Category Archives: Extremophiles

March 5, 2017

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Here are few interesting articles for your Sunday morning edition. Canadian bacteria-like fossils may be the oldest evidence of life yet.  Black carbon, one of the main components of air pollution,  is reported to drastically change the development of bacterial biofilms and key aspects of bacterial colonization and survival.  A novel organ culture system described for the mouse intestine shows that the nervous system influences the microbiome/immune system crosstalk.  And the power of alternative assays for discovery: Deep sequencing of cell-free DNA from a large patient cohort revealed previously unknown and highly prevalent microbial and viral diversity in humans.

Pregnancy and early life

Prediction of complicated disease course for children newly diagnosed with Crohn’s disease: a multicenter inception cohort study – Subra Kugathasan – The Lancet

Multi-site human microbiome

Humans are colonized by many uncharacterized and highly divergent microbes -Mark A. Kowarsky -bioRxiv

Human respiratory microbiome

Air pollution alters Staphylococcus aureus and Streptococcus pneumonia biofilms, antibiotic tolerance and colonization – Shane J. K. Hussey – Journal of Environmental Microbiology

Human vaginal microbiome

The global health impact of vaginal dysbiosis – Janneke H.H.M. van de Wijgert – Research in Microbiology

Human gut microbiome

An Intestinal Organ Culture System Uncovers a Role for the Nervous System in Microbe-Immune Crosstalk – Nissan Yissachar – Cell

Animal microbiome

Genetic and functional analysis of the bovine uterine microbiota. Part I: Metritis versus healthy cows, Part II: Purulent vaginal discharge versus healthy cows – M.L.S. Bicalho – The journal of Dairy Science

Plant, root, and soil microbiome

Review: Soil-Plant-Microbe Interactions in Stressed Agriculture Management– Shobhit Raj Vimal – Pedosphere

Water and extremophile microbiome

Evidence for early life in Earth’s oldest hydrothermal vent precipitates – Matthew S. Dodd – Nature

Microbes in the news

Study Shows Link Between Microbiome in the Gut and Parkinson’s – University of Alabama at Birmingham

A Japanese study performed by sequencing the gut microbiota of 367 healthy individuals ranging from newborn to 104 years old shows microbiome changes with age

UN issues list of 12 most worrying bacteria

Microbes on the market

Rebiotix Inc. has its lead product for C. diff. treatment granted Fast Track, Orphan Drug, and Breakthrough Therapy status by the FDA.  

February 27, 2017

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The ‘horseshoe effect’ in analyzing microbial niches; fecal microbiota transplantation (FMT) in immunocompromised individuals; effects of long-term ceftriaxone sodium administration on gut microbiota diversity; DNA extraction bias in soil microbial community analysis; and a multistrain probiotic clinical trial in NAFLD.

Events and jobs

Postdoctoral Fellow in Microbiology – University of Tennessee Health Science Center, Memphis, TN

QC Microbiology Analyst – Leidos – Frederick, MD

General microbiome
Uncovering the Horseshoe Effect in Microbial Analyses – James T. Morton – mSystems

Pregnancy and early life
Microbiome, autoimmunity, allergy, and helminth infection: The importance of the pregnancy period – Xian Chen – American Journal of Reproductive Immunology

Implications of intrapartum azithromycin on neonatal microbiota – Jenny Mei – The Lancet Infectious Diseases

Human respiratory microbiome
Restoring CFTR Function Reduces Airway Bacteria and Inflammation in People With Cystic Fibrosis and Chronic Lung Infections – Katherine B. Hisert – American Journal of Respiratory and Critical Care Medicine

Microbiome of the Lung in Patient with Idiopathic Pneumonia Syndrome (IPS) after HCT – Sachiko Seo – Biology of Blood and Marrow Transplantation

Oral and nasal microbiota in Parkinson’s disease – Pedro A.B. Pereira – Parkinsonism & Related Disorders

Human skin microbiome
N-acetylcysteine inhibits growth, adhesion and biofilm formation of Gram-positive skin pathogens – Daria Eroshenko – Microbial Pathogenesis

Human vaginal microbiome
Olegusella massiliensis gen. nov., sp. nov., strain KHD7T, a new bacterial genus isolated from the female genital tract of a patient with bacterial vaginosis – Khoudia Diop – Anaerobe

Bacterial species colonizing the vagina of healthy women are not associated with race – May A. Beamer – Anaerobe

The influence of sexual activity on the vaginal microbiota and Gardnerella vaginalis clade diversity in young women – Vodstrcil LA – PLoS One

Human gut microbiome
Long-term taxonomic and functional divergence from donor bacterial strains following fecal microbiota transplantation in immunocompromised patients – Eli Moss – bioRxiv

Long-term use of ceftriaxone sodium induced changes in gut microbiota and immune system – Yanjie Guo – Scientific Reports

Two dynamic regimes in the human gut microbiome – Sean M. Gibbons – PLoS Computational Biology

Review: The gut microbiome in human neurological disease: A review – Helen Tremlett – Annals of Neurology

The Effects of Moderate Whole Grain Consumption on Fasting Glucose and Lipids, Gastrointestinal Symptoms, and Microbiota – Danielle N. Cooper – Nutrients

Gut microbial profile is altered in primary biliary cholangitis and partially restored after UDCA therapy – Ruqi Tang – Gut

Randomised clinical trial: faecal microbiota transplantation for recurrent Clostridum difficile infection – fresh, or frozen, or lyophilised microbiota from a small pool of healthy donors delivered by colonoscopy – Z. D. Jiang – Alimentary Pharmacology and Therapeutics

Gut microbiota and systemic inflammation changes after bread consumption: The ingredients and the processing influence – Maykel Arias – Journal of Functional Foods

Review: Gut microbiome-based medical methodologies for early-stage disease prevention – Jing-Zhang Wong – Microbial Pathogenesis

The dual role of short fatty acid chains in the pathogenesis of autoimmune disease models – Mizuno M – PLoS One

Giardia duodenalis induces dysbiosis of human intestinal microbiota biofilms – Jennifer K. Beatty – International Journal for Parasitology

Animal experiments
Apple Polysaccharide inhibits microbial dysbiosis and chronic inflammation and modulates gut permeability in HFD-fed rats – Sheng Wang – International Journal of Biological Macromolecules

Animal microbiome
Metatranscriptomic profiling reveals linkages between the active rumen microbiome and feed efficiency in beef cattle – Fuyong Li – Applied and Environmental Microbiology

Plant, root, and soil microbiome
Review: Genomic dissection of host–microbe and microbe–microbe interactions for advanced plant breeding – Samuel Kroll – Current Opinion in Plant Biology

Differential sharing and distinct co-occurrence networks among spatially close bacterial microbiota of bark, mosses and lichens‬‬ – Ines Aline Aschenbrenner – Molecular Ecology

The choice of the DNA extraction method may influence the outcome of the soil microbial community structure analysis – Sylwia Zielińska – Microbiology Open

High-resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils – Adrienne B. Narrowe – Environmental Microbiology

A comprehensive phylogenetic analysis of copper transporting P1B ATPases from bacteria of the Rhizobiales order uncovers multiplicity, diversity and novel taxonomic subtypes – Ciro Cubillas – Microbiology Open

Host-parasite-bacteria triangle: the microbiome of the parasitic weed Phelipanche aegyptiaca and tomato-Solanum lycopersicum (Mill.) as a host – Lilach Iasur Kruh – Frontiers in Plant Science

Diversity of root-associated fungi of Vaccinium mandarinorum along a human disturbance gradient in subtropical forests, China – Yanhua Zhang – Journal of Plant Ecology

Loss of soil microbial diversity may increase insecticide uptake by crop – Min Zhang – Agriculture, Ecosystems & Environment

The presence of aggressive ants is associated with insect visits to coffee flowers and floral microbe communities – Rachel L. Vannette – Basic and Applied Ecology

Metagenomic assessment of methane production-oxidation and nitrogen metabolism of long term manured systems in lowland rice paddy – P. Bhattacharyya – Science of the Total Environment

The Introduction of Woody Plants For Freshwater Wetland Restoration Alters The Archaeal Community Structure in Soil – Xiao-Yan Liu – Land Degradation & Development

A distinctive root-inhabiting denitrifying community with high N2O/(N2O+N2) product ratio – Chao Ai – Soil Biology and Biochemistry

Plant cultivars imprint the rhizosphere bacterial community composition and association networks – Yuji Jiang – Soil Biology and Biochemistry

Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees – Bram Beckers – Microbiome

Water and extremophile microbiome
Development of a prototype 16S rRNA gene-based microarray for monitoring planktonic actinobacteria in shrimp ponds – Jingjing Wang – International Aquatic Research

Serpentinization-influenced groundwater harbors extremely low diversity microbial communities adapted to high pH – Katrina I. Twing – Frontiers in Microbiology

Cold adaptation of the Antarctic haloarchaea Halohasta litchfieldiae and Halorubrum lacusprofundi – Timothy J. Williams – Environmental Microbiology

Diversity of crude oil-degrading bacteria and alkane hydroxylase (alkB) genes from the Qinghai-Tibet Plateau – Haozhi Long – Environmental Monitoring and Assessment

Ubiquitous and persistent Proteobacteria and other Gram-negative bacteria in drinking water – Ivone Vaz-Moreira – Science of the Total Environment

Acidicapsa ferrireducens sp. nov., Acidicapsa acidiphila sp. nov., and Granulicella acidiphila sp. nov.: novel acidobacteria isolated from metal-rich acidic waters – Carmen Falagán – Extremophiles

Synthetic extreme environments: overlooked sources of potential biotechnologically relevant microorganisms – Timothy Sibanda – Microbial Biotechnology

Acinetobacter halotolerans sp. nov., a novel halotolerant, alkalitolerant, and hydrocarbon degrading bacterium, isolated from soil – Ram Hari Dahal – Arhives of Microbiology

Physiological and comparative genomic analysis of Acidithiobacillus ferrivorans PQ33 provides psychrotolerant fitness evidence for oxidation at low temperature – Robert Ccorahua-Santo – Research in Microbiology

Genome-resolved metagenomics of a bioremediation system for degradation of thiocyanate in mine water containing suspended solid tailings – Sumayah F. Rahman – Microbiology Open

Food microbiology
Nondairy beverage produced by controlled fermentation with potential probiotic starter cultures of lactic acid bacteria and yeast – Ana Luiza Freire – International Journal of Food Microbiology

Probiotics / prebiotics
Targeting the Microbiota-Gut-Brain Axis: Prebiotics Have Anxiolytic and Antidepressant-like Effects and Reverse the Impact of Chronic Stress in Mice – Aurelijus Burokas – Biological Psychiatry

Review: Clinical effects of probiotics in cystic fibrosis patients: A systematic review – Stephanie Van Biervliet – Clinical Nutrition ESPEN

Effects of Multistrain Probiotic Supplementation on Glycemic and Inflammatory Indices in Patients with Nonalcoholic Fatty Liver Disease: A Double-Blind Randomized Clinical Trial – Abbaszadeh Sepideh – Journal of the American College of Nutrition

Microbes in the news
Glass Microbiology at the At-Bristol Science Centre – Culture Calling

Bacteria And Babies: A Scientific Debate – Part One – American Council on Science and Health

Reference: Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns – Maria G. Dominguez-Bello – PNAS

February 24, 2017

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Bioassay-guided metabolomics reveal new polyketide macrolactams from termite-associated actinomycete, the microbiota affects host antibody repertoire, artist makes agar molds of her face and grows bacteria on them, the fecal microbiota of Old World vultures.

Events and jobs

“Research Instructor – Microbiology & Immunology” at the Medical University of South Carolina

General microbiome

Review: Carcinogenesis and therapeutics: the microbiota perspective – Matthew C. B. Tsilimigras – Nature Microbiology

Pregnancy and early life

Review: Microbiome, autoimmunity, allergy, and helminth infection: The importance of the pregnancy period – Xian Chen – American Journal of Reproductive Immunology

Impact of microbial invasion of amniotic cavity and the type of microorganisms on short-term neonatal outcome in women with preterm labor and intact membranes – Teresa Cobo – Acta Obstetricia et Gynecologica Scandinavica

Human oral microbiome

Betel nut chewing, oral premalignant lesions, and the oral microbiome – Brenda Y. Hernandez – PLOS One

Human gut microbiome

Review: Gut Microbiota: A Potential Regulator of Neurodevelopment – Paola Tognini – Frontiers in Cellular Neuroscience

New evidences on the altered gut microbiota in autism spectrum disorders – Francesco Strati – Microbiome

Massilioclostridium coli gen. nov., sp. nov., a new member of the Clostridiaceae family isolated from the left colon of a 27-year-old woman – C. I. Lo – New Microbes and New Infections

Impact of humic acids on the colonic microbiome in healthy volunteers – Alexander Swidsinski – World Journal of Gastroenterology

Animal experiments

* IgD class switching is initiated by microbiota and limited to mucosa-associated lymphoid tissue in mice – Jin Huk Choi – PNAS

An Intestinal Farnesoid X Receptor-Ceramide Signaling Axis Modulates Hepatic Gluconeogenesis in Mice – Cen Xie – Diabetes

Effects of xylanase supplementation on growth performance, nutrient digestibility, blood parameters, fecal microbiota, fecal score and fecal noxious gas emission of weaning pigs fed corn-soybean meal-based diet – Ruixia Lan – Animal Science Journal

Animal microbiome

Assessment of Ruminal Bacterial and Archaeal Community Structure in Yak (Bos grunniens) – Zhenming Zhou – Frontiers in Microbiology

Changes in Metabolically Active Bacterial Community during Rumen Development, and Their Alteration by Rhubarb Root Powder Revealed by 16S rRNA Amplicon Sequencing – Zuo Wang – Frontiers in Microbiology

Metataxonomics reveal vultures as a reservoir for Clostridium perfringens – Xiangli Meng – Emerging Microbes and Infections

The fecal microbiome of dogs with exocrine pancreatic insufficiency – Anitha Isaiah – Anaerobe

Plant, root, and soil microbiome

Host-parasite-bacteria triangle: the microbiome of the parasitic weed Phelipanche aegyptiaca and tomato-Solanum lycopersicum (Mill.) as a host – Lilach Iasur Kruh – Frontiers in Plant Science

Diversity of root-associated fungi of Vaccinium mandarinorum along a human disturbance gradient in subtropical forests, China – Yanhua Zhang – Journal of Plant Ecology

Effects of long-term heavy metals contamination on soil microbial characteristics in calcareous agricultural lands (Saiss plain, North Morocco) – A. Kouchou – Journal of Materials and Environmental Sciences

Global transcriptional response to salt shock of the plant microsymbiont Mesorhizobium loti MAFF303099 – Marta Laranjo – Research in Microbiology

Novosphingobium pokkalii sp nov, a novel rhizosphere-associated bacterium with plant beneficial properties isolated from saline-tolerant pokkali rice – Ramya Krishnan – Research in Microbiology

Assembly patterns of soil-dwelling lichens after glacier retreat in the European Alps – Juri Nascimbene – Journal of Biogeography

Soil classification predicts differences in prokaryotic communities across a range of geographically distant soils once pH is accounted for – Rachel Kaminsky – bioRxiv

Water and extremophile microbiome

Different types of diatom-derived extracellular polymeric substances drive changes in heterotrophic bacterial communities from intertidal sediments – Julio Bohorquez – Frontiers in Microbiology

Broadcast Spawning Coral Mussismilia hispida Can Vertically Transfer its Associated Bacterial Core – Deborah C. A. Leite – Frontiers in Microbiology

Built environment

Microbial diversity of a full-scale UASB reactor applied to poultry slaughterhouse wastewater treatment: integration of 16S rRNA gene amplicon and shotgun metagenomic sequencing – Tiago Palladino Delforno – MicrobiologyOpen

Metabolomics

* Macrotermycins A−D, Glycosylated Macrolactams from a Termite- Associated Amycolatopsis sp. M39 – Christine Beemelmanns – Organic Letters

compMS2Miner: an automatable metabolite identification, visualization and data-sharing R package for high-resolution LC-MS datasets – William Matthew Bell Edmands – Analytical Chemistry

More microbes

Indole production provides limited benefit to Escherichia coli during co-culture with Enterococcus faecalis – Shelly L. Pringle – Archives of Microbiology

Microbes in the news

* Art Grows on You – Lara Medlam – Nouse

Beware! Are bacteria raising your oxidative stress? – Purna Kashyap – Science Translational Medicine

Microbes on the market

Finch Therapeutics Announces Strategic Collaboration with OpenBiome to Develop Microbiome Therapies for FDA Approval – Business Wire

February 23, 2017

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Today’s selection includes an interesting review on how bacteria keep their time. Long term ceftriaxon sodium usage alters gut microbiota and immune system. Clostridium perfringens toxin genes in the gut microbiota of autistic children. Taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic. Enjoy!

General microbiome

Distinct signatures of dental plaque metabolic byproducts dictated by periodontal inflammatory status. – Akito Sakanaka – Scientific Reports

*Review: Timing the day: what makes bacterial clocks tick? – Carl Hirschie Johnson – Nature Reviews Microbiology

Human urinary microbiome

Review: The female urinary microbiota, urinary health and common urinary disorders. – Linda Brubaker – Annals of Translational Medicine

Review: Questions and challenges associated with studying the microbiome of the urinary tract – Yige Bao – Annals of Translational Medicine

Review: The association between bacteria and urinary stones. – Andrew L. Schwaderer – Annals of Translational Medicine

Human nearly-sterile sites 

The Conserved Phylogeny of Blood Microbiome – Malay Bhattacharyya – Molecular Phylogenetics and Evolution

Human gut microbiome

Review: The gut microbiome in human neurological disease: A review. – Helen Tremlett – Annals of Neurology

Review: Gut microbiome-based medical methodologies for early-stage disease prevention – Jing-Zhang Wang – Microbial Pathogenesis

Review: Gut microbiome and chronic prostatitis/chronic pelvic pain syndrome. – Hans C. Arora – Annals of Translational Medicine

*Long-term use of ceftriaxone sodium induced changes in gut microbiota and immune system. – Yanjie Guo – Scientific Reports

Note Elies Bik: This study was not performed in humans but in a horrible rat model that can only be qualified as torture. This does not test for depression but for extreme stress. Should not have performed. Proceed with extreme caution. Variations in gut microbiota and fecal metabolic phenotype associated with depression by 16S rRNA gene sequencing and LC/MS-based metabolomics. – Meng Yu – Journal of Pharmaceutical and Biomedical Analysis

Specific inulin-type fructan fibers protect against autoimmune diabetes by modulating gut immunity, barrier function and microbiota homeostasis. – Kang Chen – Molecular Nutrition and Food Research

Gut microbiota and oxalate homeostasis. – Marguerite Hatch – Annals of Translational Medicine

Tryptophan: A gut microbiota-derived metabolites regulating inflammation. – Lucie Etienne-Mesmin –  World Journal of Gastrointestestinal Pharmacology

*Detection of Clostridium perfringens toxin genes in the gut microbiota of autistic children. – Sydney M. Finegold – Anaerobe

Animal experiments

Butyrate restores HFD induced adaptations in brain function and metabolism in mid-adult obese mice – Ilse A. C. Arnoldussen – International Journal of Obesity

Toxin-positive Clostridium difficile latently infect mouse colonies and protect against highly pathogenic C. difficile. – Lucie Etienne-Mesmin – Gut

Animal microbiome

Individual Signatures Define Canine Skin Microbiota Composition and Variability. – Anna Cuscó – Frontiers in Veterinary Science

Plant, root, and soil microbiome

Differential sharing and distinct co-occurrence networks among spatially close bacterial microbiota of bark, mosses and lichens‬‬. – Ines Aline Aschenbrenner – Molecular Ecology

Links between soil microbial communities and plant traits in a species-rich grassland under long-term climate change. – Lin Li – Ecology and Evolution

Water and extremophile microbiome

*Metagenomic survey of the taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic. – Etienne Yergeau – Scientific Reports

High-resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils. – Adrienne Narrowe – Environmental Microbiology

Food microbiology

Enhanced Control of Listeria monocytogenes by Enterococcus faecium KE82, a Multiple Enterocin–Producing Strain, in Different Milk Environments. – Elpinki Vandera – Journal of food protection

Probiotics / prebiotics

Review: Probiotics for prevention of urinary stones. – John C. Lieske – Annals of Translational Medicine

Review: Review of the mechanisms of probiotic actions in the prevention of colorectal cancer. – Sandra A. dos Reis – Nutrition Research

Phages and viruses

The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses – Lisa Zeigler Allen – mSystems

Microbes in the news 

The Future Of Skin Care: Lotions That Feed Our Microbiome

Collapse of Aztec society linked to catastrophic salmonella outbreak

Smart’ bacteria remodel their genes to infect our intestines

Smallest CRISPR So Far Comes from Food Poisoning Bacteria

Anitha’s non-microbiology picks 

An epigenetics gold rush: new controls for gene expression

Scientists discover 7 ‘Earthlike’ planets orbiting a nearby star

February 20, 2017

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This Monday we have some quite interesting news about microbes! Microbes found inside giant crystals in caves in Chihuahua, Mexico, may have survived there for tens of thousands of years, while meadows of underwater seagrass plants might lower levels of harmful bacteria in nearby ocean waters making the whole ecosystem — from corals to fish to humans — healthier. Enjoy your reading..

Pregnancy and early life

Adenoid bacterial colonization in a paediatric population – João Subtil – European Archives of Oto-Rhino-Laryngology

Human gut microbiome

Review: NLRP6: A Multifaceted Innate Immune Sensor – Maayan Levy – Trends in Immunology

Prebiotic inulin-type fructans induce specific changes in the human gut microbiota – Doris Vandeputte – Gut

Gut microbial profile is altered in primary biliary cholangitis and partially restored after UDCA therapy – Ruqi Tang – Gut

Multidonor intensive faecal microbiota transplantation for active ulcerative colitis: a randomised placebo-controlled trial – Sudarshan Paramsothy – The Lancet

Reinforcement of intestinal epithelial barrier by arabinoxylans in overweight and obese subjects: A randomized controlled trial: Arabinoxylans in gut barrier – Bouke N. Salden – Clinical Nutrition

Diet-induced obesity, gut microbiota and bone, including alveolar bone loss – Sathima Eaimworawuthikul – Archives of Oral Biology

Animal experiments

Dietary Prebiotics and Bioactive Milk Fractions Improve NREM Sleep, Enhance REM Sleep Rebound and Attenuate the Stress-Induced Decrease in Diurnal Temperature and Gut Microbial Alpha Diversity – Robert S. Thompson – Frontiers in  Behavioral Neuroscience

Plant, root, and soil microbiome

Plant community and nitrogen deposition as drivers of α- and β-prokaryotic diversity in reconstructed oil-sands soils and natural boreal forest soils – Jacynthe Masse – Applied and Environmental Microbiology

Plant-microbial association in petroleum and gas exploration sites in the state of Assam, north-east India—significance for bioremediation – Hemen Sarma – Environmental Science and Pollution Research

The choice of the DNA extraction method may influence the outcome of the soil microbial community structure analysis – Sylwia Zielińska – Microbiology Open

Water and extremophile microbiome

Seagrass ecosystems reduce exposure to bacterial pathogens of humans, fishes, and invertebrates – Joleah B. Lamb – Science

Phages and viruses

Cyanophage-encoded lipid-desaturases: oceanic distribution, diversity and function – Sheila Roitman – bioRxiv

Techniques

Effects of gelling agent and extracellular signaling molecules on the culturability of marine bacteria – Anita Mac Rygaard – Applied and Environmental Microbiology

A tool named Iris for versatile high-throughput phenotyping in microorganisms – George Kritikos – Nature Microbiology

Microbes in the news 

Microbes survived inside giant cave crystals for up to 50,000 years – Science News

Three-way dance between herbivores, plants and microbes unveiled  – Phys.org

Synthetic antibiotic developed by Sask. researchers to combat drug-resistant bacteria – CBC News

Salmonella ‘can kill cancer’: How bacteria that cause food poisoning could be used to attack tumour cells – Colin Fernandez for Daily Mail, UK

Brazilian peppertree packs power to knock out antibiotic-resistant bacteria – Science Daily

Bacteria Hysteria

Drug-resistant deadly bacteria more widespread than previously thought, study finds – News Medical

 

February 9, 2017

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Metabolomic analysis to determine affects of antibiotic treatment on the microbiome, capsular polysaccharide structure from marine bacterium, altering soil bacterial communities from use of organic-inorganic fertilization, new CRISPR-Cas systems discovered in uncultivated microbes.

General microbiome

Metabolic effects of Lactobacillus reuteri DSM 17938 in people with type 2 diabetes: A randomized controlled trial – Reza Mobini – Diabetes, Obesity and Metabolism

Pregnancy and early life

Diversity and composition of vaginal microbiota of pregnant women at risk for transmitting Group B Streptococcus treated with intrapartum penicillin – Luiz Fernando Wurdig Roesch – PLOS ONE

Human oral microbiome

Isolation and identification methods of Rothia species in oral cavities – Osamu Tsuzukibashi – Journal of Microbiological Methods

Association of oral microbiome with type 2 diabetes risk – J Long – Journal of Periodontal Research

Human skin microbiome

Microbiome precision editing: Using PEG as a selective fermentation initiator against methicillin-resistant Staphylococcus aureus – Ming-Shan Kao – Biotechnology Journal

Human gut microbiome

Comparative study on the in vitro effects of Pseudomonas aeruginosa and seaweed alginates on human gut microbiota – Shaofeng Bai – PLOS ONE

Rett Syndrome: A Focus on Gut Microbiota – Elisa Borghi – International Journal of Molecular Sciences

Colonization with enterotoxigenic Bacteroides fragilis is associated with early-stage colorectal neoplasia – Rachel V Purcell – PLOS ONE

Gut dysbiosis is associated with metabolism and systemic inflammation in patients with ischemic stroke – Kazuo Yamashiro – PLOS ONE

Glycomacropeptide sustains microbiota diversity and promotes specific taxa in an artificial colon model of elderly gut microbiota – Alexandra Ntemiri – Journal of Agricultural and Food Chemistry

Animal experiments

* Early life antibiotic exposure affects pancreatic islet development and metabolic regulation – Jiaying Li – Scientific Reports

Reduction of Abeta amyloid pathology in APPPS1 transgenic mice in the absence of gut microbiota – T Harach – Scientific Reports

Animal microbiome

Comparative study of the gut microbiome potentially related to milk protein in Murrah buffaloes (Bubalus bubalis) and Chinese Holstein cattle – Jiachao Zhang – Scientific Reports

Fish Intestinal Microbiome: Diversity and Symbiosis Unraveled by Metagenomics – AM Tarnecki – Journal of Applied Microbiology

Plant, root, and soil microbiome

Exploring the symbiont diversity of ancient western redcedars: arbuscular mycorrhizal fungi of long-lived hosts – Monika A Gorzelak – Molecular Ecology

Community-level physiological profiling analyses show potential to identify the copiotrophic bacteria present in soil environments – Salvador Lladó – PLOS ONE

Arbuscular mycorrhiza enhance the rate of litter decomposition while inhibiting soil microbial community development – Heng Gui – Scientific Reports

Bacterial Community Structure after Long-term Organic and Inorganic Fertilization Reveals Important Associations between Soil Nutrients and Specific Taxa Involved in Nutrient Transformations – Fang Li – Frontiers in Microbiology

The effects of fluoride based fire-fighting foams on soil microbiota activity and plant growth during natural attenuation of perfluorinated compounds – Renato Nallin Montagnolli – Environmental Toxicology and Pharmacology

Chapter: Phytostimulation and Biocontrol by the Plant-Associated Bacillus amyloliquefaciens FZB42: An Update – Rainer Borriss – Bacilli and Agrobiotechnology

Chapter: New Insights in Plant-Associated Paenibacillus Species: Biocontrol and Plant Growth-Promoting Activity – Sadhana Lal – Bacilli and Agrobiotechnology

Variations of soil microbial community structures beneath broadleaved forest trees in temperate and subtropical climate zones – Sihang Yang – Frontiers in Microbiology

Water and extremophile microbiome

The effects of elevated seawater temperatures on Caribbean gorgonian corals and their algal symbionts, Symbiodinium spp. – Tamar L. Goulet – PLOS ONE

* Structural characterization of an all-aminosugar-containing capsular polysaccharide from Colwellia psychrerythraea 34H – Angela Casillo – Antonie van Leeuwenhoek

Illumina sequencing-based analysis of sediment bacteria community in different trophic status freshwater lakes – Yu Wan – Microbiology Open

Bacterial communities in sediment of a Mediterranean Marine Protected Area – Valentina Catania – Canadian Journal of Microbiology

Metagenomic survey of the taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic – Etienne Yergeau – Scientific Reports

The effect of top-predator presence and phenotype on aquatic microbial communities – Karen E. Sullam – Ecology and Evolution

Metabolomics

Divergent Relationships between Fecal Microbiota and Metabolome following Distinct Antibiotic-Induced Disruptions – Jocelyn M. Choo – mSphere

Techniques

A novel LCMSMS method for quantitative measurement of short-chain fatty acids in human stool derivatized with 12C- and 13C-labelled aniline – James Chun Yip Chan – Journal of Pharmaceutical and Biomedical Analysis

More microbes

* New CRISPR–Cas systems from uncultivated microbes – David Burstein – Nature

Adaptation of genetically monomorphic bacteria: evolution of copper resistance through multiple horizontal gene transfers of complex and versatile mobile genetic elements – D Richard – Molecular Ecology

Microbes in the news

Microbial Molecules from the Multitudes within Us – Matthew R. Redondo – Cell Metabolism

Boston Children’s Hospital and uBiome to Investigate Premature Births – PRWeb

Cholera bacteria stab and poison enemies at predictable rates – Georgia Institute of Technology – ScienceDaily

ADA funds Kostic Lab to create model linking the microbiome to type 1 diabetes – EurekAlert

February 6, 2017

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General Microbiome

Microbiome sharing between children, livestock and household surfaces in western Kenya – Emily Mosites – PLoS ONE

 

Human Gut Microbiome

The Fecal Microbial Community of Breast-fed Infants from Armenia and Georgia – Zachery T Lewis – Scientific Reports

 

Animal Experiments

Dietary biofloc supplementation in black tiger shrimp, Penaeus monodon: effects on immunity, antioxidant and metabolic enzyme activities – Panantharayil Sudhayam Shyne Anand – Aquaculture Research

 

Animal Microbiome

Rainbow trout (Oncorhynchus mykiss) secretory component binds to commensal bacteria and pathogens – Cecelia Kelly – Scientific Reports

Effect of three commercial microbial products on bacterial community in a freshwater fish polyculture system – Tao Zhou – Aquaculture Research

 

Plant, Soil and Root Microbiome

Arsenic-hyperaccumulator Pteris vittata Efficiently Solubilized Phosphate Rock to Sustain Plant Growth and As Uptake – Jing–Wei Fu – Journal of Hazardous Materials

Synthesis: The next frontier of plant-soil feedback research: unraveling context dependence across biotic and abiotic gradients – Lauren M. Smith-Ramesh – Journal of Vegetation Science

Survival of Xanthomonas campestris pv. campestris in the phyllosphere and rhizosphere of weeds – J. C. Silva – Plant Pathology

Microbial catabolic diversity in and beyond the rhizosphere of plant species and plant genotypes – Karst M. Brolsma – Pedobiologia

 

Water  and Extremophile Microbiome

Ecotype Diversification of an Abundant Roseobacter Lineage – Ying Sun – Environmental Microbiology

Sticking together: inter-species aggregation of bacteria isolated from iron snow is controlled by chemical signaling – Jiro F Mori – ISME

Multiple metabolisms constrain the anaerobic nitrite budget in the Eastern Tropical South Pacific – Andrew R. Babbin – Global Biogeochemical Cycles

 

Techniques

Review: Infection control in the new age of genomic epidemiology – Patrick Tang – American Journal of Infection Control

Elucidating the biosynthetic pathways of volatile organic compounds in Mycobacterium tuberculosis through a computational approach – Purva Bhatter – Mol. Bio Syst.

Production of diatom–bacteria biofilm isolated from Seriola lalandi cultures for aquaculture application – María Teresa Mata – Aquaculture Research

 

Microbes in the News

Statoviruses, A novel taxon of RNA viruses present in the gastrointestinal tracts of diverse mammals – Andrew B. Janowski – Virology

Complete genome sequence of Serratia sp. YD25 (KCTC 42987) presenting strong antagonistic activities to various pathogenic fungi and bacteria – Chun Su – Journal of Biotechnology

Researcher creates molecular diagnostic system that can quickly identify dangerous bacteria – Brett Etchebarne – News Medical LifeSciences

Spain’s Balearic Islands hit by deadly olive tree bacteria – Mateu Ginard – Phys.org

USDA Funds Study of Plant and Animal Phenomics and Microbiomes – USDA – Pork Network

Probiotics in salads probed as solution to Salmonella outbreaks in bagged mixes – Mark Turner – abc.net

Bacteria to improve sanitation on Southeast Asia’s largest lake –  Hakley Ke  –  Channel NewsAsia

February 5, 2017

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General Microbiome

Chlamydia retesting and retest positivity rates: results from a state-wide laboratory data linkage study in Tasmania, 2012–13 – Nicola Stephens – Sexual Health

 

Human Gut Microbiome

Gut metagenomes of type 2 diabetic patients have characteristic single-nucleotide polymorphism distribution in Bacteroides coprocola – Yaowen Chen – Microbiome

 

Animal Microbiome

Influence of different inclusion levels and chain length of inulin on microbial ecology and the state of mucosal protective barrier in the large intestine of young pigs – M. Barszcz – Animal Production Science

The role and interaction of gut microflora and local immune response in Campylobacter jejuni infection in chicken – Zifeng Han – University of Veterinary Medicine Hannover Clinic for Poultry

 

Plant, Root and Soil Microbiome

Changes in soil microbial communities due to biological invasions can reduce allelopathic effects – Yang-Ping Li – Journal of Applied Ecology

 

Water and extremophile microbiome

Cyanobacterial Contribution to Travertine Deposition in the Hoyoux River System, Belgium – Julia Kleinteich – Microbial Ecology

Sulfur-Oxidizing Bacteria Mediate Microbial Community Succession and Element Cycling in Launched Marine Sediment – Hideyuki Ihara – Aquatic Microbiology 

 

Built Environment Microbiology

Draft genome sequences of eight bacteria isolated from the indoor environment: Staphylococcus capitis strain H36, S. capitis strain H65, S. cohnii strain H62, S. hominis strain H69, Microbacterium sp. strain H83, Mycobacterium iranicum strain H39, Plantibacter sp. strain H53, and Pseudomonas oryzihabitans strain H72 – Despoina S. Lymperopoulou – Standards in Genomic Sciences

 

Techniques

High throughput 16SrRNA gene sequencing reveals the correlation between Propionibacterium acnes and sarcoidosis – Meng-Meng Zhao – Respiratory Research

Critical issues in mycobiota analysis – Bettina Halwachs – Microbial Symbioses

 

Microbiome in News

Abstract A18: Gut microbiota changes in response to treatment with ursodeoxycholic acid (UDCA) – Talima Pearson – Cancer Research

The AGA’s Fecal Microbiota Transplantation National Registry: An Important Step Toward Understanding Risks and Benefits of Microbiota Therapeutics – Colleen R. Kelly – Gastroenterology

Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica – Zhemin Zhou – bioRxiv

Patterns of genomic variation in the opportunistic pathogen Candida glabrata suggest the existence of mating and a secondary association to the human host – Laia Carreté – bioRxiv

February 2, 2017

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Did you ever wonder about vitamin B12 role in microbiome organization and function? using a chemical probe mimic of vitamin B12, the authors reveal a light- and B12-dependent DNA regulator and predict that organismal interdependencies for B12 may be critical to microbiome stability and overall function.  On the extremophiles front, a study provides an analysis of the genomic content of the most abundant bacterial inhabitants of the salt-secreting desert tree Tamarix aphylla.  An interesting paper reinforced linkages between the colonization of the foodborne pathogen E. coli O157:H7 in cattle and the nature of the microbial community inhabiting the digestive tract of super-shedders. And as for future generations, if you want to get your kids or students excited about microbiology, try an interactive tool created by Stanford bioengineers: the 3D printed microscope powered by your smartphone.

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January 22, 2017

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Events and Jobs

PhD scholarship in Molecular Microbiology– University of Copenhagen-Last Date: February 8, 2017

Quality Control Associate-Microbiology–US-CA-Del Mar

General Microbiome

Impacts of chemical gradients on microbial community structure-Jianwei Chen-The ISME Journal

Human Skin

Proteomic and peptidomic analysis of human sweat with emphasis on proteolysis-Yijing Yu-Journal of Proteomics

Human Respiratory Microbiome

Nasopharyngeal Microbiome Diversity Changes over Time in Children with Asthma–Marcos Pérez-Losada-PLOS One

Adherence of Pseudomonas aeruginosa to cystic fibrosis buccal epithelial cells–Meike Lingner-ERJ

Human Vaginal Microbiome

The interaction between vaginal microbiota, cervical length, and vaginal progesterone treatment for preterm birth risk-Lindsay M. Kindinger-Microbiome

Human Gut Microbiome

Role of Gastrointestinal Microbiota on Kidney Injury and the Obese Condition-Keerati Wanchai-The American Journal of the Medical Sciences

Review-Altered Molecular Signature of Intestinal Microbiota in Irritable Bowel Syndrome Patients Compared with Healthy Controls: a Systematic Review and Meta-analysis-Hai Ning Liu-Digestive and Liver Disease

Animal Microbiome

Bacterial community composition and fermentation in the rumen of Xinjiang brown cattle (Bos taurus), Tarim red deer (Cervus elaphus yarkandensis), and Karakul sheep (Ovis aries)-Wenxi Qian-Canadian Journal of Microbiology

The Gut Microbiome of the Vector Lutzomyia longipalpis Is Essential for Survival of Leishmania infantum–Stephen M. Beverley-mBio

The normal vaginal and uterine bacterial microbiome in giant pandas (Ailuropoda melanoleuca)-Xin Yang-Microbiological Research

Pathogen-mediated manipulation of arthropod microbiota to promote infection–Nabil M. Abraham-PNAS

The gastrointestinal tract of farmed mink (Neovison vison) maintains a diverse mucosa-associated microbiota following a 3-day fasting period-Martin I. Bahl-Microbiology Open

Ovarian cycling and reproductive state shape the vaginal microbiota in wild baboons–Elizabeth A. Miller-BMC Microbiome

Plant, root, and soil microbiome

A decade of irrigation transforms the soil microbiome of a semi-arid pine forest-Martin Hartmann-Molecular Ecology

Methane Emissions and Microbial Communities as Influenced by Dual Cropping of Azolla along with Early Rice-Jingna Liu-Scientific Reports

Differential responses of soil bacterial communities to long-term N and P inputs in a semi-arid steppe-Ning Ling-Geoderma

Mineralization of “non-metabolizable” glucose analogues in soil: potential chemosensory mimics of glucose-Kyle Mason-Jones-Journal of Plant Nutrition and Soil Science

Deciphering composition and function of the root microbiome of a legume plant-Kyle Hartman-BMC Microbiome

Isolation and characterization of Rhizobium sp. strain YS-1r that degrades lignin in plant biomass-Colin A. Jackson-Journal of Applied Microbiology

Metagenomic insights into effects of spent engine oil perturbation on the microbial community composition and function in a tropical agricultural soil–Lateef B. Salam-Environmental Science and Pollution Research

Biocontrol effects of Brevibacillus laterosporus AMCC100017 on potato common scab and its impact on rhizosphere bacterial communities-Shengfu Chen-Biological Control

Co-inoculation with Enterobacter and Rhizobacteria on Yield and Nutrient Uptake by Wheat (Triticum aestivum L.) in the Alluvial Soil Under Indo-Gangetic Plain of India-Ashok Kumar-Journal of Plant Growth Regulation

 Ornamental flowers in new light: Artificial lighting shapes the microbial phyllosphere community structure of greenhouse grown sunflowers (Helianthus annuus L.)–Beatrix W. Alsanius–Scientia Horticulturae

Extremophiles

Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats-Meinhard Simon-ISME

Review: Marine Bacterioplankton Seasonal Succession Dynamics-Carina Bunse-Trends in Microbiology

Review: Stress response physiology of thermophiles–Preeti Ranawat-Archives of Microbiology

The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights-Emanuele Bosi-BMC Genomics

Sulfur compound oxidation and carbon co-assimilation in the haloalkaliphilic sulfur oxidizers Thioalkalivibrio versutus and Thioalkalimicrobium aerophilum-Wee Kiong Ang-Research in Microbiology

Geological and Geochemical Controls on Subsurface Microbial Life in the Samail Ophiolite, Oman–Kaitlin R. Rempfert-Extreme Microbiology

Microbial character related sulfur cycle under dynamic environmental factors based on the microbial population analysis in sewerage system-Qian Dong-Aquatic Microbiology

Similar community assembly mechanisms underlie similar biogeography of rare and abundant bacteria in lakes on Yungui Plateau, China-Jingqiu Liao-Limnology and Oceanography

Unraveling the microbial processes of black band disease in corals through integrated genomics-Yui Sato-Scientific Reports

Preliminary Phylogenetic Analysis of Thermophilic Bacteria Producing Protease isolated from Kuantan Malaysia -Essam A. Makky-JBSR

Identification of a novel fatty acid in the cell membrane of Chryseobacterium frigidisoli PB4T isolated from an East Antarctic glacier forefield-Kai Mangelsdorf-Organic Geochemistry

Phosphorus removal by marine bacterium enhanced with iron in the presence of silicon–Yanru Wang-Journal of Chemical Technology and Biotechnology

 Built Environment Microbiology

Developing Evidence-based Tools for Designing and Evaluating Hospital Inpatient Rooms–Xiaobo Quan-Journal of Interior Design

Building-related symptoms are linked to the in vitro toxicity of indoor dust and airborne microbial propagules in schools: A cross-sectional study-J T Salin-Environmental Research

Techniques

Review:  Application of meta-omics techniques to understand greenhouse gas emissions originating from ruminal metabolism-Robert J. Wallace-Genetics Selection Evolution

Balance Trees Reveal Microbial Niche Differentiation–James T. Morton-Ecological and Evolutionary Science

Virus

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

Virome of US bovine calf serum-Mohammadreza Sadeghi-Biologicals

More Microbes

Bacillus zeae sp. nov. isolated from the rhizosphere of Zea mays– Peter Kämpfer-International Journal of Systematic and Evolutionary Microbiology

Microbes in News

Capnophilic Enterobacteriaceae-JM. Sahuquillo Arce-Diagnostic Microbiology and Infectious Disease