June 25, 2017

Lots of interesting pre-prints in this post that might be worth following! Also a blog post on some cool science art with kombucha, as well as a lot of articles on rhizosphere-microbe interactions.

Events and jobs

Research Opportunities in Molecular Microbiology – Washington University in St. Louis

PhD scholarship in Metagenomics analysis and systems biology – Danmarks Tekniske Universitet

General microbiome

Microbiome yarns: microbial forensics for auditing provenance in global food chains – Timmis et al. – Microbial Biotechnology

Adjuncts and alternatives in the time of antibiotic resistance and in-feed antibiotic bans – Brüssow – Microbial Biotechnology

Human gut microbiome

Bacteria facilitate viral co-infection of mammalian cells and promote genetic recombination – Erickson et al. – bioRXiv

Chemical transformation of xenobiotics by the human gut microbiota – Koppel et al. – Science

Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer – Purcell et al. – bioRXiv

Animal microbiome

Whole genome sequencing-based detection of antimicrobial resistance and virulence in non-typhoidal Salmonella enterica isolated from wildlife – Thomas et al. – bioRXiv

 

Plant, root, and soil microbiome

Antagonism between two root-associated beneficial Pseudomonas strains does not affect plant growth promotion and induced resistance against a leaf-chewing herbivore – Pangesti et al. – FEMS Microbiology Ecology

Bioelectrochemical approach for control of methane emission from wetlands – Liu et al. – Bioresource Technology

The biocontrol agent Pseudomonas chlororaphis PA23 primes Brassica napus defenses through distinct gene networks – Duke et al. – BMC Genomics

Delftia rhizosphaerae sp. nov. isolated from the rhizosphere of Cistus ladanifer – Carro et al. – International Journal of Systematic and Evolutionary Microbiology

Synthesis and Secretion of Isoflavones by Field-Grown Soybean – Sugiyama et al. – Plant Cell Physiology

The Variation in the Rhizosphere Microbiome of Cotton with Soil Type, Genotype and Developmental Stage – Qiao et al. – Scientific Reports

Complete Genome Sequence of Bacillus paralicheniformis MDJK30, a Plant Growth -Promoting Rhizobacterium with Antifungal Activity – Wang et al. – Genome Anouncements

Extensive Overlap of Tropical Rainforest Bacterial Endophytes between Soil, Plant Parts, and Plant Species – Haruna et al. – Microbial Ecology

Phytoavailability of Cr in Silene vulgaris: The role of soil, plant genotype and bacterial rhizobiome – García-Gonzalez et al. – Ecotoxicology and Environmental Safety

Water and extremophile microbiome

Sulfolobus islandicus meta-populations in Yellowstone National Park hot springs – Campbell et al. – Environmental Microbiology

Bottled aqua incognita: Microbiota assembly and dissolved organic matter diversity in natural mineral waters – Lesaulnier et al. – bioRXiv

Techniques

Rapid whole genome amplification and sequencing of low cell numbers in a bacteraemia model – Anscombe et al. – bioRXiv

Microbes in the news

Do Probiotics Really Work? – Ferris Jabr – Scientific American

Fungi and bacteria team up in dental plaque – Evans – LabRoots

Scientists spy on the secret inner life of bacteria – Saey – Science News

Biofilms: The eradication has begun – McGill University Health Centre – Science Daily

Bacteria and Mental Health: Gut Bacteria Linked to Bipolar Disorder – Villamil – Medical News Bulletin

The Kombucha Craze Steps into Art and the Science of the Microbiome – Fernández – Labiotech

Microbes on the market

Global Microbiome Drugs Industry Market Research Report 2017 – Medgadget

June 17, 2017

Today: A few job searches, a lot of microbes in the news (as we all ponder our bread choices), and some articles about microbes in the wild.

Events and jobs

Assistant Professor-Microbiology (Tenure-Track) – The College of New Jersey

Microbiology Technician – Matchtech, England

Microbiology Analyst – Stericycle, Massachusetts

Animal microbiome

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

Water and extremophile microbiome

Undocumented Potential For Primary Productivity In A Globally-Distributed Bacterial Photoautotroph – Graham et al, bioRxiv (pre-print)

Microbes in the news

White or Whole Wheat Bread Study May Shed Light on Diet Failure – Patrick Keeffe, HealthLine

Gene transfer keeps bacteria fit – University of Basel, Phys.org

In dying, blood-starved heart, bacteria injections offer cellular life support – Beth Mole, Ars Technica

New antibiotic effective against drug-resistant bacteria – Rutgers University, Science Daily

May 21, 2017

Events and jobs

FULLY FUNDED POSTDOCTORAL FELLOW POSITION TO STUDY MICROBIOME-BEHAVIOR INTERACTIONS: PORTUGAL

General microbiome

Bioinorganic antimicrobial strategies in the resistance era – Regiel-Futyra et al, Coordination Chemistry Reviews

Biofilm microenvironment induces a widespread adaptive amino-acid fermentation pathway conferring strong fitness advantage in Escherichia coli – Letoffe et al, PLoS Genetics

A bloodstream infection by Ruminococcus gnavus in a patient with a gall bladder perforation – Kim et al, Anerobe

Microbial community compositional analysis for membrane bioreactor treating antibiotics containing wastewater – Zhu et al, Chemical Engineering Journal

Thermophilic Moorella thermoautotrophica-immobilized cathode enhanced microbial electrosynthesis of acetate and formate from CO2 – Yu et al, Bioelectrochemistry

Arumberiamorph structure in modern microbial mats: implications for Ediacaran palaeobiology – Kolesnikov et al, Bulletin de la Société Géologique de France

Succession in the petroleum reservoir microbiome through an oil field production lifecycle – Vigneron et al, ISME

Human respiratory microbiome

Population Genomic Analysis of 1,777 Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolates, Houston, Texas: Unexpected Abundance of Clonal Group 307 – Long et al, Mbio

Human oral microbiome

Pro-resolving mediators in the regulation of periodontal disease – Van Dyke, Molecular Aspects of Medicine

A structure-derived snap-trap mechanism of a multispecific serpin from the dysbiotic human oral microbiome – Goulas et al, Journal of Biological Chemistry

Human gut microbiome

Is frozen fecal microbiota transplantation as effective as fresh fecal microbiota transplantation in patients with recurrent or refractory clostridium difficile infection: a meta-analysis? – Tang et al, Diagnostic Microbiology and Infectious Disease

Weight-loss interventions and gut microbiota changes in overweight and obese patients: a systematic review – Seganfredo et al, Obesity Reviews

 

Dysbiosis of Gut Microbiome and Its Impact on Epigenetic Regulation – Lee et al, Journal of Clinical Epigenetics

Hypoxia and Inactivity Related Physiological Changes (Constipation, Inflammation) Are Not Reflected at the Level of Gut Metabolites and Butyrate Producing Microbial Community: The PlanHab Study – Sket et al, Frontiers in Physiology

Is there a potential role of fecal microbiota transplantation in the treatment of inflammatory bowel disease? – Eun, Intestinal Research

Diet and contaminants: driving the rise to obesity epidemics? – Di Ciaula and Portincasa, Current Medical Chemistry

How to: Establish and run a stool bank – Terveer et al, Clinical Microbiology and Infection

Animal experiments

Transforming growth factor β: a master regulator of the gut microbiota and immune cell interactions – Bauche and Marie, Clinical and Translational Immunology

Aloin, a Component of the Aloe Vera Plant Leaf, Induces Pathological Changes and Modulates the Composition of Microbiota in the Large Intestine of F344/N Male Rats – Boudraeu et al, Toxicology Science

Diabetes-associated microbiota in fa/fa rats is modified by Roux-en-Y gastric bypass – Arora et al, ISME

Absorption and degradation of sulfated polysaccharide from pacific abalone in in vitro and in vivo models – Ai et al, Journal of Functional Foods

Dietary ZnO nanoparticles alters intestinal microbiota and inflammation response in weaned piglets – Xia et al, Oncotarget

Dietary delta-tocotrienol favors abundance and diversity of beneficial microbiomes in obese male mice – Shen et al, FASEB

Bile acid binding resin prevents fat accumulation through intestinal microbiota in high-fat diet-induced obesity in mice – Kusumoto et al, Metabolism

In vitro ability of mastitis causing pathogens to form biofilms – Schonborn et al, Journal of Dairy Research

Dysbiosis of Intestinal Microbiota and Decreased Antimicrobial Peptide Level in Paneth Cells during Hypertriglyceridemia-Related Acute Necrotizing Pancreatitis in Rats – Huang et al, Frontiers in Microbiology

Effects of replacing Leymus chinensis with whole-crop wheat hay on Holstein bull apparent digestibility, plasma parameters, rumen fermentation, and microbiota – Niu et al, Scientific Reports

Physiological responses of insects to microbial fermentation products: insights from the interactions between Drosophila and acetic acid – Kim et al, Journal of Insect Physiology

Animal microbiome

Molecular detection by analysis of the 16S rRNA gene of fecal coliform bacteria from the two Korean Apodemus species (Apodemus agrarius and A. peninsulae) – Rahman et al, Genetics and Molecular Research

Detection and genetic characterization of Pasteurella multocida from alpaca (Vicugna pacos) pneumonia cases – Rimac et al, Tropical Animal Health and Production

Plant, root, and soil microbiome

Soil depth and crop determinants of bacterial communities under ten biofuel cropping systems – Zhang et al, Soil Biology and Biochemistry

Ground cover and slope exposure effects on micro- and mesobiota in forest soils – Gomez-Brandon et al, Ecological Indicators

Root chemical traits and their roles in belowground biotic interactions – Tsunoda and van Dam, Pedobiologia

Proteomics analysis of Fusarium proliferatum under various initial pH during fumonisin production – Li et al, Journal of Proteomics

Culturable bacterial diversity from the chestnut (Castanea sativa Mill.) phyllosphere and antagonism against the fungi causing the chestnut blight and ink diseases – Valverde et al, AIMS Microbiology

Water and extremophile microbiome

The removal of nitrogen compounds from farming wastewater – The effect of different carbon substrates and different microbial activators – Mankiewicz-Boczek et al, Ecological Engineering

How do physicochemical properties influence the toxicity of silver nanoparticles on freshwater decomposers of plant litter in streams? – Batista et al, Ecotoxicology and Environmental Safety

The heterogeneity of composition and assembly processes of the microbial community between different nutrient loading lake zones in Taihu Lake – Zhao et al, Applied Microbiology and Biotechnology

Towards a sustainable biobased industry – Highlighting the impact of extremophiles – Kruger et al, New Biotechnology

Distribution and genetic diversity of microbial populations in the pilot-scale biofilter for simultaneous removal of ammonia, iron and manganese from real groundwater – Cheng et al, Chemosphere

Pilot plant demonstration of stable and efficient high rate biological nutrient removal with low dissolved oxygen conditions – Keene et al, Water Research

Study on The Removal of Hexavalent Chromium from Contaminated Groundwater using Emulsified Vegetable Oil – Wen et al, Process Safety and Environmental Protection

A Novel Roseosiphophage Isolated from the Oligotrophic South China Sea – Yang et al, Viruses

Oxidative Stickland reactions in an obligate aerobic organism — amino acid catabolism in the Crenarchaeon Sulfolobus solfataricus – Stark et al, FEBS

Microbial Diversity in Extreme Marine Habitats and Their Biomolecules – Poli et al, Microorganisms

Methanogenic community was stable in two contrasting freshwater marshes exposed to elevated atmospheric CO2 – Lin et al, Frontiers in Microbiology

Plant-microbial interactions in agriculture and the use of farming systems to improve diversity and productivity – Ishaq, AIMS Microbiology

Effect of arbuscular mycorrhizal fungi on survival and growth of micropropagated Comanthera mucugensis spp. mucugensis (Eriocaulaceae) – Pereira et al, African Journal of Agricultural Research

Native communities of arbuscular mycorrhizal fungi associated with Capsicum annuum L. respond to soil properties and agronomic management under field conditions – Carballar-Hernandez et al, Agriculture, Ecosystems & Environment

Food microbiology

Microbial cell-free extracts affect the biochemical characteristics and sensorial quality of sourdough bread – Cavallo et al, Food Chemistry

Analysis of the microbiota of refrigerated chopped parsley after treatments with a coating containing enterocin AS-48 or by high-hydrostatic pressure – Burgos et al, Food Research International

Microorganisms Found in MPR and Packaged Produce and Their Detection Methods – Acar and Soyer, Minimally Processed Refridgerated Fruits and Vegetables, Food Engineering Series

Applications of Kluyveromyces marxianus in Biotechnology – Varela et al, Yeast Diversity in Human Welfare

Mucin- and carbohydrate-stimulated adhesion and subproteome changes of the probiotic bacterium Lactobacillus acidophilus NCFM – Celebioglu et al, Journal of Proteomics

Techniques

Metaproteomics-guided selection of targeted enzymes for bioprospecting of mixed microbial communities – Speda et al, Biotechnology Biofuels

Microbes in the news

Probiotics are popular, but some questions remain – Reading Eagle

April 23, 2017

Water and extremophile microbiome

Size fractionated phytoplankton biomass and net metabolism along a tropical estuarine gradient – Sara Soria-Píriz – Limnology and Oceanography

Tropical mangrove swamp metagenome reveals unusual abundance of ecologically important microbes – Zahidah Ismail – Current Science

Techniques

HirBin: high-resolution identification of differentially abundant functions in metagenomes – Tobias Österlund – BMC Genomics

Microbes in the news

Using elements of viruses, antibodies to fight resistant bacteria – Chris Dall – CIDRAP News

Lower Hutt officials investigate bacteria in water – Newshub

Stowaway Bacteria Could Be Even More Contagious in Space Than We Thought – Peter Dockrill – Science Alert

April 16, 2017

A post with an overgrowth of gut and skin microbiome papers. Talk about dysbiosis!

 

General microbiome

The ovarian cancer oncobiome – Sagarika Banerjee – Oncotarget

A metagenomic approach to decipher the indigenous microbial communities of arsenic contaminated groundwater of Assam – Saurav Das – Genomics Data

Applying the design-build-test paradigm in microbiome engineering – Hoang Long Pham – Current Opinion in Biotechnology

Microbiota and their affiliation with physiochemical characteristics of different subsurface petroleum reservoirs – Xiao-Xiao Li – International Biodeterioration & Biodegradation

Sampling, sequencing and the SAD – Sharon Bewick – Ecological Complexity

Pregnancy and early life

The Maternal Diet, Gut Bacteria, and Bacterial Metabolites during Pregnancy Influence Offspring Asthma – Lawrence E. K. Gray – Frontiers in Immunology

Deficiency Leads to Dysbiosis and Bacterial Translocation in the Newborn Intestine – Jason Fawley – Journal of Surgical Research

Human respiratory microbiome

The microbiome of the lung and its extracellular vesicles in nonsmokers, healthy smokers and COPD patients – Hyun Jung Kim – Experimental & Molecular Medicine

Human skin microbiome

The Molecular Revolution in Cutaneous Biology: Investigating the Skin Microbiome – Heidi H. Kong – Journal of Investigative Dermatology

Microbiome controls mast cell differentiation in the skin – Z. Wang – Journal of Investigative Dermatology

Inflammatory gene expression in keratinocytes is regulated by HDAC8 and HDAC9 and is modulated by metabolites from the microbiome – J. Sanford – Journal of Investigative Dermatology

Ultraviolet radiation alters the skin microbiome composition – H. Ahmed – Journal of Investigative Dermatology

Isolation and Identification of the follicular microbiome: Implications for acne research – Amanda Nelson – Journal of Investigative Dermatology

Role of the cutaneous microbiome in the pathogenesis of psoriasis – D. Yan – Journal of Investigative Dermatology

Skin microbiome and psoriasis: Staphylococcus induces robust biofilm formation by Aspergillus – Pranab Mukherjee – Journal of Investigative Dermatology

Microbiome-free fatty acid cross-talk in the human pilosebaceous gland – S. Singh – Journal of Investigative Dermatology

Changes of lesional and non-lesional skin microbiome in the treatment course of atopic dermatitis – J. Na – Journal of Investigative Dermatology

Human gut microbiome

Clinical, functional, behavioural and epigenomic biomarkers of obesity – Claudio L. Lafortuna – Frontiers in Bioscience

‘Collinsella phocaeensis’ sp. nov., ‘Clostridium merdae’ sp. nov., ‘Sutterella massiliensis’ sp. nov., ‘Sutturella timonensis’ sp. nov., ‘Enorma phocaeensis’ sp. nov., ‘Mailhella massiliensis’ gen. nov., sp. nov., ‘Mordavella massiliensis’ gen. nov., sp. nov. and ‘Massiliprevotella massiliensis’ gen. nov., sp. nov., 9 new species isolated from fresh stool samples of healthy French patients – S. Ndongo – New Microbes and New Infections

Editorial: Understanding Crohn’s Disease: Immunity, Genes and Microbes – Amelia Sarmento – Frontiers in Immunology

Human Derived Gut Microbiota Modulates Colonic Secretion in Mice by Regulating 5-HT3 Receptor Expression via Acetate Production – Yogesh Bhattarai – American Journal of Physiology: Gastrointestinal and Liver Physiology

Gastroparesis and lipid metabolism-associated dysbiosis in Wistar Kyoto rats – Julie E Dalziel – American Journal of Physiology: Gastrointestinal and Liver Physiology

How do they stick together? Bacterial adhesins implicated in the binding of bacteria to the human gastrointestinal mucins – Bélinda Ringot-Destrez – Biochemical Society Transactions

Relationships between gut microbiota, plasma metabolites, and metabolic syndrome traits in the METSIM cohort – Elin Org – BioMed Central Genome Biology

Gut microbiota plays a role in the development of alopecia areata – Lekha Nair – Journal of Investigative Dermatology

Dysbiosis of gut microbiota by ampicillin exacerbates vitiligo – S. Akhtar – Journal of Investigative Dermatology

More frequent hemodialysis does not effectively clear protein-bound azotemic solutes derived from gut microbiome metabolism – Andrew Davenport – Kidney International

Gut microbiota and Hepatitis B virus-Induced Chronic Liver Disease: implications for faecal microbiota transplantation therapy – Yongbo Kang – Journal of Hospital Infection

The effect of probiotics as a treatment for constipation in elderly people: a systematic review – Maria Isabel Martínez-Martínez – Archives of Gerontology and Geriatrics

Colonic microbiota encroachment correlates with dysglycemia in humans – Benoit Chassaing – Cellular and Molecular Gastroenterology and Hepatology

Animal microbiome

Liver microbiome of Peromyscus leucopus, a key reservoir host species for emerging infectious diseases in North America – Adrien André – Infection, Genetics and Evolution

Plant, root, and soil microbiome

Conversion of rainforest into agroforestry and monoculture plantation in China: Consequences for soil phosphorus forms and microbial community – Jinchuang Wang – Science of the Total Environment

Tuber indicum shapes the microbial communities of ectomycorhizosphere soil and ectomycorrhizae of an indigenous tree (Pinus armandii) – Qiang Li – PLoS ONE

Draft Genome Sequence of Chryseobacterium sp. JV274 Isolated from Maize Rhizosphere – Jordan Vacheron – Genome Anouncements

Wars between microbes on roots and fruits – Ben Lugtenberg – F1000Research

Food microbiology

Metagenomic assessment of the microbial diversity in ground pork products from markets in the North Central Region of South Korea – Ok-Kyung Koo – Journal
Journal of Environmental Science and Health

Growth of selected probiotic bacterial strains with fructans from Nendran banana and garlic – Ravichandran Shalini – LWT: Food Science and Technology

Techniques

Suitability of various DNA extraction methods for a traditional Chinese paocai system
Nan Zhao – Bioengineered

Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies – William W. Greenwald – BioMed Central Genomics

Microbes in the news

IISc makes two potent molecules to fight TB – Ravindranath Prasad – The Hindu

Essential California: Inside UC Irvine hospital’s bacteria outbreak among infants – Benjamin Oreskes and Shelby Grad – Los Angeles Times

April 2, 2017

An article on the transfer of Rickettsia via ticks and news articles on various pathogens in the news!

Events and jobs

Bioengineering researcher – Shell Oil Company

Animal microbiome

Catalase is a determinant of the colonization and transovarial transmission of Rickettsia parkeri in the Gulf Coast tick Amblyomma maculatum – Khemraj Budachetri – Insect Molecular Biology

Microbes in the News

Bacteria could be cause of dolphin stranding deaths on Cape – Mary Ann Bragg – Cape Cod Times

Bacteria found in drinking water flushed – Marianne Napoles – Champion Newspapers

NICU at Maryland hospital to reopen after investigation of Pseudomonas bacteria – Arelis R. Hernández – Albuquerque Journal

February 4, 2017

Today: articles on the nutrient niches that exist in the gut, how bifidobacterium might be functioning as a probiotic, and probiotic treatment in Bactrocera cucurbitae (melon fly), and astronaut’s gut bacteria in flight.

General microbiome

Effect of fermentation temperature on hydrogen production from xylose and the succession of hydrogen-producing microflora – Chunsheng Qiu – Journal of Chemical Technology and Biotechnology

Dental and periodontal health, and microbiological and salivary conditions in patients with or without diabetes undergoing haemodialysis – Gerhard Schmalz – International Dental Journal

Human gut microbiome

Microbial nutrient niches in the gut – Fátima C. Pereira – Environmental Microbiology

MicroRNAs at the epicenter of intestinal homeostasis – Antoaneta Belcheva – BioEssays

Oscillospira and related bacteria – From metagenomic species to metabolic features – Uri Gophna – Environmental Microbiology

Association between small-intestinal bacterial overgrowth and deep vein thrombosis in patients with spinal cord injuries – X. Cheng – Journal of Thrombosis and Haemostasis

Prioritization of polysaccharide utilization and control of regulator activation in Bacteroides thetaiotaomicron – Nathan D. Schwalm III – Molecular Microbiology

Animal experiments

Malondialdehyde epitopes are sterile mediators of hepatic inflammation in hypercholesterolemic mice – Clara Jana-Lui Busch – Hepatology

Time- and strain-specific downregulation of intestinal EPAS1 via miR-148a by Bifidobacterium bifidum – Amel Taibi – Molecular Nutrition and Food Research

Animal microbiome

Enhanced fitness of a Bactrocera cucurbitae genetic sexing strain based on the addition of gut-isolated probiotics (Enterobacter spec.) to the larval diet – Mingyan Yao – Entomologia Experimentalis et Applicata

Water and extremophile microbiome

Chemotype diversity in Planktothrix rubescens (cyanobacteria) populations is correlated to lake depth – Danka Haruštiaková – Environmental Microbiology Reports

Genomic and physiological analyses of ‘Reinekea forsetii’ reveal a versatile opportunistic lifestyle during spring algae blooms – Burak Avcı – Environmental Microbiology

Techniques

DNA metabarcoding reveals that 200-μm-size-fractionated filtering is unable to discriminate between planktonic microbial and large eukaryotes – Lemian Liu – Molecular Ecology Resources

Microbes in the news

Change in astronaut’s gut bacteria attributed to spaceflight

Oral dose of phage cocktail prevents infection and cholera-like symptoms in animal model

UNH researchers ID bacteria contaminating seafood

Tap Water Free of Diarrhea-Causing Bacteria: Pittsburgh Mayor

Science in the News series kicks off with ‘Big Bacteria, Big Pharma, Big Problems’

Salicylic acid promotes nasal mucosa colonization by Staphylococcus aureus