September 22, 2017

Human Microbiome

Microbiome profile of the amniotic fluid as a predictive biomarker of perinatal outcome – Daichi Urushiyama – Scientific Reports

Role of gut microbiota on cardio-metabolic parameters and immunity in coronary artery disease patients with and without type-2 diabetes mellitus – Lidia Sanchez-Alcoholado – Frontiers in Microbiology

Perspective: Linking the gut microbial ecosystem with the environment: does gut health depend on where we live? – Nishat Tasnim – Frontiers in Microbiology

Effect of caloric restriction on gut permeability, inflammation markers, and fecal microbiota in obese women – Beate Ott – Scientific Reports

Perspective: The immunology of the allergy epidemic and the hygiene hypothesis – Bart N Lambrecht – Nature Immunology

Pearls: The microbiome and the hallmarks of cancer – Laura E. Fulbright – PLoS Pathogens

Exploring the salivary microbiome of children stratified by the oral hygiene index – Izumi Mashima – PLoS ONE

 

Built Site Microbiome

Metagenomic characterization of ambulances across the USA – Niamh B. O’Hara – Microbiome (BMC)

 

Food Microbiome

Review: A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies – Yu Cao – Frontiers in Microbiology

Bottled aqua incognita: microbiota assembly and dissolved organic matter diversity in natural mineral waters – Celine C. Lesaulnier – Microbiome (BMC)

 

Pathogen Research

An engineered bispecific DNA-encoded IgG antibody protects against Pseudomonas aeruginosa in a pneumonia challenge model – Ami Patel – Nature Communications

Illusions regarding Helicobacter pylori clinical trials and treatment guidelines – David Y Graham – Gut (BMJ)

 

Beneficial Microbes

Akkermansia muciniphila May Determine the Ameliorating or Aggravating Effects of Chondroitin Sulfate on Osteoarthritis – Qing-Ping Zeng – Frontiers in Microbiology

Minireview: Next-Generation Beneficial Microbes: The Case of Akkermansia muciniphila – Patrice D. Cani – Frontiers in Microbiology

The PGPR Stenotrophomonas maltophilia SBP-9 augments resistance against biotic and abiotic stress in wheat plants – Prabhat N. Jha – Frontiers in Microbiology

 

Beneficial Molecules

pH-dependant antifungal activity of valproic acid against the human fungal pathogen Candida albicans – Julien Chaillot – Frontiers in Microbiology

Dietary teasaponin ameliorates alteration of gut microbiota and cognitive decline in diet-induced obese mice – Sen Wang – Scientific Reports

Mulberry leaf alleviates streptozotocin-induced diabetic rats by attenuating NEFA signaling and modulating intestinal microflora – Yao Sheng – Scientific Reports

 

Microbial Evolution

New Insights into the Diversity of the Genus Faecalibacterium – Leandro Benevides – Frontiers in Microbiology

 

Environmental Microbiology

Insights into microalga and bacteria interactions of selected phycosphere biofilms using metagenomic, transcriptomic and proteomic approaches – Ines Krohn-Molt – Frontiers in Microbiology

 

Bioinformatics, Genomics and Methodologies

Genomic GC-content affects the accuracy of 16S rRNA gene sequencing based microbial profiling due to PCR bias – Martin I. Bahl – Frontiers in Microbiology

Preprint: Optimizing scoring function of dynamic programming of pairwise profile alignment using derivative free neural network – Kazunori D. Yamada – BioRxiv

Improving contig binning of metagenomic data using dS2 oligonucleotide frequency dissimilarity – Ying Wang – BMC Bioinformatics

A Laboratory Methodology for Dual RNA-Sequencing of Bacteria and their Host Cells In Vitro – James W. Marsh – Frontiers in Microbiology

 

Other

Review: A review of the relationship between the gut microbiota and amino acid metabolism – Rui Lin – Amino Acids (Springer)

 

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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

 

 

September 11, 2017

General microbiome

The evolutionary logic of sepsis – Lajos Rózsa, Infection, Genetics and Evolution

Pan-genome analysis of Bacillus for microbiome profiling – Yihwan Kim, Scientific Reports

Using CRISPR-Cas systems as antimicrobials – David Bikard, Current Opinion in Microbiology

Pregnancy and early life

The composition of the vaginal microbiome in first trimester pregnant women influences the level of autophagy and stress in vaginal epithelial cells – Dimitrios Nasioudis, Journal of Reproductive Immunology

Multi-site human microbiome

Veterinary antibiotics in food, drinking water, and the urine of preschool children in Hong Kong – Na Li, Environment International

Acne vulgaris patients have a distinct gut microbiota in comparison with healthy controls – Y. Deng, Journal of Investigative Dermatology

Immune mechanisms of food allergy and its prevention by early intervention – Victor Turcanu, Current Opinion in Immunology

Intestinal microbiome-gut-brain axis and irritable bowel syndrome – Moser G., Wiener Medizinische Wochenschrift

Human skin microbiome

Integrated metabolome-microbiome analyses to evaluate the alleviating effects of short-term green tea supplementation for UVB-induced erythema – E. Jung, Journal of Investigative Dermatology

Isomerization of urocanic acid by ultraviolet radiation and its role in modulation of skin microbiome, antimicrobial peptides, and immune function – V. Patra, Journal of Investigative Dermatology

Universal transcriptomic analysis of host-microbiome interactions in psoriasis – T. Furnholm, Journal of Investigative Dermatology

Skin microbiota alteration link to skin symptoms after a harsh cleanser – A.G. Gueniche, Journal of Investigative Dermatology

Forensic human identification using skin microbiomes – Sarah E. Schmedes, Applied Environmental Microbiology

Human gut microbiome

“Clostridium mediterraneense” a new bacterial species isolated from the human gut – Sokhna Ndongo, New Microbes and New Infections

Definition, Pathogenesis and Management of that cursed Dyspepsia – Pramoda Koduru, Clinical Gastroenterology and Hepatology

Gastrointestinal Conditions in the Female Athlete – Barry Kent Diduch, Clinics in Sports Medicine

Human oral microbiome

Location-Specific Oral Microbiome Possesses Features Associated with Chronic Kidney Disease – Jianzhong Hu, Kidney International Reports

The salivary microbiome is consistent between subjects and resistant to impacts of short-term hospitalization – Damien J. Cabral, Scientific Reports

Animal experiments

Effects of dietary fructooligosaccharide on the growth, antioxidants, immunity and disease resistance of Chinese mitten crab – Erteng Jia, Aquaculture

The microbiota influences cell death and microglial colonization in the perinatal mouse brain – Alexandra Castillo-Ruiz, Brain, Behavior, and Immunity

Differences in amino acid catabolism by gut microbes with/without prebiotics inclusion in GDDY-based diet affect feed utilization in rainbow trout – Omolola C. Betiku, Aquaculture

Effects of organic acids and essential oils blend on growth, gut microbiota, immune response and disease resistance of Pacific white shrimp (Litopenaeus vannamei) against Vibrio parahaemolyticus – Wangquan He, Fish & Shellfish Immunology

Imazalil exposure induces gut microbiota dysbiosis and hepatic metabolism disorder in zebrafish – Cuiyuan Jin, Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology

Local immune response of two mucosal surfaces of the European seabass, Dicentrarchus labrax, fed tryptophan- or methionine-supplemented diets – R. Azeredo, Fish & Shellfish Immunology

Segment specific responses of intestinal epithelium transcriptome to in-feed antibiotics in pigs – Kaifan Yu, Physiological Genomics

Animal microbiome

Inside the guts of the city: Urban-induced alterations of the gut microbiota in a wild passerine – Aimeric Teyssier, Science of The Total Environment

Bacterial microbiota associated with Rhipicephalus sanguineus(s.l.) ticks from France, Senegal and Arizona – Magalie René-Martellet, Parasites & Vectors

Introduced ascidians harbor highly diverse and host-specific symbiotic microbial assemblages – James S. Evans, Scientific Reports

The interactions between gut microbiota and entomopathogenic fungi: a potential approach for biological control of Blattella germanica (L.) – Fan Zhang, Pest Management Science

Plant, root, and soil microbiome

Volatiles of roots of wild-growing and cultivated Armoracia macrocarpa and their antimicrobial activity, in comparison to horseradish, A. rusticana – Silvana Petrović, Industrial Crops and Products

Rhizospheric metagenome of the terrestrial mangrove fern Acrostichum from Indian Sunderbans – Sayak Ganguli, Genomics Data

Paddy soil microbial communities driven by environment- and microbe-microbe interactions: A case study of elevation-resolved microbial communities in a rice terrace – Weimin Sun, Science of The Total Environment

Identifying the active microbiome associated with roots and rhizosphere soil of oilseed rape – Konstantia Gkarmiri, Applied Environmental Microbiology

Effect of Extracellular Electron Shuttles on Arsenic-Mobilizing Activities in Soil Microbial Communities – Shigeki Yamamura, Journal of Hazardous Materials

Water and extremophile microbiome

Microbiological studies of hot springs in India: a review – Poddar A., Archives of Microbiology

Impact of pyrene and cadmium co-contamination on prokaryotic community in coastal sediment microcosms – Qifang Ding, Chemosphere

Food microbiology

Analysis of bacterial and fungal communities in Marcha and Thiat, traditionally prepared amylolytic starters of India – Shankar Prasad Sha, Scientific Reports

Probiotics / prebiotics

Passion fruit by-product and fructooligosaccharides stimulate the growth and folate production by starter and probiotic cultures in fermented soymilk – Marcela Albuquerque Cavalcanti Albuquerque, International Journal of Food Microbiology

Gut microbiota alterations from different Lactobacillus probiotic-fermented yoghurt treatments in slow-transit constipation – Chen-Jian Liu, Journal of Functional Foods

Microbes in the news

Scientists to Study Health of Plant-Bacteria Symbiosis in California –  Iqbal Pittalwala, UCR Today

Sugars in breast milk may fight harmful bacteria directly – Laura Sanders, Science News

Atopic dermatitis associated with different bacteria depending on disease severity – Andrew Bowser, Dermatology Times

Park Service using lasers to remove Jefferson Memorial’s grimy coating – Jack Moore, WTOP

Startups focus on the microbiome as an organic solution to increase crop yields – Jonathan Shieber, Tech Crunch

September 9, 2017

 

Pregnancy and early life

Pre-pregnancy weight, gestational weight gain, and the gut microbiota of mothers and their infants – MA Stanislawski – Microbiome

 

Human oral microbiome

The tongue microbiome in healthy subjects and patients with intra-oral halitosis – SK Seerangaiyan – Journal of Breath Research

Effects of lactoferrin and lactoperoxidase-containing food on the oral microbiota in the elderly – M Nakano – Microbiology & Immunology

Unraveling the human salivary microbiome diversity in Indian populations – A Sarkar – PLoS One

 

 

Human gut microbiome

Review: Influence of gut microbiota on the development and progression of nonalcoholic steatohepatitis – F de Faria Ghetti – European Journal of Nutrition

Markers of intestinal permeability are already altered in early stages of non-alcoholic fatty liver disease: Studies in children – A Nier – PLoS One

Review: the human intestinal virome in health and disease – SR Carding – AP &T

Meds Modify Microbiome, Mediating Their Effects – NM Koropatkin – Cell Metabolism

 

Animal experiments

Maternal treatment with short-chain fatty acids modulates the intestinal microbiota and immunity and ameliorates type 1 diabetes in the offspring – JC Needell – PLoS One

The intestinal microbiota determines the colitis-inducing potential of T-bet-deficient Th cells in mice – J Zimmermann – European Journal of Immunology

A study of the prebiotic-like effects of tomato juice consumption in rats with diet-induced non-alcoholic fatty liver disease (NAFLD). – FJ García-Alonso – Food & Function

Patterns of host gene expression associated with harboring a foregut microbial community. – KD Kohl – BMC Genomics

 

Animal microbiome 

Bacterial community composition and distribution in different segments of the gastrointestinal tract of wild-caught adult Penaeus monodon – P Mongkol – Aquaculture Research

Enrichment of beneficial bacteria in the skin microbiota of bats persisting with white-nose syndrome – V Lemieux-Labonté – Microbiome

 

Plant, root, and soil microbiome

Soil microbiomes associated with Verticillium wilt suppressive broccoli and chitin amendments are enriched with potential biocontrol agents.  – P Inderbitzin – Phytopathology

Olive mill waste and glyphosate-based herbicide addition to olive grove soils: effects on microbial activities and their responses to drying–rewetting cycles – N Boukhdoud – Soil Use and Management

Changes in soil microbial communities after 10 years of winter wheat cultivation versus fallow in an organic-poor soil in the Loess Plateau of China – H Tian – PLoS One

Host Genotype and Nitrogen Form Shape the Root Microbiome of Pinus radiata. – M Gllart – Microbial Ecology

Microbacterium hibisci sp. nov., isolated from rhizosphere of mugunghwa (Hibiscus syriacus L.). – ZF Yan – Int. J. Syst. Evol. Microbiol.

 

Water microbiome and extremophile 

Microbial ecological associations in the surface sediments of Bohai strait –  B Wang – Chinese Journal of Oceanology and Limnology

Contrasting seasonal drivers of virus abundance and production in the North Pacific Ocean. – PJ Gainer – PLoS One

 

Built environment 

Bacteria and archaea communities in full-scale thermophilic and mesophilic anaerobic digesters treating food wastewater: key process parameters and microbial indicators of process instability – J Lee – Bioresource Technology

 

 

Phages and viruses

Temperate phages as frequency-dependent weapons in bacterial competition – XY Li – bioRxiv

 

Techniques

A novel approach for predicting microbe-disease associations by bi-random walk on the heterogeneous network. – S Zou – PLoS One

Machine learning leveraging genomes from metagenomes identifies influential antibiotic resistance genes in the infant gut microbiome – SF Rahman – bioRxiv

Application of real-time PCR (qPCR) for characterization of microbial populations and type of milk in dairy food products. – C Agrimonti – Critical Reviews in Food Science and Nutrition

Identification of regulatory targets for the bacterial Nus factor complex – G Baniulyte – bioRxiv

Early nasopharyngeal microbial signature associated with severe influenza in children: a retrospective pilot study – S Langevin – The Journal of General Virology

Infection via mosquito bite alters Zika virus replication kinetics in rhesus macaques – D Dudley – bioRxiv

Denitrifying metabolism of the methylotrophic marine bacterium Methylophaga nitratireducenticrescens strain JAM1 – F Mauffrey – bioRxiv

 

Microbes in the news 

Mimicry: by gut bacteria metabolites – Nutra Ingredients

Bacterial ‘aphrodisiac’ sends single-celled organism into mating frenzy – Nature News

Bacteria Use Brainlike Bursts of Electricity to Communicate – Quanta Magazine

Bacteria in Children’s Throats Found Strongly Associated with Bone and Joint Infections – Geneng News

How Farmers Can Help Ensure That We Don’t All Die From Super-Powered Bacteria – Fast Company

Harvey’s Floodwaters Contaminated With Nasty, Dangerous Bacteria – Houston Press

FOR THE FIRST TIME, GUT BACTERIA HAS BEEN SPOTTED EATING CHEMICALS IN THE BRAIN – Collective Evolution

University of Idaho research may slow antibiotic resistance to drugs – The Spokesman

 

August 31, 2017

Today we have a lot of interesting job offers, a lot of news, many papers from Nature’s Scientific Reports and several reviews from Immunological Reviews and to mention each time more and more papers dealing with wastewater treatments. Enjoy your (still) summer microbiome reading.

Events and jobs

Laboratory Manager (Microbiology), Sydney, Australia

Algae Technician, MBD Energy Limited, Townsville 

PhD position: Synthetic Microbiology/Biotechnology, Germany

PhD position (m/f) in the field of microbiota-host interaction in laying hens, Germany

PhD position in the field of microbial ecology of the fowl gastrointestinal tract,  Germany

Post-Doctoral Research Associate, King’s College London , UK

Synthetic Biologist / Geneticist: Ginkgo Bioworks, Boston, MA

General microbiome

Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA – Mark Kowarsky – PNAS

Maintenance of microbial cooperation mediated by public goods in single and multiple traits scenarios – Özhan Özkaya – Journal of Bacteriology

Pregnancy and early life

The oral microbiome and adverse pregnancy outcomes – Charles M Cobb – International Journal of Women’s Health

Human respiratory microbiome

The nasal microbiota of dairy farmers is more complex than oral microbiota, reflects occupational exposure, and provides competition for staphylococci – Sanjay K. Shukla –  PLOS One

Sphenoid sinus microbiota in pituitary apoplexy: a preliminary study – Gavin J. Humphreys – Pituitary

Oral microbiology

Review: Studying the human oral microbiome: challenges and the evolution of solutions – Angela ML Benn – Australian Dental Journal

Human vaginal microbiome

The human vaginal microbial community – Mario Vaneechoutte – Research in Microbiology

Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women – Benjamin J. Callahan – PNAS

Comparison of vaginal microbiota sampling techniques: cytobrush versus swab – Anita Mitra – Scientific Reports

Human nearly-sterile sites 

Dominance of ST131 Escherichia coli carrying blaCTX-M in patients with bloodstream infections caused by cephalosporin-resistant strains in Australia, New Zealand and Singapore: whole genome analysis of isolates from a randomised trial –  Patrick Harris – bioRxiv

Temporal Stability and Composition of the Ocular Surface Microbiome – Jerome Ozkan – Scientific Reports

Human gut microbiome

Review:Interactions between bile salts, gut microbiota, and hepatic innate immunity – Kristin Schubert – Immunological Reviews

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

Review: Gut microbiota: Role in pathogen colonization, immune responses, and inflammatory disease – Joseph M. Pickard – Immunological Reviews

Gut microbiota and chronic kidney disease: implications for novel mechanistic insights and therapeutic strategies – Wei Pan –  International Urology and Nephrology

Ecophylogenetics Reveals the Evolutionary Associations between Mammals and their Gut Microbiota – Christopher Andrew Gaulke -bioRxiv

Unveiling the gut microbiota composition and functionality associated with constipation through metagenomic analyses – Leonardo Mancabelli –  Scientific Reports

Influence of gut microbiota on neuropsychiatric disorders – María Carmen Cenit – World Journal of Gastroenterology

Fecal microbiota transplantation for Clostridium difficile infection in patients with ileal pouches – Nan Lan – Gastroenterology Report

The Intestinal Microbiome in Infectious Diseases: The Clinical Relevance of a Rapidly Emerging Field – Vanessa C Harris – Open Forum Infectious Diseases

A novel approach for the prediction of species-specific biotransformation of xenobiotic/drug molecules by the human gut microbiota – Ashok K. Sharma – Scientific Reports

Animal experiments

Metagenomic Analysis of Cecal Microbiome Identified Microbiota and Functional Capacities Associated with Feed Efficiency in Landrace Finishing Pigs – Zhen Tan – Frontiers in Microbiology

Characterization of the ecological role of genes mediating acid resistance in Lactobacillus reuteri during colonization of the gastrointestinal tract – Janina A. Krumbeck – Environmental Microbiology

Animal microbiome

High Spatial and Temporal Variations of Microbial Community along the Southern Catfish Gastrointestinal Tract: Insights into Dynamic Food Digestion – Zhimin Zhang – Frontiers in Microbiology

Unraveling the gut microbiome of the long-lived naked mole-rat – Tewodros Debebe – Scientific Reports

Plant, root, and soil microbiome

Effects of cationic surfactant on the bioaccumulation of polycyclic aromatic hydrocarbons in rice and the soil microbial community structure – Ni Ni – RSC Advances

The impact of adsorption on the exposure assessment of Bacillus thuringiensis in the water-sediment system: a mathematical model approach – Stefano Cervelli – Biology and Fertility of Soils

Phylogenetic diversity and antagonistic traits of root and rhizosphere pseudomonads of a bean from Iran for controlling Rhizoctonia solani – Vahid Keshavarz-Tohid – Research in Microbiology

Petroleum Contamination and Plant Identity Influence Soil and Root Microbial Communities While AMF Spores Retrieved from the Same Plants Possess Markedly Different Communities – Bachir Iffis – Frontiers in Microbiology

Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence – Y. Colin – Scientific Reports

Microbial communities with distinct denitrification potential in spruce and beech soils differing in nitrate leaching – Jiří Bárta – Scientific Reports

The rhizospheric microbial community structure and diversity of deciduous and evergreen forests in Taihu Lake area, China – Wei Z – PLOS One

Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence – Y. Colin – Scientific Reports

Water and extremophile microbiome 

Seasonal Succession and Spatial Patterns of Synechococcus Microdiversity in a Salt Marsh Estuary Revealed through 16S rRNA Gene Oligotyping – Katherine R. M. Mackey – Frontiers in Microbiology

Independent Shifts of Abundant and Rare Bacterial Populations across East Antarctica Glacial Foreland – Wenkai Yan – Frontiers in Microbiology

Microbial community structure and diversity within hypersaline Keke Salt Lake environments – Rui Han – Canadian Journal of Microbiology

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

A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities – Bennett S. Lambert –  Nature Microbiology

Anaerobic methanotrophic communities thrive in deep submarine permafrost – Matthias Winkel – bioRxiv

Microbial communities in peatlands along a chronosequence on the Sanjiang Plain, China – Xue Zhou – Scientific Reports

Microbial communities in marine sediments modify success of an invasive macrophyte – Paul E. Gribben – Scientific Reports

Built environment 

Novosphingobium clariflavum sp. nov., isolated from a household product plant –  Xin Zhang – International Journal of Systematic and Evolutionary Microbiology

Probiotics / prebiotics

Bifidobacterium longum W11: an antibiotic-resistant probiotic – Francesco Di Pierro – Nutrafoods

Lactobacillus plantarum LP‑Onlly alters the gut flora and attenuates colitis by inducing microbiome alteration in interleukin‑10 knockout mice – Hongqi Chen – Molecular Medicine Reports

Bacillus As Potential Probiotics: Status, Concerns, and Future Perspectives – Fouad M. F. Elshaghabee – Frontiers in Microbiology

Probiotics administration following sleeve gastrectomy surgery: A randomized double-blind trial – S Sherf-Dagan – International Journal of Obesity

Phages and viruses

Infection with purified Piscine orthoreovirus demonstrates a causal relationship with heart and skeletal muscle inflammation in Atlantic salmon – Øystein Wessel  – PLOS One

HPeV-3 predominated among Parechovirus A positive infants in the summer of 2013-2014 in Queensland, Australia – Donna M. McNeale – bioRxiv

Review: A bacteriophages journey through the human body – Jeremy J. Barr – Immunological Reviews

Mouse hepatitis virus nsp14 exoribonuclease activity is required for resistance to innate immunity – James Brett Case – bioRxiv

Bioinformatics

microPop: Modelling microbial populations and communities in R – Helen Kettle – Methods in Ecology and Evolution

Biotechnology

Biodegradation of mono-, di- and trifluoroacetate by microbial cultures with different origins – Diogo A.M. Alexandrino – New Biotechnology

Metagenomic mining pectinolytic microbes and enzymes from an apple pomace-adapted compost microbial community – Man Zhou – Biotechnology for Biofuels

Wastewater microbiology

Unravelling diversity and metabolic potential of microbial consortia at each stage of leather sewage treatment – Hebin Liang – RSC Advances

Influence of microbial community diversity and function on pollutant removal in ecological wastewater treatment – Yaohui Bai – Applied Microbiology and Biotechnology

Techniques

A Comparison of Methods to Analyze Aquatic Heterotrophic Flagellates of Different Taxonomic Groups – Alexandra Jeuck – Protist

Fast and Simple Tool for the Quantification of Biofilm-Embedded Cells Sub-Populations From Fluorescent Microscopic Images – Mikhail Bogachev – bioRxiv

Microbes in the news 

Gut bacteria that “talk” to human cells may lead to new treatments

Gut Microbiome Differences in REM Sleep Behavior Disorder, Parkinson’s, and Healthy Controls

Scientists Made Music From the Human Microbiome, and It’s Seriously Cool

Over 50% of Bacteria and Viruses inside Human Body are Unknown to Science

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 23, 2017

Human Microbiome

The vaginal microbiome of pregnant women is less rich and diverse, with lower prevalence of Mollicutes, compared to non-pregnant women – Aline C. Freitas – Scientific Reports

The IBD interactome: an integrated view of aetiology, pathogenesis and therapy – Heitor S. P. de Souza – Nature Reviews Gastroenterology & Hepatology

Changes in the intestinal microbiota following the administration of azithromycin in a randomised placebo-controlled trial among infants in south India – Edward P. K. Parker – Scientific Reports

High intake of dairy during energy restriction does not affect energy balance or the intestinal microflora compared to low dairy intake in overweight individuals in a Randomized Controlled Trial – Line Quist Bendtsen – Applied Physiology, Nutrition, and Metabolism

Metabolic and functional paths of lactic acid bacteria in plant foods: get out of the labyrinth – Pasquale Filannino –  Current Opinion in Biotechnology

Differences of lung microbiome in patients with clinically stable and exacerbated bronchiectasis – Min Kwang Byun – PLoS ONE

Precision Nutrition: A Review of Personalized Nutritional Approaches for the Prevention and Management of Metabolic Syndrome – Juan de Toro-Martín – Nutrients

 

Animal Microbiome

Soy Improves Cardiometabolic Health and Cecal Microbiota in Female Low-Fit Rats – Tzu-Wen L. Cross – Scientific Reports

Modulatory influence of segmented filamentous bacteria on transcriptomic response of gnotobiotic mice exposed to TCDD – Robert Stedtfeld – Frontiers in Microbiology

Comparative analysis of the gut microbiota composition between captive and wild forest musk deer – Yimeng Li – Frontiers in Microbiology

Modulation of gut microbiome composition and function in experimental colitis treated with Sulphasalazine – Haihui Zheng – Frontiers in Microbiology

Respiratory Commensal Bacteria Corynebacterium pseudodiphtheriticum Improves Resistance of Infant Mice to Respiratory Syncytial Virus and Streptococcus pneumoniae Superinfection – Paulraj Kanmani – Frontiers in Microbiology

 

Pathogen research

Whole-genome sequencing for national surveillance of Shigella flexneri – Marie Anne Chattaway – Frontiers in Microbiology

SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data – Lennard Epping –  BioRxiv

In Vitro Antibacterial Activity of Unconjugated and Conjugated Bile Salts on Staphylococcus aureus – Thippeswamy H. Sannasiddappa –  Frontiers in Microbiology

Environmental Microbiology

Alleviation of heavy metal stress in plants and remediation of soil by rhizosphere microorganisms – Jitendra Mishra – Frontiers in Microbiology

From surface to deep-sea: Bacterial distribution to polymetallic nodule fields at 4000 m in the Clarion-Clipperton Zone of the Pacific Ocean – Markus V. Lindh – Frontiers in Microbiology

Analysis of Microbial Functions in the Rhizosphere Using a Metabolic-Network Based Framework for Metagenomics Interpretation – Shany Ofaim – Frontiers in Microbiology

 

Bioinformatics

Contradictory Results: Low rate of index hopping on the Illumina HiSeq X platform – Tom van der Valk – BioRxiv

Analyzing contentious relationships and outlier genes in phylogenomics – Joseph F. Walker – BioRxiv

Other

Metabolic Reconstruction and Modeling Microbial Electrosynthesis – Christopher W. Marshall – Scientific Reports

Receptor Uptake Arrays For Vitamin B12, Siderophores And Glycans Shape Bacterial Communities – Steven A. Frank – BioRxiv

Diversity of microbiota associated with symptomatic and non-symptomatic bacterial wilt-diseased banana plants determined using 16S rRNA metagenome sequencing – Nurul Shamsinah Mohd Suhaimi – World Journal of Microbiology and Biotechnology

News

Antarctic mystery microbe could tell us where viruses came from – Michael Marshall – New Scientist

Even the Eye Has a Microbiome – Jeff Lyon – JAMA

The Surprising Things Your Microbiome Reveals About You – Ashley Lewis – Readers Digest

Linking mental health and the gut microbiome – MedicalXpress

 

Non-microbiology picks

How to share data for collaboration – Shannon E Ellis – PeerJ preprints