September 16, 2017

Events and jobs

Interim Microbiology Manager – Central Belt – North Lanarkshire, Scotland, UK

 

General microbiome

Haloarchaea: worth exploring for their biotechnological potential – A Singh – Biotechnology Letters

 

Pregnancy and early life

Rotavirus Vaccine Response Correlates with the Infant Gut Microbiota Composition in Pakistan – V Harris – Gut Microbes

 

 

Human gut microbiome

Infections by human gastrointestinal helminths are associated with changes in faecal microbiota diversity and composition – TP Jenkins – PLoS One

 

Animal experiments 

Review: Gut Microbial Influences on the Mammalian Intestinal Stem Cell Niche. – BCE Peck – Stem Cells International

Caloric restriction promotes rapid expansion and long-lasting increase of Lactobacillus in the rat fecal microbiota – C Fraumene – Gut Microbes

SMV1, an extremely stable thermophilic virus platform for nanoparticle trafficking in the mammalian GI tract – KB Uldahl – Journal of Applied Microbiology

Fungal derived 15-keto-prostaglandin E₂ activates host peroxisome proliferator-activated receptor gamma (PPAR-γ) to promote C. neoformans growth during infection. – RJ Evans – bioRxiv

The effect of regular or reduced-fat distillers grains with solubles on rumen methanogenesis and the rumen bacterial community – E Castillo-Lopez – Journal of Applied Microbiology

Role of Microbiota in Strengthening Ocular Mucosal Barrier Function Through Secretory IgA – A Kugadas – IOVS

 

Animal microbiome 

Virome analysis for identification of novel mammalian viruses in bats from Southeast China. – D Hu – Scientific Reports

 

Plant, root, and soil microbiome

Long-term no-till: A major driver of fungal communities in dryland wheat cropping systems – D Sharma-Poudyal – PLoS One

Nitrile-Degrading Bacteria Isolated from Compost – R Egelkamp – Frontiers in Environmental Science

Application of compost and clay under water-stressed conditions influences functional diversity of rhizosphere bacteria – BS Mickan – Biology and Fertility of Soils

High-yield production of indole-3-acetic acid by Enterobacter sp. DMKU-RP206, a rice phyllosphere bacterium that possesses plant growth-promoting traits – P Nutaratat – 3 Biotech

Structural and functional variability in root-associated bacterial microbiomes of Cd/Zn hyperaccumulator Sedum alfredii – J Luo – Applied Microbiology and Biotechnology

 

Water microbiome and extremophile 

Microbial Diversity in a Hypersaline Sulfate Lake: A Terrestrial Analog of Ancient Mars – A Pontefract – Frontiers in Microbiology

Bacterial community in ancient permafrost alluvium at the Mammoth Mountain (Eastern Siberia) – A Brouchkov – Gene

Bacterial, Archaeal, and Eukaryotic Diversity across Distinct Microhabitats in an Acid Mine Drainage – V Mesa – Frontiers in Microbiology

 

 

Techniques

Review: Recent Advances in the Etiopathogenesis of Inflammatory Bowel Disease: The Role of Omics – E Stylianou – Molecular Diagnosis & Therapy 

Formation of functional, non-amyloidogenic fibres by recombinant Bacillus subtilis TasA – E Erskine – bioRxiv

IN VITRO AND IN VIVO CHARACTERISATION OF ISOLATES OF CRYPTOCOCCUS NEOFORMANS CAUSING MENINGITIS IN HIV-INFECTED AND UNINFECTED PATIENTS IN VIETNAM – TT Lam – bioRxiv

Morphological and Transcriptomic analysis reveals the osmoadaptive response of endophytic fungus Aspergillus montevidensis ZYD4 to high salt stress – KH Liu – Frontiers in Microbiology

Multilocus and SSU rRNA gene phylogenetic analyses of available cyanobacterial genomes, and their relation to the current taxonomic system – J Mareš – Hydrobiologia

Analysis of Bacterial Community Composition of Corroded Steel Immersed in Sanya and Xiamen Seawaters in China via Method of Illumina MiSeq Sequencing – X Li – Frontiers in Microbiology

Deep nirS amplicon sequencing of San Francisco Bay sediments enables prediction of geography and environmental conditions from denitrifying community composition – JA Lee – Environmental Microbiology

 

Microbes in the news 

WITH DESIGNER BACTERIA, CROPS COULD ONE DAY FERTILIZE THEMSELVES – Wired

Popular health supplements contaminated with faecal bacteria – Irish Examiner

Omega 3 intake linked to greater gut microbial diversity – Nutra Ingredients

Scientists Just Discovered Organisms That Are Distinct From Any Life Forms Known to Science – Futurism

 

 

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September 13,2017

Our midweek digest is a treat for wine drinkers- two studies looking at vineyard microbiomes and news of how Nestlé is moving into microbiome research. Lastly, read about an exciting workflow that makes it easier to map the resistome.

General Microbiome

Microbial communities in placentas from term normal pregnancy exhibit spatially variable profiles.

Parnell LA .Scientific Reports

Human gut microbiome

Host-microbe interaction in the gastrointestinal tract.

Parker A.Environmental Microbiology Report

Gut microbiota composition is associated with polypharmacy in elderly hospitalized patients.

Ticinesi A.Scientific Reports

Microbes in Infant Gut Development: Placing Abundance Within Environmental, Clinical and Growth Parameters.

Obermajer T.Scientific Reports

Animal experiments and microbiome

Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models.

Cekanaviciute E, PNAS

The microbiota influences cell death and microglial colonization in the perinatal mouse brain.

Castillo-Ruiz A. Brain, Behaviour, and Immunity

Microbial colonization is required for normal neurobehavioral development in zebrafish.

Phelps D,.Scientific Reports

Biotechnology 

Ozone-cathode microbial desalination cell; An innovative option to bioelectricity generation and water desalination.

Gholizadeh A. Chemosphere.

Plant and soil microbiome

Grape microbiome as a reliable and persistent signature of field origin and environmental conditions in Cannonau wine production.

Mezzasalma V. PLoS One.

Is microbial terroir related to geographic distance between vineyards?

Miura T. Environmental Microbiology Reports

Bacteria utilising plant-derived carbon in the rhizosphere of Triticum aestivum change in different depths of an arable soil.

Uksa M. Environmental Microbiology Reports

Mining the Volatilomes of Plant-Associated Microbiota for New Biocontrol Solutions.

Bailly A. Frontiers in Microbiology

More than 2500 years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis.

Michas A. Microbiome

Lung Microbiome

Functional characterization of the Mycobacterium abscessus genome coupled with condition specific transcriptomics reveals conserved molecular strategies for host adaptation and persistence.

Miranda-CasoLuengo AA.BMC Genomics

Mechanistic insight into the function of the microbiome in lung diseases.

Ubags NDJ. European Respiratory Journal

Antibiotics

A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity.

Ruiz VE.Nature Communications

Resistome

The recent emergence in hospitals of multidrug-resistant community-associated sequence type 1 and spa type t127 methicillin-resistant Staphylococcus aureus investigated by whole-genome sequencing: Implications for screening.

Earls MR. PLoS One

Rapid resistome mapping using nanopore sequencing.

van der Helm E.Nucleic Acids Research  

Network of microbial and antibiotic interactions drive colonization and infection with multidrug-resistant organisms

Wang J. PNAS

News

Nestlé moves into gut microbiome tests.

News- Nature Biotechnology

Protocol

Shotgun metagenomics, from sampling to analysis.

Quince C,Nature Biotechnology

Erratum 

Erratum to: Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey Species.

Hale VL. Microbial Ecology

September 2, 2017

General microbiome

Nutrient stoichiometry shapes microbial coevolution – ML Larsen – bioRxiv

Review: Interplay of innate lymphoid cells and the microbiota – L Britanova – Immunological Reviews

 

 

Human gut microbiome

The intestinal microbiota: Antibiotics, colonization resistance, and enteric pathogens – S Kim – Immunological Reviews

 

Animal experiments

Effect of Propionibacterium acidipropionici P169 on the rumen and faecal microbiota of beef cattle fed a maize-based finishing diet – E Azad – Beneficial Microbes

The Effects of an Environmentally Relevant Level of Arsenic on the Gut Microbiome and its Functional Metagenome – L Chi – Toxicological Sciences

 

Animal microbiome 

Skin bacterial microbiome of a generalist Puerto Rican frog varies along elevation and land use gradients – MC Hughey – PeerJ

Effects of probiotic on microfloral structure of live feed used in larval breeding of turbot Scophthalmus maximus – Y Jiang – Chinese Journal of Oceanology and Limnology

 

Plant, root, and soil microbiome

Synergistic rhizosphere degradation of γ-hexachlorocyclohexane (lindane) through the combinatorial plant-fungal action – MD Asemoloye – PLoS One

Bacillus kiskunsagensis sp. nov., a novel alkaliphilic and moderately halophilic bacterium isolated from soda soil – AK Borsodi – International Journal of Systematic and Evolutionary Microbiology

 

Water microbiome and extremophiles 

Natronoarchaeum persicum sp. nov., a haloarchaeon isolated from a hypersaline lake – A Naghoni – International Journal of Systematic and Evolutionary Microbiology

Geographical variations in bacterial communities associated with soft coral Scleronephthya gracillimum – S Woo – PLoS One

Biogeochemical conversion of sulfur species in saline lakes of Steppe Altai – SV Borzenko – Chinese Journal of Oceanology and Limnology

Role of heavy metals in structuring the microbial community associated with particulate matter in a tropical estuary – VA Sheeba – Environmental Pollution

 

Probiotics / prebiotics

Review: To add or not to add probiotics to infant formulae? An updated systematic review – A Skórka – Beneficial Microbes

 

Phages and viruses

Biogeography & Environmental Conditions Shape Phage & Bacteria Interaction Networks Across The Human Microbiome – GD Hannigan – bioRxiv

ReviewImpact of transmission cycles and vector competence on global expansion and emergence of arboviruses – A Agarwal – Reviews in Medical Virology

 

Techniques

Validation of RT-qPCR approaches to monitor Pseudomonas syringae gene expression during infection and exposure to pattern-triggered immunity – A Smith – bioRxiv

Review: Deciphering interactions between the gut microbiota and the immune system via microbial cultivation and minimal microbiomes – T Clavel – Immunological Reviews

 

Microbes in the news 

Could an altered microbiome predict Parkinson’s disease – Nutra Ingredients

Could faecal microbiota transplantation be used to tackle asthma – Nutra Ingredients

Probiotics effective in preventing sepsis in infants – Healio

Start made on revealing scale of gut bugs’ hijacking our signalling – Chemistry World

Dietary Indoles May Help Extend Lifespan – Emax Health

Baby Bottle Soap Recalled Due to ‘Harmful Bacteria’ – Fortune

Multi-drug resistant bacteria proliferating through poultry waste – TOI

 

August 24, 2017

Bacterial paleontology of iron formations, gene expression from bacteria and archaea in the Amazon River, indoles promote a “youthful” gene expression profile in their host.

Events and jobs

Podcast: Branding Bacteria – Carla Brown

General microbiome

Preprint: Metabolic Model-Based Analysis of the Emergence of Bacterial Cross-Feeding through Extensive Gene Loss – Colin P McNally – bioRxiv

Pregnancy and early life

Breast Milk Transforming Growth Factor β Is Associated With Neonatal Gut Microbial Composition – Alexandra R Sitarik – Journal of Pediatric Gastroenterology and Nutrition

Human gut microbiome

Increased Tryptophan Metabolism is Associated With Activity of Inflammatory Bowel Diseases – Susanna Nikolaus – Gastroenterology

Animal experiments

Indoles from commensal bacteria extend healthspan – Robert Sonowal – PNAS

Plant, root, and soil microbiome

Soil C and N statuses determine the effect of maize inoculation by plant growth-promoting rhizobacteria on nitrifying and denitrifying communities – Alessandro Florio – Scientific Reports

Changes in Soil Microbial Community and Its Effect on Carbon Sequestration Following Afforestation on the Loess Plateau, China – Yun Xiang – International Journal of Environmental Research and Public Health

Rapid peat accumulation favours the occurrence of both fen and bog microbial communities within a Mediterranean, free-floating peat island – Giuseppe Concheri – Scientific Reports

Influence of film mulching on soil microbial community in a rainfed region of northeastern China – Wenyi Dong – Scientific Reports

Secondary compound hypothesis revisited: Selected plant secondary metabolites promote bacterial degradation of cis-1,2-dichloroethylene (cDCE) – Serena Fraraccio – Scientific Reports

Adaptive evolution of rhizobial symbiotic compatibility mediated by co-evolved insertion sequences – Ran Zhao – The ISME Journal

Micropredator niche differentiation between bulk soil and rhizosphere of an agricultural soil depends on bacterial prey – Lu Zhang – FEMS Microbiology Ecology

Water and extremophile microbiome

Predicting blooms of toxic cyanobacteria in eutrophic lakes with diverse cyanobacterial communities – Aleksandra Bukowski – Scientific Reports

Patterns of Bacterial and Archaeal Gene Expression through the Lower Amazon River – Brandon M Satinsky – Frontiers in Marine Science

Probiotics/prebiotics

Protocol for a randomised, placebo-controlled pilot study for assessing feasibility and efficacy of faecal microbiota transplantation in a paediatric ulcerative colitis population: PediFETCh trial – Nikhil Pai – Gastroenterology and Hepatology

More microbes

Bacterial paleontology of the Neoarchean banded iron formations of Karelia and the Kola Peninsula – M M Astafieva – Paleontological Journal

Microbes in the news

Cyborg bacteria covered in solar panels can beat plants at photosynthesis – Angela Chen – The Verge

Gut bacteria influence the brain indirectly, study shows – Maria Cohut – Medical News Today

Scientists uncover two-layer identification among soil bacteria – Amy Wallace – UPI.com

We May Have Just Found The Hormone That Lets Gut Bacteria Talk to The Brain – Peter Duckbill – Science Alert

August 22, 2017

Jobs

Postdoctoral Research Fellow in Microbiology/Molecular Ecology : Bremen, Germany (Soil microbial community interactions)

Postdoctoral Training Fellow : London, United Kingdom (M. tuberculosis and immunity)

 

Human Microbiome

Review: Human genetic variation and the gut microbiome in disease – Andrew Brantley Hall – Nature Reviews Genetics

Long-term taxonomic and functional divergence from donor bacterial strains following fecal microbiota transplantation in immunocompromised patients – Eli L. Moss – PLoS ONE

Intestinal colonisation patterns in breastfed and formula-fed infants during the first 12 weeks of life reveal sequential microbiota signatures – Harro M. Timmerman  – Scientific Reports

A prospective analysis of mucosal microbiome-metabonome interactions in colorectal cancer using a combined MAS 1HNMR and metataxonomic strategy – James Kinross – Scientific Reports

Inflammatory colonic innate lymphoid cells are increased during untreated hiv-1 infection and associated with markers of gut dysbiosis and mucosal immune activation – Stephanie Dilon- JAIDS Journal of Acquired Immune Deficiency Syndromes

The Maternal Infant Microbiome: Considerations for Labor and Birth – Alexis Dunn – MCN, American Journal of Maternal Child Nursing

Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome – Francesco Beghini – The ISME Journal

 

Animal Microbiome

The Maturing Development of Gut Microbiota in Commercial Piglets during the Weaning Transition – Limei Chen – Frontiers in Microbiology

Moderate-intensity exercise affects gut microbiome composition and influences cardiac function in myocardial infarction mice – Zuheng Liu – Frontiers in Microbiology  

Unveiling bifidobacterial biogeography across the mammalian branch of the tree of life – Christian Milani – The ISME Journal

 

Probiotics

In Vitro Evaluation of the Impact of the Probiotic E. coli Nissle 1917 on Campylobacter jejuni’s Invasion and Intracellular Survival in Human Colonic Cells – Yosra A. Helmy – Frontiers in Microbiology

 

Food Microbiology

Cell surface properties of Lactococcus lactis reveal milk protein binding specifically evolved in dairy isolates – Mariya Tarazanova – Frontiers in Microbiology

 

Pathogen Research

Metagenomic sequencing to replace semi-quantitative urine culture for detection of urinary tract infections: a proof of concept – Victoria A. Janes – BioRxiv

Burkholderia cenocepacia Infections in Cystic Fibrosis Patients: Drug Resistance and Therapeutic Approaches – Viola C. Scoffone –  Frontiers in Microbiology

 

Environmental Microbiome

Marine Microbial Gene Abundance and Community Composition in Response to Ocean Acidification and Elevated Temperature in Two Contrasting Coastal Marine Sediments – Ashleigh R. Currie – Frontiers in Microbiology

Heat Stress Dictates Microbial Lipid Composition along a Thermal Gradient in Marine Sediments – Miriam Sollich – Frontiers in Microbiology

Actinobacterial Rare Biospheres and Dark Matter Revealed in Habitats of the Chilean Atacama Desert – Hamidah Idris – Scientific Reports

A pivotal role for ocean eddies in the distribution of microbial communities across the Antarctic Circumpolar Current – – PLoS ONE

Microbial community analysis of apple rhizosphere around Bohai Gulf – Jihang Jiang – Scientific Reports

From virus isolation to metagenome generation for investigating viral diversity in deep-sea sediments – Cinzia Corinaldesi – Scientific Reports

 

Bioinformatics

PANINI: Pangenome Neighbor Identification for Bacterial PopulationsKhalil Abudahab  – BioRxiv

 

 

Non-Microbiology picks

The prehistory of biology preprints: a forgotten experiment from the 1960s – Matthew Cobb – PeerJ preprints

August 19, 2017

Today, a short Digest but with interesting features: effects of intestinal cleanout on microbiota, changes in K vitamin derivatives in human, reviews about Streptococcus group B and effect of FMT on Clostridium difficile, and more.

Human microbiome

Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment – Julia Fukuyama – PLoS Computational Biology

Research Highlight: Gut microbiota: Gas-induced GLP1 release – David Holmes – Nature Reviews Endocrinology

Maternal obesity is associated with gut microbial metabolic potential in offspring during infancy  – Tomás Cerdó – Journal of Physiology and Biochemistry

Fecal concentrations of bacterially derived vitamin K forms are associated with gut microbiota composition but not plasma or fecal cytokine concentrations in healthy adults – J Philip Karl – The American Journal of Clinical Nutrition

Temporal Stability of the Healthy Human Skin Microbiome Following Dead Sea Climatotherapy – Michael Brandwein – Acta Dermato-Venereologica

Review: Intrinsic Maturational Neonatal Immune Deficiencies and Susceptibility to Group B Streptococcus Infection – Michelle L. Korira – Clinical Microbiological Reviews

Systematic review: Faecal microbiota transplantation for Clostridium difficile infection: a multicentre study of non-responders – Paul Moayyedi – Medical Journal of Australia

 

Forensic microbiome

Daily thanatomicrobiome changes in soil as an approach of postmortem interval estimation: An ecological perspective – Joe Adserias Garriga – Forensic Science International

 

Animal microbiome

Correlations of age and growth rate with microbiota composition in Atlantic cod (Gadus morhua) larvae – Ly T. T. Trinh – Scientific Reports

Microbial community composition along the digestive tract in forage- and grain-fed bison – Gaddy T. Bergmann – BMC Veterinary Research

The effect of storage at ambient temperature on the feline fecal microbiota – Moran Tal – BMC Veterinary Research

Performance, biochemical and haematological responses, and relative organ weights of laying hens fed diets supplemented with prebiotic, probiotic and synbiotic  – Shirley Gee Hoon Tang – BMC Veterinary Research

Mosapride Stabilizes Intestinal Microbiota to Reduce Bacterial Translocation and Endotoxemia in CCl4-Induced Cirrhotic Rats – Hong Xu – Digestive Diseases and Sciences

Transition of the intestinal microbiota of cats with age – Hiroaki Masuoka – PLoS ONE

 

Pathogen research

Draft Genome Sequences of Two Enterobacter cloacae subsp. cloacae Strains Isolated from Australian Hematology Patients with Bacteremia – Lex E. X. Leonga – Genome Announcements

The impact of the Staphylococcus aureus virulome on infection in a developing country: a cohort study – Marthe Lebughe – Frontiers in Microbiology

 

 

Bioactive compounds

Regulative effects of curcumin spice administration on gut microbiota and its pharmacological implications – Liang Shen – Food & Nutrition Research

Identification of Secondary Metabolite Gene Clusters in the Pseudovibrio Genus Reveals Encouraging Biosynthetic Potential toward the Production of Novel Bioactive Compounds – Lynn M. Naughton – Frontiers in Microbiology

 

Other

Characterizing a thermostable Cas9 for bacterial genome editing and silencing – Ioannis Mougiakos – BioRxiv

Determination of geochemical bio-signatures in Mars-like basaltic environments – Karen Olsson-Francis – Frontiers in Microbiology

 

August 17, 2017

After two days of holidays on Microbiome Digest, today our blog is a bit longer with many papers in the part of water, soil and gut microbiome. Moreover, check new tools which can be used to deal with microbiome data (MicrobiomeDB and MetaMeta) and some interesting news about microbes in the “Microbes in the news” section. Enjoy the summer (in the lab or on the beach) while reading what is new in microbial world.

Events and jobs

Quality Control Manager, Microbiology, Technical Operations, Marlborough, Massachusetts, US

Assistant/Associate Professor – Microbiology and Immunology (Job ID #83258), Chicago, US

General microbiome

A macroecological theory of microbial biodiversity – William R. Shoemaker – Nature Ecology & Evolution

Community structure follows simple assembly rules in microbial microcosms – Jonathan Friedman – Nature Ecology & Evolution

Solagigasbacteria: Lone genomic giants among the uncultured bacterial phyla – Eric Becraft – bioRxiv

Review: Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life – Anja Spang – Science

Temperature-Dependent Alkyl Glycerol Ether Lipid Composition of Mesophilic and Thermophilic Sulfate-Reducing Bacteria – Arnauld Vinçon-Laugier – Frontiers in Microbiology

Advances in the analysis of “less-conventional” human body fluids: an overview of the ce- and hplc-ms applications in the years 2015–2017 – Monica Di Venere – Electrophoresis

Pregnancy and early life

Comparison of commercially-available preservatives for maintaining the integrity of bacterial DNA in human milk – Kimberly A.Lackey – Journal of Microbiological Methods

Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants – Danping Zhu – Scientific Reports

Multi-site human microbiome

Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid –  Philipp Kirstahler – bioRxiv

Oral microbiome

Oral microbial community assembly under the influence of periodontitis – Hongju Chen – PLOS One

Subgingival Microbiome of Gingivitis in Chinese Undergraduates – Ke Deng – Chinese Journal of Dental Research

Human skin microbiome

Review: What is new in the pathophysiology of acne, an overview – B. Dréno – Journal of the European Academy of Dermatology and Venerology

The Role of the Skin and Gut Microbiome in Psoriatic Disease – Di Yan – Current Dermatology Reports

Human vaginal microbiome

The Vaginal Microbiome and its Potential to Impact Efficacy of HIV Pre-exposure Prophylaxis for Women –  Jennifer Velloza – Current HIV/AIDS Reports

The urinary microbiota of men and women and its changes in women during bacterial vaginosis and antibiotic treatment – Cornelia Gottschick – Microbiome

 

Human gut microbiome

Interactions between species introduce spurious associations in microbiome studies – Rajita Menon – bioRxiv

Bacteriophages in the gastrointestinal tract and their implications – Marzanna Łusiak-Szelachowska- Gut Pathogens

Analysis of intestinal microbial communities of cerebral infarction and ischemia patients based on high throughput sequencing technology and glucose and lipid metabolism –  Wenzhen Ji – Molecular Medicine Reports

Brain-gut-microbiota axis and mental health – Timothy G. Dinan – Psychosomatic Medicine

Integrated Analysis of Biopsies from Inflammatory Bowel Disease Patients Identifies SAA1 as a Link Between Mucosal Microbes with TH17 and TH22 Cells – Mei San Tang – Inflamatory Bowel Diseases

Gut microbiome response to short-term dietary interventions in reactive hypoglycemia subjects – Sara Quercia –  Diabetes Metabolism Research and Reviews

The Impact of Western Diet and Nutrients on the Microbiota and Immune Response at Mucosal Interfaces – Donjete Statovci –  Frontiers in Immunology

Comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects – Elena Buelow – Microbiome

Future prospect of faecal microbiota transplantation as a potential therapy in asthma – Y Kang  – Allergologia et Immunopathologia

Evidence of the Immune Relevance of Prevotella copri, a Gut Microbe, in Patients With Rheumatoid Arthritis – Annalisa Pianta – Arthritis & Rheumatology

Bacteriophages in the gastrointestinal tract and their implications – Marzanna Łusiak-Szelachowska – Gut Pathogens

The impact of age and gut microbiota on Th17 and Tfh cells in K/BxN autoimmune arthritis – Fei Teng – Arthritis Research & Therapy

Amoxapine Demonstrates Incomplete Inhibition of β-Glucuronidase Activity from Human Gut Microbiota – Wei Yang –  SLAS Discovery

Animal experiments 

Role of intestinal microbiome in American ginseng-mediated colon cancer protection in high fat diet-fed AOM/DSS mice –  C.-Z. Wang –  Clinical and Translational Oncology

The influence of the gut microbiota composition on Campylobacter jejuni colonization in chickens – Zifeng Han – Infection and Immunity

Animal microbiome 

Microbiota of little penguins and short-tailed shearwaters during development – Meagan L. Dewar – PLOS One

Transition of the intestinal microbiota of cats with age – Hiroaki Masuoka – PLOS One

Brief Communication: Climate warming reduces gut microbiota diversity in a vertebrate ectotherm – Elvire Bestion – Nature Ecology & Evolution

Patterns of seasonality and group membership characterize the gut microbiota in a longitudinal study of wild Verreaux’s sifakas (Propithecus verreauxi) – Andrea Springer – Ecology and Evolution

Comparison of the microbial population in rabbits and guinea pigs by next generation sequencing – Edward J. Crowley – PLOS One

Effects of contaminants of emerging concern on Megaselia scalaris (Lowe, Diptera: Phoridae) and its microbial community – Marcus J. Pennington – Scientific Reports

Plant, root, and soil microbiome

Influence of heavy metals on rhizosphere microbial communities of Siam weed (Chromolaena odorata (L.)) using a 16S rRNA gene amplicon sequencing approach – Thanyaporn Ruangdech – Agriculture and Natural Resources

Soil microbial community composition is correlated to soil carbon processing along a boreal wetland formation gradient – Eric J. Chapman – European Journal of Soil Biology

Bacteria from the rhizosphere and tissues of As-hyperaccumulator Pteris vittata and their role in arsenic transformation – Yong-HeHan – Chemosphere

Soil Characteristics Overwhelm Cultivar Effects on the Structure and Assembly of Root-Associated Microbiomes of Modern Maize – LinChen – Pedosphere

Comparative Transcriptomics of Bacillus mycoides Strains in Response to Potato-Root Exudates Reveals Different Genetic Adaptation of Endophytic and Soil Isolates – Yanglei Yi – Frontiers in Microbiology

Soil features in rookeries of Antarctic penguins reveal sea to land biotransport of chemical pollutants – Anna C. Santamans – PLOS One

Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism – Elias Broman – Microbiome

Effects of Short-Term Set-Aside Management Practices on Soil Microorganism and Enzyme Activity in China – Guangyu Li – International Journal of Environmental Research and Public Health

Microbial volatile compounds alter the soil microbial community – Jun Yuan –  Environmental Science and Pollution Research

Metagenomes from deep Baltic Sea sediments reveal how past and present environmental conditions determine microbial community composition – Ian P.G. Marshall – Marine Genomics

A More Comprehensive Community of Ammonia-Oxidizing Archaea (AOA) Revealed by Genomic DNA and RNA Analyses of amoA Gene in Subtropical Acidic Forest Soils – Ruo-Nan Wu – Microbial Ecology

Biophysical processes supporting the diversity of microbial life in soil – Robin Tecon – FEMS Microbiology Reviews

Water and extremophile microbiome 

Effect of short-term, diel changes in environmental conditions on active microbial communities in a salt marsh pond – Patrick J. Kearns – Aquatic Microbial Ecology

Linking Phylogenetic Identity and Biogeochemical Function of Uncultivated Marine Microbes with Novel Mass Spectrometry Techniques –  Samuel Bryson – Thesis, Oregon State University

Effects of alkali types on waste activated sludge (WAS) fermentation and microbial communities – Xiaoling Li – Chemosphere

Cyanobacterial Allelochemicals But Not Cyanobacterial Cells Markedly Reduce Microbial Community Diversity – Filipa Dias – Frontiers in Microbiology

Marinobacter aquaticus sp. nov., a moderately halophilic bacterium from a solar saltern –  María José León –  International Journal of Systematic and Evolutionary

Exploring the microbial diversity in Jordanian hot springs by comparative metagenomic analysis – Emad I. Hussein – Microbiology Open

Development of the first gene expression system for Salinicoccus strains with potential application in bioremediation of hypersaline wastewaters – Dahe Zhao – Applied Microbiology and Biotechnology

Bacterial biomes and potential human pathogens in irrigation water and leafy greens from different production systems described using pyrosequencing – M Jongman – Journal of Applied Microbiology

Report: Metabolic Flexibility Underpins Growth Capabilities of the Fastest Growing Alga – Haim Treves – Current Biology

The effects of morphology and neighbouring seaweeds on macroalgal microbiota – Thesis, The University of British Columbia

Relationships between and formation dynamics of the microbiota of consumers, producers, and the environment in an abalone aquatic system – Jing-Zhe Jiang – PLOS One

Vertical gradients in species richness and community composition across the twilight zone in the North Pacific Subtropical Gyre – Stephanie A. Sommer – Molecular Ecology

Metagenomic Insights into The Diversity and Functions of Microbial Assemblages in Tasik Kenyir Ecosystem – Mohd Ezhar Mohd Noor –  bioRxiv

The organizing effects of elevated CO2 on competition among estuarine primary producers – Craig S. Young – Scientific Reports

Microbial Community Structure and the Persistence of Cyanobacterial Populations in Salt Crusts of the Hyperarid Atacama Desert from Genome-Resolved Metagenomics – Kari M. Finstad – Frontiers in Microbiology

Draft Genome Sequence of Thiohalobacter thiocyanaticus Strain FOKN1, a Neutrophilic Halophile Capable of Thiocyanate Degradation – Mamoru Oshiki – Genome Announcements

Environmental drivers of a microbial genomic transition zone in the ocean’s interior – Daniel R. Mende – Nature Microbiology

Early photosynthetic eukaryotes inhabited low-salinity habitats – Patricia Sánchez-Baracaldo – PNAS

Microbial dynamics in petroleum oilfields and their relationship with physiological properties of petroleum oil reservoirs – Sunita J.Varjani – Bioresource Technology

Probiotics / prebiotics

Label-free quantitative proteomic analysis of Lactobacillus fermentum NCDC 400 during bile salt exposure – Gurjeet Kaur – Journal of Proteomics

Timely Use of Probiotics in Hospitalized Adults Prevents Clostridium difficile Infection: A Systematic Review With Meta-Regression Analysis – Nicole T. Shen – Gastroenterology

Phages and viruses

Phage in urban wastewater have the potential to disseminate antibiotic resistance – Gayathri Upeksha Gunathilaka – International Journal of Antimicrobial Agents

Bioinformatics

MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments – Francislon Silva de Oliveira – bioRxiv

MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling – Vitor C. Piro – Microbiome

A bioarchitectonic approach to the modular engineering of metabolism – Cheryl A. Kerfeld – Philosophical Transactions of the Royal Society B

Techniques

Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems – Joanne B. Emerson – Microbiome

A Note: A simple methodology to collect culturable bacteria from feces of Anopheles darlingi (Diptera: Culicidae) – Andrelisse Arruda – Journal of Microbiological Methods

Biotechnology

Predicting Microbial Fuel Cell Biofilm Communities and Bioreactor Performance using Artificial Neural Networks – Keaton Larson – Environmental Science & Technology

Microbial communities as biosensors for monitoring urban environments – Fangqiong Ling – Microbial Biotechnology

Perspectives for microbial community composition in anaerobic digestion: from abundance and activity to connectivity – Jo De Vrieze – Environmental Microbiology

Review: Purification and reuse of non-point source wastewater via Myriophyllum-based integrative biotechnology: A review – Liu F – Bioresource Technology

Improvements in algal lipid production: a systems biology and gene editing approach –  Avik Banerjee – Critical Reviews in Biotechnology

Microbes in the news 

Scientists Make Food From Bacteria, Water, Electricity, and a Whole Lot of Patience

Are you lonesome tonight? Why we, like Elvis, turn to food for comfort

Scientists See Bacteria Responding Electrically to Physical Stimuli for the First Time

Killing bacteria by hacking plastics with silver and electricity

Human Gut Microbes May Help Suppress MS, New Research Suggests 

Unexpected Microbial Life in Glacial Clay Could Offer Antibiotic Solutions