Medicine

Human respiratory microbiome

Airway microbial dysbiosis in asthmatic patients: A target for prevention and treatment? – Kian Fan Chung – Journal of Allergy and Clinical Immunology

Oral microbiome

Measuring nitrate reductase activity from human and rodent tongues – Khandaker Ahtesham Ahmed – Nitric Oxide

Streptococcal adhesin SspA/B analogue peptide inhibits adherence and impacts biofilm formation of Streptococcus mutans – Tatsuro Ito – PLOSOne

Characterization of growth inhibition of oral bacteria by sophorolipid using a microplate-format assay – Daniel K.Y. Solaiman – Journal of Microbiological Methods

Salivary microbiome of an urban Indian cohort and patterns linked to subclinical inflammation  – Aneesha Acharya – Oral Diseases

Second Era of OMICS in Caries Research: Moving Past the Phase of Disillusionment – M.M. Nascimento – Journal of Dental Research

Human skin microbiome

Bacterial communities on facial skin of teenage and elderly Thai females – Naraporn Somboonna – Archives of Microbiology

Skin microbiome and mast cells – Satomi Igawa – Translational Research

Human vaginal microbiome
Microbial profiling of cpn60 universal target sequences in artificial mixtures of vaginal bacteria sampled by nylon swabs or self-sampling devices under different storage conditions – John J. Schellenberg – Journal of Microbiological Methods

‘Anaerococcus mediterraneensis’ sp. nov., a new species isolated from human female genital tract – K. Diop – New Microbes and New Infections

Human gut microbiome

Functional relevance of microbiome signatures: The correlation era requires tools for consolidation – Ludovica F. Buttó – Journal of Allergy and Clinical Immunology

Physiochemical Tuning of Potent Escherichia coli Anti-Adhesives by Microencapsulation and Methylene Homologation – Dimitri Alvarez Dorta – ChemMedChem

Gut microbiota functions: metabolism of nutrients and other food components –  Ian Rowland – European Journal of Nutrition

Evaluation of the impact of gut microbiota on uremic solute accumulation by a CE-TOFMS–based metabolomics approach – Eikan Mishima – Kidney International

Animal experiments

Starch-enriched diet modulates the glucidic profile in the rat colonic mucosa – Maria Gabriella Gabrielli – European Journal of Nutrition

The influence of diet on the grass carp intestinal microbiota and bile acids – Jing Zhang – Aquaculture Research

Characterization of the Fecal Bacterial Microbiota of Healthy and Diarrheic Dairy Calves – D.E. Gomez – Journal of Veterinary Internal Medicine

Gut Microbiota Modulation Attenuated the Hypolipidemic Effect of Simvastatin in High-Fat/Cholesterol-Diet Fed Mice – Xuyun He – Journal of Proteome Research

 

Animal microbiome

Host Genotype and Microbiota Contribute Asymmetrically to Transcriptional Variation in the Threespine Stickleback Gut – Clayton M. Small – Genome Biology and Evolution

The structured diversity of specialized gut symbionts of the New World army ants – Piotr Łukasik – Molecular Ecology

Microbial composition of spiny ants (Hymenoptera: Formicidae: Polyrhachis) across their geographic range – Manuela Oliveira Ramalho – BMC Evolutionary Biology

Plant, root, and soil microbiome

Isolation, identification, and environmental adaptability of heavy-metal-resistant bacteria from ramie rhizosphere soil around mine refinery – Jie Jiang – Biotech

Autogenic succession and deterministic recovery following disturbance in soil bacterial communities – Stephanie D. Jurburg – Scientific Reports

Microbial community response to hydration-desiccation cycles in desert soil – Adam Šťovíček – Scientific Reports

Water and extremophile microbiome

Development of an economical, autonomous pHstat system for culturing phytoplankton under steady state or dynamic conditions – Rachel L. Golda – Journal of Microbiological Methods

Microbial Diversity of Browning Peninsula, Eastern Antarctica Revealed Using Molecular and Cultivation Methods – Sarita Pudasaini – Frontiers in Microbiology

Subduction zone forearc serpentinites as incubators for deep microbial life – Oliver Plümper – PNAS

Ferrous iron- and ammonium-rich diffuse vents support habitat-specific communities in a shallow hydrothermal field off the Basiluzzo Islet (Aeolian Volcanic Archipelago) – G. Bortoluzzi – Geobiology

Microbial biotechnology

Characterization of a Chlorophyta microalga isolated from a microbial mat in Salar de Atacama (northern Chile) as a potential source of compounds for biotechnological applications – Gladys Hayashida – Phycological Research

Real-time iTRAQ-based proteome profiling revealed the central metabolism involved in nitrogen starvation induced lipid accumulation in microalgae – Vineeta Rai – Scientific Reports

Food microbiology

Microbial communities associated with the anthropogenic, highly alkaline environment of a saline soda lime, Poland – Agnieszka Kalwasińska – Antonie van Leeuwenhoek

Probiotics / prebiotics

Genome Sequences of Potential Probiotic Lactobacillus rhamnosus Isolates from Human Infants – Jason W. Arnold – Genome Announcements

Phages and viruses

Review: Phage injection establishes CRISPR immunity – Shimona Starling – Nature Reviews Microbiology

Giant viruses with an expanded complement of translation system components – Frederik Schulz – Science

Bioinformatics

The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism – Garrett W. Birkel – BMC Bioinformatics

Techniques

Identification of microorganisms grown on chromogenic media by MALDI-TOF MS – Petra Lüthje – Journal of Microbiological Methods

The impact of fecal sample processing on prevalence estimates for antibiotic-resistant Escherichia coli – Sylvia Omulo – Journal of Microbiological Methods

Chapter in the book: New Generation DNA Sequencing (NGS): Mining for Genes and the Potential of Extremophiles – Bhagwan Rekadwad – Microbial Applications Vol.1

Novel micelle PCR-based method for accurate, sensitive and quantitative microbiota profiling – Stefan A. Boers – Scientific Reports
Microbes in the news 

Bacteria to the Future – Mizzou News (University of Missouri)

April 5, 2017

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Today’s digest features interesting research on the dynamic microbiome evolution in social bees and the alteration in quorum Sensing, cell motility, stress Response, and carbohydrate metabolism  of gut microbiome by the organophosphate pesticide Diazinon. Low dose penicillin in early life can induce long term changes in mice gut microbiota, brain cytokines and behavior. Interesting reviews on the microbiome and human biology, and role of gut microbiota in the development of hypertension, including that associated with obstructive sleep apnea.

General microbiome

*Review: The Microbiome and Human Biology – Rob Knight – Annual Review of Genomics and Human Genetics

*Dynamic microbiome evolution in social bees – Waldan K. Kwong – Science Advances

Anaerobic Bacterial Fermentation Products Increase Tuberculosis Risk in Antiretroviral-Drug-Treated HIV – Leopoldo N. Segal – Cell Host & Microbe

Pregnancy and early life

Vancomycin treatment is a risk factor for vancomycin-nonsusceptible Staphylococcus capitis sepsis in preterm neonates – Marine Butin – Clinical Microbiology and Infection

Human oral microbiome

Relative abundance of total subgingival plaque-specific bacteria in salivary microbiota reflects the overall periodontal condition in patients with periodontitis – Shinya Kageyama – Plos One

Review: Biofilm over teeth and restorations: What do we need to know? – Nancy J. Lin – Dental Materials

Human skin microbiome

Cutaneous Burn Injury Promotes Shifts in the Bacterial Microbiome in Autologous Donor Skin: Implications for Skin Grafting Outcomes – Jennifer K. Plichta – Shock

Human gut microbiome

Review : The gut microbiota: a possible factor influencing systemic lupus erythematosus – Hadar Neuman – Current Opinion in Rheumatology

*Organophosphate Diazinon Altered Quorum Sensing, Cell Motility, Stress Response, and Carbohydrate Metabolism of Gut Microbiome – Bei Gao -Toxicological Sciences

Baseline gut microbiota predicts clinical response and colitis in metastatic melanoma patients treated with ipilimumab – N. Chaput – Oncology

*Review: Obstructive Sleep Apnea-Induced Hypertension: Role of the Gut Microbiota – David J. Durgan – Current Hypertension Reports

Review: The Gut Microbiota and Alzheimer’s Disease – Chunmei Jiang – Journal of Alzheimer’s Disease

Fecal Microbiota Transplantation

Fecal Microbiota Transplantation in Patients with Blood Disorders Inhibits Gut Colonization with Antibiotic-Resistant Bacteria: Results of a Prospective, Single-Center Study – Jaroslaw Bilinski – Clinical Infectious Diseases

Animal microbiome

Multi-Omics Analysis Reveals a Correlation between the Host Phylogeny, Gut Microbiota and Metabolite Profiles in Cyprinid Fishes – Tongtong Li – Frontiers in Microbiology

Diurnal Dynamics of Gaseous and Dissolved Metabolites and Microbiota Composition in the Bovine Rumen – Henk J. van Lingen – Frontiers in Microbiology

Microbial Biogeography and Core Microbiota of the Rat Digestive Tract – Dongyao Li – Scientific Reports

Animal experiments

Bifidobacterium in the gut microbiota confer resilience to chronic social defeat stress in mice – Chun Yang – Scientific Reports

Lack of Evidence That Selenium-Yeast Improves Chicken Health and Modulates the Caecal Microbiota in the Context of Colonization by Campylobacter jejuni – Alexandre Thibodeau – Frontiers in Microbiology

Review : Outstanding animal studies in allergy II: from atopic barrier and microbiome to allergen-specific immunotherapy – Erika Jensen-Jarolim – Current Opinion in Allergy & Clinical Immunology

Faecalibacterium prausnitzii treatment improves hepatic health and reduces adipose tissue inflammation in high-fat fed mice – Eveliina Munukka – ISME Journal

*Low-dose penicillin in early life induces long-term changes in murine gut microbiota, brain cytokines and behavior –  Sophie Leclercq – Nature Communications

Nod2 and Nod2-regulated microbiota protect BALB/c mice from diet-induced obesity and metabolic dysfunction – Ivan Rodriguez-Nunez – Scientific Reports

Plant, root, and soil microbiome

Aluminum-tolerant bacteria improve the plant growth and phosphorus content in ryegrass grown in a volcanic soil amended with cattle dung manure – María de la Luz Mora- Applied Soil Ecology

Invisible but consequential: root endophytic fungi have variable effects on belowground plant–insect interactions – Huyijuie Gan – Ecosphere

Land-use types and soil chemical properties influence soil microbial communities in the semiarid Loess Plateau region in China – Qin Tian – Scientific Reports

Phylogenetic conservation of substrate use specialization in leaf litter bacteria – Kristin L. Dolan – Plos ONE

Root biomass and exudates link plant diversity with soil bacterial and fungal biomass – Nico Eisenhauer – Scientific Reports

Water and extremophile microbiome

Discrimination of Four Marine Biofilm-Forming Bacteria by LC-MS Metabolomics and Influence of Culture Parameters – Laurie Favre – Journal of Proteome Research

Iron assimilation and utilization in anaerobic ammonium oxidizing bacteria – Christina Ferousi – Current Opinion in Chemical Biology

*Potential sources of bacteria colonizing the cryoconite of an Alpine glacier – Andrea Franzetti – PLOS ONE

Spatio-Temporal Variations of Marine Biofilm Communities Colonizing Artificial Substrata Including Antifouling Coatings in Contrasted French Coastal Environments – Jean-François Briand – Microbial Ecology

Metabolomics

Review: Metabolomics: Strategies to Define the Role of Metabolism in Virus Infection and Pathogenesis – Marianne Manchester – Advances in Virus Research

Effect of Major Royal Jelly Proteins on Spatial Memory in Aged Rats: Metabolomics Analysis in Urine – Di Chen -Journal of Agricultural and Food Chemistry

Food microbiology

Sourdough authentication: quantitative PCR to detect the lactic acid bacterial microbiota in breads – Erica Pontonio – Scientific Reports

Probiotics / prebiotics

Evaluation of Potential Probiotics Isolated from Human Milk and Colostrum – Quésia S. Damaceno – Probiotics and Antimicrobial Proteins

Bioinformatics

SLIMM: species level identification of microorganisms from metagenomes – Temesgen Hailemariam Dadi – PeerJ

Techniques

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area – Kazuma Nakano – Human Cell

High-pressure microscopy for tracking dynamic properties of molecular machines – Masayoshi Nishiyama – Biophysical Chemistry

Gut Microbiome Standardization in Control and Experimental Mice – Kathy D. McCoy – Current Protocols in Immunology

Diastereomer-specific Quantification of Bioactive Hexosylceramides from Bacteria and Mammals – Johanna von Gerichten – Journal of Lipid Research

Microbes in the news

Genetically engineered microbes make their own fertilizer, could feed the world’s poorest

The Next Plague (5) Bacteria: The Coming And Going And Coming Again Of Bacterial Plagues

Latest Helicobacter pylori breakthrough could lead to eradication of bacteria

Science, publishing, and career

Journal editor calls for ‘culture change’ around clinical trial data

Anitha’s non-microbiology picks

In the quest of Planet 9