Category Archives: Microbial Ecology

March 9, 2017

Posted on by

A variety of reviews about the oral microbiome and periodontal disease, a perspective piece on secondary metabolites mediating symbiotic interactions in the new Nature Reviews Chemistry journal, Akkermansia muciniphila’s involvement in host immune homeostasis, new insight into how raindrops disperse bacteria from soil into the air.

General microbiome

* Perspective: Hijacking exogenous signals to generate new secondary metabolites during symbiotic interactions – Rurun Wang – Nature Reviews Chemistry

Cooperation of Gastric Mononuclear Phagocytes with Helicobacter pylori during Colonization – Monica Viladomiu – Journal of Immunology

Human respiratory microbiome

Longitudinal sampling of the lung microbiota in individuals with cystic fibrosis – Fiona J. Whelan – PLoS ONE

Human oral microbiome

Review: Role of microbial communities in the pathogenesis of periodontal diseases and caries – Alex Mira – Journal of Clinical Periodontology

Review: Dental biofilm: ecological interactions in health and disease – P. D. Marsh – Journal of Clinical Periodontology

Review: The oral cavity microbiota: between health, oral disease and cancers of the aerodigestive tract – Pierre Le Bars – Canadian Journal of Microbiology

A new mathematical model of bacterial interactions in two-species oral biofilms – Bénédicte Martin – PLoS ONE

Human urinary microbiome

Alterations of Urinary Microbiota in Type 2 Diabetes Mellitus with Hypertension and/or Hyperlipidemia – Fengping Liu – Frontiers in Physiology

Human gut microbiome

Impact of Bariatric Surgery on Metabolic and Gut Microbiota Profile: a Systematic Review and Meta-analysis – Dimitrios E. Magouliotis – Obesity Surgery

Commensal gut bacteria modulate phosphorylation-dependent PPARγ transcriptional activity in human intestinal epithelial cells – Malgorzata Nepelska – Scientific Reports

* Pili-like proteins of Akkermansia muciniphila modulate host immune responses and gut barrier function – Noora Ottman – PLoS ONE

Altered intestinal microbiota in patients with chronic pancreatitis: implications in diabetes and metabolic abnormalities – Sai Manasa Jandhyala – Scientific Reports

Disease-Associated Changes in Bile Acid Profiles and Links to Altered Gut Microbiota – Susan A. Joyce – Digestive Diseases

One-year calorie restriction impacts gut microbial composition but not its metabolic performance in obese adolescents – Alicia Ruiz – Environmental Microbiology

Dysbiosis of Gut Microbiota Associated with Clinical Parameters in Polycystic Ovary Syndrome – Rui Liu – Frontiers in Microbiology

Animal experiments

Bifidobacterium breve with α-linolenic acid alters the composition, distribution and transcription factor activity associated with metabolism and absorption of fat – Elaine Patterson – Scientific Reports

Exploring gastric bacterial community in young pigs – Vincenzo Motta – PLoS ONE

Animal microbiome

Parasitism perturbs the mucosal microbiome of Atlantic Salmon – M. S. Llewellyn – Scientific Reports

The microbiome composition of Aedes aegypti is not critical for Wolbachia-mediated inhibition of dengue virus – Michelle D. Audsley – PLoS Neglected Tropical Diseases

Endosymbiotic calcifying bacteria across sponge species and oceans – Leire Garate – Scientific Reports

Bacterial communities associated with Shinkaia crosnieri from the Iheya North, Okinawa Trough: Microbial diversity and metabolic potentials – Jian Zhang – Journal of Marine Systems

Diet affects arctic ground squirrel gut microbial metatranscriptome independent of community structure – Jasmine J. Hatton – Environmental Microbiology

Plant, root, and soil microbiome

Microbial Communities as Environmental Indicators of Ecological Disturbance in Restored Carbonate Fen-Results of 10 Years of Studies – Tomasz Mieczan – Microbial Ecology

Rhizospheric microbial community of Caesalpinia spinosa (Mol.) Kuntze in conserved and deforested zones of the Atiquipa fog forest in Peru – Irene Cordero – Applied Soil Ecology

Abundance and diversity of ammonia-oxidizing archaea and bacteria in the rhizosphere soil of three plants in the Ebinur Lake wetland – Yuan He – Canadian Journal of Microbiology

Alphaproteobacteria fix nitrogen in a Sphagnum-dominated peat bog using molybdenum-dependent nitrogenase – Melissa J. Warren – bioRxiv

Water and extremophile microbiome

Quantifying the importance of the rare biosphere for microbial community response to organic pollutants in a freshwater ecosystem – Yuanqi Wang – Applied and Environmental Microbiology

Comparison of Prokaryotic Diversity in Cold, Oligotrophic Remote Lakes of Chilean Patagonia – Paulina Aguayo – Current Microbiology

Plasmid DNA analysis of pristine groundwater microbial communities reveal extensive presence of metal resistance genes – Ankita Kothari – bioRxiv

Food microbiology

Characterization of microbial population of breba and main crops (Ficus carica) during cold storage: Influence of passive modified atmospheres (MAP) and antimicrobial extract application – María del Carmen Villalobos – Food Microbiology

Genetic diversity, safety and technological characterization of lactic acid bacteria isolated from artisanal Pico cheese – M. F. P. Domingos-Lopes – Food Microbiology

Probiotics/prebiotics

A proliferative probiotic Bifidobacterium strain in the gut ameliorates progression of metabolic disorders via microbiota modulation and acetate elevation – Ryo Aoki – Scientific Reports

More microbes

* Bioaerosol generation by raindrops on soil – Young Soo Joung – Nature Communications

Cooperation in carbon source degradation shapes spatial self-organization of microbial consortia on hydrated surfaces – Robin Tecon – Scientific Reports

Microbes in the news

The ‘Dark Matter’ of the Microbial World – Sarah Zhang – The Atlantic

Scientists Make Art From Objects Invisible to the Naked Eye – Marissa Fessenden – Smithsonian

March 6, 2017

Posted on by

Interesting articles on the how the interactions between bacteria and fungi influence N cycling in soils. Also, fecal sample collection methods influence microbial community structure.

General microbiome

The National Biome Initiative: An Allergy Perspective. Furuta GT. Journal of Allergy and Clinical Immunology

The Microbiome in Allergic Disease: Current Understanding and Future Opportunities – 2017 PRACTALL Document of the American Academy of Allergy, Asthma & Immunology and the European Academy of Allergy and Clinical Immunology. Huang YJ. Journal of Allergy and Clinical Immunology

Oral and nasal microbiome

Community analysis of dental plaque and endotracheal tube biofilms from mechanically ventilated patients.      Marino PJ. Journal of Critical Care

Oral and nasal microbiota in Parkinson’s disease. Pereira PA. Parkinsonism and Related Disorders

Gut microbiome

The effect of omeprazole treatment on the gut microflora and neutrophil function. Kostrzewska M. Clinics and Research in Hepatology and Gastroenterology

Water and extremophile microbiome

Bacterial interactions and implications for oil biodegradation process in mangrove sediments. Grativol AD. Marine Pollution Bulletin

Quantifying the importance of the rare biosphere for microbial community response to organic pollutants in a freshwater ecosystem. Wang Y. Applied and Environmental Microbiology

Probiotics

Probiotic treatment reduces depressive-like behaviour in rats independently of diet. Abildgaard A. Psychoneuroendocrinology

Techniques

Comparison of fecal collection methods for microbiota studies in Bangladesh. Vogtmann E. Applied and Environmental Microbiology

Plant, root, and soil microbiome

How interacting fungal species and mineral nitrogen inputs affect transfer of nitrogen from litter via arbuscular mycorrhizal mycelium. He Y. Environmental Science and Pollution Research

Salmonella Senftenberg adaptation to linalool and its association with antibiotic resistance and environmental persistence. Hollander K. Applied and Environmental Microbiology

Fungal and bacterial contributions to nitrogen cycling in cheatgrass-invaded and uninvaded native sagebrush soils of the western USA.  DeCrappeo NM. Plant and Soil

Native soil organic matter as a decisive factor to determine the arbuscular mycorrhizal fungal community structure in contaminated soils. Montiel-Rozas. Biology and Fertility of Soils

February 24, 2017

Posted on by

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

Posted on by

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 10, 2017

Posted on by

Today’s digest features fascinating  research articles on the potential of glycomacropeptide in modulating human gut microbiota of elderly, identifying IBD-like microbiome in at-risk healthy relatives of IBD patients with no clinical signs of inflammation,  long-term climate change affects soil microbial communities and  a reviews on the potential role of transglutaminases in autoimmunity.

General 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

The microbiome of the octocoral Lobophytum pauciflorum: minor differences between sexes and resilience to short-term stress – Wiebke Wessels – FEMS Microbiol Ecology

Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas – Hannah Wang- Genome Medicine

Microbiota composition of simultaneously colonized mice housed under either a gnotobiotic isolator or individually ventilated cage regime – Randi Lundberg – Scientific Reports

Microbial strain-level population structure and genetic diversity from metagenomes – Duy Tin Truong – Genome Research

*Review: Transglutaminases in Dysbiosis As Potential Environmental Drivers of Autoimmunity – Aaron Lerner- Frontiers in Microbiology

Pregnancy and early life

Perspective: The maternal microbiome: Cause or consequence of obesity risk in the next generation? – Jacob E. Friedman – Obesity

Review: Charting the Maternal and Infant Microbiome: What Is the Role of Diabetes and Obesity in Pregnancy? – Sirtaj Singh – Current Diabetes Reports

Human skin microbiome

Skin Microbiome in Small- and Large-plaque Parapsoriasis – Alexander Salava – Acta Dermato-Venereologica

Human gut microbiome

*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

A Disease-Associated Microbial and Metabolomics State in Relatives of Pediatric Inflammatory Bowel Disease Patients – Jonathan P. Jacobs – Cellular and Molecular Gastroenterology and Hepatology

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

Review: Gut microbiota modulation and anti-inflammatory properties of dietary polyphenols in IBD: new and consolidated perspectives.  – Angelo Santino – Current Pharmaceutical Design

Animal experiments 

Changes in Microbiota in Rumen Digesta and Feces Due to a Grain-Based Subacute Ruminal Acidosis (SARA) Challenge – Jan C. Plaizier – Microbial Ecology

A maternal Western diet during gestation and lactation modifies offspring’s microbiota activity, blood lipid levels, cognitive responses, and hippocampal neurogenesis in Yucatan pigs – David Val-Laillet – FASEB Journal

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

Plant, root, and soil microbiome

Plants Assemble Species Specific Bacterial Communities from Common Core Taxa in Three Arcto-Alpine Climate Zones – Manoj Kumar – Frontiers in Microbiology

*Links between soil microbial communities and plant traits in a species-rich grassland under long-term climate change – Emma J. Sayer – Ecology and Evolution

Specificity of root microbiomes in native-grown Nicotiana attenuata and plant responses to UVB increase Deinococcus colonization – Rakesh Santhanam – Molecular Ecology

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

Phages and viruses

Things Are Getting Hairy: Enterobacteria Bacteriophage vB_PcaM_CBB – Colin Buttimer – Frontiers in Microbiology

Techniques

Successive DNA extractions improve characterization of soil microbial communities – Mauricio R. Dimitrov – PeerJ

Microbes in the news

Bacteria fed synthetic iron-containing molecules turn into electrical generators

Method to identify bacteria in blood samples works in hours instead of days

Characterizing Cervical Cancer by HPV Strain, Mutations, and Molecular Features

Phage In The Time Of Cholera

An Innovative New Cancer Therapy Hijacks Bacteria to Fight Tumors

Microbes on the market

Chan Zuckerberg Biohub funds first crop of 47 investigators

Anitha’s non-microbiology picks 

Could this pollinating drone replace butterflies and bees?

The physics of why valve amps sound better

Circuits survive on Venus, electronics powered by stomach acid

February 9, 2017

Posted on by

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 4, 2017

Posted on by

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

February 2, 2017

Posted on by

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.

Continue reading →

January 29, 2017

Posted on by

A post on fecal transplats, the gut microbiome of cranes, fungal diversity of soils, and much more.

Events and Jobs

Assistant Professor of Microbiology, Immunology & Tropical Medicine at George Washington University

General microbiome

The Stromal Intervention: Regulation of Immunity and Inflammation at the Epithelial-Mesenchymal Barrier – Roni Nowarski – Cell

Effect of adsorbants on in vitro biohydrogenation of 22:6n-3 by mixed cultures of rumen microorganisms – Marlene Escobar – Animal

Pregnancy and early life

Airway Microbial Community Turnover Differs by BPD Severity in Ventilated Preterm Infants – Brandie D. Wagner – PLoS One

Mode of Delivery and Its Influence on the Acquisition of Streptococcus mutans in Infants – Ritu G. Ubeja – International Journal of Clinical Pediatric Dentistry

Human gut microbiome

Blood Trimethylamine-N-Oxide Originates from Microbiota Mediated Breakdown of Phosphatidylcholine and Absorption from Small Intestine – Wolfgang Stremmel – PLoS One

Challenges in Fecal Donor Selection and Screening for Fecal Microbiota Transplantation: A Review – Michael H. Woodworth – Gut Microbes

Animal experiments

Peptostreptococcus anaerobius Induces Intracellular Cholesterol Biosynthesis in Colon Cells to Induce Proliferation and Causes Dysplasia in Mice – Ho Tsoi – Journal of AGA Institute: Gastroenterology Special Issure

Animal microbiome

The gut microbiome of hooded cranes (Grus monacha) wintering at Shengjin Lake, China – Guanghong Zhao – Wiley

Linking Peripartal Dynamics of Ruminal Microbiota to Dietary Changes and Production Parameters – Hooman Derakhashani – Frontiers in Microbiology

Effect of antibiotic on survival and development of Spodoptera litura (Lepidoptera: Noctuidae) and its gut microbial diversity – Abhinay Thakur – Bullitin of Entomological Research

Plant, root, and soil microbiome

Fungal diversity in soils across a gradient of preserved Brazilian Cerrado – Ademir Sergio Ferreira de Araujo – Journal of Microbiology

Synthetic photosynthetic consortia define interactions leading to robustness and photoproduction – Stephanie G. Hays – Journal of Biomedical Engineering

Translocation of Bacillus thuringiensis in Phaseolus vulgaris tissues and vertical transmission in Arabidopsis thaliana – Rosalina García-Suárez – Journal of Applied Microbiology

Transport Capabilities of Environmental Pseudomonads for Sulfur Compounds – Sarah Zerbs – Protein Science

Water and extremophile microbiome

Molecular-biological sensing in aquatic environments: recent developments and emerging capabilities – Jonathan S McQuillan – Current Opinion in Biotechnology

Probiotics / prebiotics

Nutritional stimulation of commensal oral bacteria suppresses pathogens: the prebiotic concept – Vera Slomka – Wiley

Microbes in the news

Rebalancing gut microbiome lengthens survival in mouse model of ALS

What We’ve Learned From Studying Microbiomes

Microbiota Transfer Therapy Could Help Children With Autism

Bacteria’s sneaky way to spread by getting you to eat more

Studies show prevalence of multi-drug resistant bacteria in China

Researchers discover molecule that could fight ‘superbug’ bacteria

Microbes on the market

New Market Analysis: The global clinical microbiology market is projected to reach USD 5.77 Billion by 2021

Bacteria Hysteria

SHOCKING: You won’t BELIEVE how many GERMS are on your hands

January 27, 2016

Posted on by

Reviews on prenatal bacterial microbiota, mycobiome in the lower respiratory tract and interesting articles on association of HPV infection with vaginal microbiota; prebiotic and bioactive milk fraction improving NREM sleep.

General microbiome

Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data – Kelly M. Robinson – Microbiome

Pregnancy and early life

*Review: Does a prenatal bacterial microbiota exist? – M Hornef  -Mucosal Immunology

Human respiratory microbiome

*Review: Mycobiome in the Lower Respiratory Tract – A Clinical Perspective – Robert Krause- Frontiers in microbiology

Human vaginal microbiome

*Association of HPV infection and clearance with cervicovaginal immunology and the vaginal microbiota – B Shannon – Mucosal Immunology

Human gut microbiome

Review: Advances in Gut Microbiome Research, Opening New Strategies to Cope with a Western Lifestyle – Gina P. Rodriguez-Castaño – Frontiers in Genetics

Helicobacter pylori infection is associated with an altered gastric microbiota in children – K M Brawner – Mucosal Immunology

*Colonic Absorption of Low-Molecular-Weight Metabolites Influenced by the Intestinal Microbiome: A Pilot Study – Mitsuharu Matsumoto – PLoS One

Review: Advances in Gut Microbiome Research, Opening New Strategies to Cope with a Western Lifestyle – Gina P. Rodriguez-Castaño – Frontiers in Genetics

Animal experiments 

Effect of Lactobacillus Strains on Intestinal Microflora and Mucosa Immunity in Escherichia coli O157:H7-Induced Diarrhea in Mice – Xin Bian  – Current Microbiology

Modulation of gut microbiota and increase in fecal water content in mice induced by administration of Lactobacillus kefiranofaciens DN1 -Dana Jeong – Food & Function

Plant, root, and soil microbiome

Bacterial, fungal, and plant communities exhibit no biomass or compositional response to two years of simulated nitrogen deposition in a semiarid grassland – Theresa A. McHugh- Environmental Microbiology

Water and extremophile microbiome

Temporal and Spatial Variations of Bacterial and Faunal Communities Associated with Deep-Sea Wood Falls – Petra Pop Ristova – PLoS One

Probiotics / prebiotics

*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

Changes in the Gut Microbiota After Early Administration of Oral Synbiotics to Young Infants in India – DS Chandel -Journal of Pediatric Gastroenterology Nutrition

Techniques

Home-made cost effective preservation buffer is a better alternative to commercial preservation methods for microbiome research – Sebastian Menke- Frontiers in microbiology

Furosemide enhances the sensitivity of urinary metabolomics for assessment of kidney function – Isaie Sibomana – Metabolomics

Impact of sample processing on human airways microbial metagenomes – Lutz Wiehlmann – Journal of Biotechnology

Microbes in the news 

Scientists develop new flu vaccines for dogs

New Insight Describes Connection between Salmonella Infection and Appetite Loss

Anitha’s non-microbiology picks

Tiny Satellites to Make Big Contributions to Science

First report of metallic hydrogen on earth – Hydrogen turned into metal in stunning act of alchemy that could revolutionise technology and spaceflight