May 25, 2017

A review on the “vine and wine” microbiomes, a fungus that can infect and kill mosquitos through interaction with the gut microbiota, an introduction to the viruses of coral reefs.

General microbiome

The Role of Microbiota and Immunobiotics in Granulopoiesis of Immunocompromised Hosts – Susana Salva – Frontiers in Immunology

Successive range expansion promotes diversity and accelerates evolution in spatially structured microbial populations – Felix Goldschmidt – The ISME Journal

Human gut microbiome

TGF-β in inflammatory bowel disease: a key regulator of immune cells, epithelium, and the intestinal microbiota – Sozaburo Ihara – Journal of Gastroenterology

Review: Towards an Integrative Understanding of Diet–Host–Gut Microbiome Interactions – Mark N Read – Frontiers in Immunology

Review: Genes, emotions and gut microbiota: The next frontier for the gastroenterologist – Arturo Panduro – World Journal of Gastroenterology

Animal experiments

Modulation of the gut microbiota impacts non-alcoholic fatty liver disease: a potential role for bile acids – Aafke WF Janssen – Journal of Lipid Research

Antimicrobial peptides extend lifespan in Drosophila – Gerrit Loch – PLOS ONE

Animal microbiome

Bacterial diversity of cosmopolitan Culex pipiens and invasive Aedes japonicus from Germany – Sina Zotzmann – Parasitology Research

Comparison of Microbiomes between Red Poultry Mite Populations (Dermanyssus gallinae): Predominance of Bartonella-like Bacteria – Jan Hubert – Microbial Ecology

* Insect pathogenic fungus interacts with the gut microbiota to accelerate mosquito mortality – Ge Wei – PNAS

Plant, root, and soil microbiome

Leaf bacterial diversity mediates plant diversity and ecosystem function relationships – Isabelle Laforest-Lapointe – Nature

Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling – Linwei Wu – The ISME Journal

Review: From Vineyard Soil to Wine Fermentation: Microbiome Approximations to Explain the “terroir” Concept – Ignacio Belda – Frontiers in Microbiology

Phages and viruses

Differentiation and Structure in Sulfolobus islandicus Rod-Shaped Virus Populations – Maria A Bautista – Viruses

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

Metabolomics

Inter-individual Recovery of the Microbiota and Metabolome Over Time Following Fecal Microbiota Transplantation in Patients with Recurrent Clostridium difficile Infection – Anna M Seekatz – bioRxiv

Metabolic profiling by gas chromatography-mass spectrometry of energy metabolism in high-fat diet-fed obese mice – Daxesh P Patel – PLOS ONE

Review: Livestock metabolomics and the livestock metabolome: A systematic review – Seyed Ali Goldansaz – PLOS ONE

Techniques

Review: A diverse community to study communities: integration of experiments and mathematical models to study microbial consortia – Antonella Succurro – Journal of Bacteriology

More microbes

Decoding and reprogramming fungal iterative nonribosomal peptide synthetases – Dayu Yu – Nature Communications

Microbes in the news

Companies Pursue Diagnostics that Mine the Microbiome – Andrea Anderson – The Scientist

The fungal microbiome contributes to alcohol-induced liver damage in mice – EurekAlert

May 24, 2017

Human Microbiome

Non-pylori Helicobacters (NHPHs) induce shifts in gastric microbiota in Helicobacter pylori-infected patients – Peng et al. – Frontiers in Microbiology

Association between body mass index and Firmicutes/Bacteroidetes ratio in an adult Ukrainian population – Koliada et al. – BMC Microbiology

The effect of heritability and host genetics on the gut microbiota and metabolic syndrome – Young Lim et al. – Gut (BMJ)

Fungal microbiota dysbiosis in IBD – Sokol et al. – Gut (BMJ)

A tale of two risks: smoking, diabetes and the subgingival microbiome – Ganesan et al. – The ISME Journal

Animal Microbiome

The Structural and Functional Capacity of Ruminal and Cecal Microbiota in Growing Cattle Was Unaffected by Dietary Supplementation of Linseed Oil and Nitrate  – Popova et al. – Frontiers in Microbiology

Probiotics – Prebiotics

Gut Bacteria Missing in Severe Acute Malnutrition, Can We Identify Potential Probiotics by Culturomics? – Tidjani Alou et al – Frontiers in Microbiology

Detection and Physicochemical Characterization of Membrane Vesicles (MVs) of Lactobacillus reuteri DSM 17938 –  Grande et al. – Frontiers in Microbiology

Review: Resistant Starch Regulates Gut Microbiota: Structure, Biochemistry and Cell Signalling – Yang et al. – Cellular Physiology and Biochemistry

Food Microbiology

A Functional Metagenomic Analysis of Tetracycline Resistance in Cheese Bacteria – Flórez et al. – Frontiers in Microbiology

Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria – Bonham et al. – BioRxiv

Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access – Taboada et al. – Frontiers in Microbiology

In vitro assessment of Pediococcus acidilactici Kp10 for its potential use in the food industry – Abbasiliasi et al. – BMC Microbiology

Pathogen Research

In-depth Profiling of MvfR-Regulated Small Molecules in Pseudomonas aeruginosa after Quorum Sensing Inhibitor Treatment – Allegretta et al. – Frontiers in Microbiology

Metabolic anticipation in Mycobacterium tuberculosis – Eoh et al. – Nature Microbiology

Predicting Drug Resistance Evolution: Antimicrobial Peptides Vs. Antibiotics – Yi et al. – BioRxiv

Environmental Microbiology

Undocumented Potential For Primary Productivity In A Globally-Distributed Bacterial Photoautotroph – Graham et al. – BioRxiv

Epibionts dominate metabolic functional potential of Trichodesmium colonies from the oligotrophic ocean – Frischkorn et al. – The ISME Journal

Bioinformatics

BSocial: Deciphering Social Behaviors within Mixed Microbial Populations – Purswani et al. – Frontiers in Microbiology

A Phylogenetic Method To Perform Genome-Wide Association Studies In Microbes That Accounts For Population Structure And Recombination – Collins and Didelot – BioRxiv

Association Mapping From Sequencing Reads Using K-mers – Rahman et al. – BioRxiv

MATAM: Reconstruction Of Phylogenetic Marker Genes From Short Sequencing Reads In Metagenomes – Pericard et al. – BioRxiv

Other

Perspective: Our path to better science in less time using open data science tools – Stewart Lowndes et al. – Nature Ecology & Evolution

Teaching genetics prior to teaching evolution improves evolution understanding but not acceptance –  Mead et al. – PLoS Biology

Review: Adaptations of archaeal and bacterial membranes to variations in temperature, pH and pressure – Siliakus et al. – Extremophiles

May 19, 2017

Microbiome research

Exploring a possible link between the intestinal microbiota and feed efficiency in pigs

Ursula M. McCormack et al., Applied and Environmental Microbiology

Modulation of the Gut Microbiota by Krill Oil in Mice Fed a High-Sugar High-Fat Diet

Chenyang Lu et al., Frontiers in Microbiology

Opinion: Gut microbiome as a clinical tool in gastrointestinal disease management: are we there yet?

Eamonn M. M. Quigley, Nature Reviews Gastroenterology & Hepatology (Online since March 30, 2017; however this has not been pointed out here before)

 

Pathogen microbiology

Mini review: The Role of Ribonucleases and sRNAs in the Virulence of Foodborne Pathogens

Rute G. Matos et al., Frontiers in Microbiology

Pathogenic Characteristics of Staphylococcus aureus Endovascular Infection Isolates from Different Clonal Complexes

Dafne Pérez-Montarelo et al., Frontiers in Microbiology

Pseudomonas aeruginosa Exolysin promotes bacterial growth in lungs, alveolar damage and bacterial dissemination

Stéphanie Bouillot et al., Scientific Reports (Nature)

Intrinsic Toxin-Derived Peptides Destabilize and Inactivate Clostridium difficile TcdB

Jason L. Larabee et al., mBio

 

Probiotics – Prebiotics

Vaginal Lactobacillus Inhibits HIV-1 Replication in Human Tissues Ex Vivo

Rogers A. Ñahui Palomino et al., Frontiers in Microbiology

Assessing the Risk of Probiotic Dietary Supplements in the Context of Antibiotic Resistance

Min Zheng et al., Frontiers in Microbiology

Review: Lactic Acid Bacteria and Bifidobacteria with Potential to Design Natural Biofunctional Health-Promoting Dairy Foods

Daniel M. Linares et al., Frontiers in Microbiology

In silico Prediction, in vitro Antibacterial Spectrum, and Physicochemical Properties of a Putative Bacteriocin Produced by Lactobacillus rhamnosus Strain L156.4

Letícia de C. Oliveira et al., Frontiers in Microbiology

Health benefit of vegetable/fruit juice-based diet: Role of microbiome

Susanne M. Henning et al., Scientific Reports (Nature)

Characterization of bile salt hydrolase from Lactobacillus gasseri FR4 and demonstration of its substrate specificity and inhibitory mechanism using molecular docking analysis

Rizwana Parveen Rani et al., Frontiers in Microbiology

Lactobacillus johnsonii ameliorates intestinal, extra-intestinal and systemic pro-inflammatory immune responses following murine Campylobacter jejuni infection

Stefan Bereswill et al., Scientific Reports (Nature)

News and Views: Paediatrics: Are human milk oligosaccharides the magic bullet for necrotizing enterocolitis?

Michael S. Caplan, Nature Reviews Gastroenterology & Hepatology

Assessing the Challenges in the Application of Potential Probiotic Lactic Acid Bacteria in the Large-Scale Fermentation of Spanish-Style Table Olives

Francisco Rodríguez-Gómez et al., Frontiers in Microbiology

 

Antimicrobials

A broad-spectrum bactericidal lipopeptide with anti-biofilm properties

Ohad Meir et al., Scientific Reports (Nature)

The anticancer peptide TAT-RasGAP317-326 exerts broad antimicrobial activity

Mathieu Heulot et al., Frontiers in Microbiology

 

Genomics

Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655

Sang Woo Seo et al., Scientific Reports (Nature)

High-Definition Electronic Genome Maps From Single Molecule Data

John S. Oliver et al., BioRxiv

Local genes for local bacteria: evidence of allopatry in the genomes of transatlantic Campylobacter populations

Ben Pascoe et al., PeerJ (not peer reviewed)

Feature: Mining microbes: Creating genomic tools to fight disease

Amber Dance, Science

 

Microbiology – Other

Variation in soil microbial community structure associated with different legume species is greater than that associated with different grass species

Yang Zhou et al.,  Frontiers in Microbiology

Microbial Community Dynamics in Soil Depth Profiles Over 120,000 Years of Ecosystem Development

Stephanie Turner et al., Frontiers in Microbiology

Autotrophic and heterotrophic acquisition of carbon and nitrogen by a mixotrophic chrysophyte established through stable isotope analysis

Ramon Terrado et al., The ISME Journal

Hypothesis & Theory: The hyperarid core of the Atacama Desert, an extremely dry and carbon deprived habitat of potential interest for the field of carbon science

Armando Azua-Bustos et al., Frontiers in Microbiology

 

non-Microbiology picks

Divergent prebiotic synthesis of pyrimidine and 8-oxo-purine ribonucleotides

Shaun Stairs et al., Nature Communications

Virus origin could relate to the act of prey among primitive life forms

Eslam Abbas, PeerJ (not peer reviewed)

Beyond the protein-only hypothesis: A novel mineral-lipid hypothesis in prion and protein-misfolding disease

Kavitha Reddy, PeerJ (not peer reviewed)

Feature: Introducing ORCID

John Bohannon and Kirk Doran, Science

 

May 12, 2017

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

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 9, 2017

Today’s digest is full of exciting papers that look at how climate change is influencing the gut microbiome of lizards, biogeography of bacteria along the Amazon river, lastly how going to the gym might be bad for you.

Human gut microbiome

Preprint : The Landscape Of Type VI Secretion Across Human Gut Microbiomes Reveals Its Role In Community Composition. Verster A. bioRxiv

Ocean, river, and stream microbiome

Disentangling multi‐scale environmental effects on stream microbial communities. Jyrkänkallio‐Mikkola J. Journal of Biogeography

Bacterial biogeography across the Amazon river-ocean continuum  Doherty M. Frontiers in Microbiology

Spatial variation of microbial communities in sediments along the environmental gradients from Xiaoqing River to Laizhou Bay.   Yu SX.  Marine Pollution Bulletin

The impact of long-term water level draw-down on microbial biomass: A comparative study from two peatland sites with different nutrient status Mpamah PA. European Journal of Soil Biology

The metabolic potential of the single cell genomes obtained from the Challenger Deep, Mariana Trench within the Candidate Superphylum Parcubacteria (OD1). León‐Zayas. Environmental Microbiology

Plant, soil, and air microbiome

Postmortem microbial communities in burial soil layers of skeletonized humans. Thomas TB. Journal of Forensic and Legal Medicine

Metagenomic Analysis of Bacterial Communities in the Rhizosphere of Leguminous Crops and Trees. Ahrenhoerster C. The FASEB Journal

Animal gut microbiome

Can fecal samples be used to inform about microbial communities of the equine hindgut? Reed KJ. Journal of Equine Veterinary Science

Normal variation and changes over time in the equine intestinal microbiome Martin EJ. Journal of Equine Veterinary Science

Climate warming reduces gut microbiota diversity in a vertebrate ectotherm. Bestion E. Nature:Ecology and Evolution

Effect of dietary supplementation with Lactobacillus acidophilus D2/CSL (CECT 4529) on caecum microbioma and productive performance in broiler chickens De Cesare A. PLoS One

Biotechnology 

Editorial Petroleum Microbial Biotechnology: Challenges and Prospects Ismail WA.Frontiers in Microbiology

Antibiotic 

Networks of exchanging antibiotic resistance between environmental, commensal, and pathogenic microbes Dantas G- The FASEB Journal

Extreme environment 

Decoupling of microbial carbon, nitrogen, and phosphorus cycling in response to extreme temperature events Mooshammer M. Science Advances

Faecal microbiome 

pH-Mediated Microbial and Metabolic Interactions in Fecal Enrichment Cultures Ilhan ZE. mSpehere

Anemia During Infancy Affects the Fecal Microbiome and Fecal and Serum Metabolomes McClorry S. The FASEB Journal

Microbes in the news

Southern California beaches get bacteria warnings after rain

Monterey County Herald

The Amount Of Bacteria On Gym Equipment Will Make Sure You Never Forget To Wipe Down The Elliptical Again

Bustle


 

April 28, 2017

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