Category Archives: Uncategorized

February 13, 2017

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Today ‘s digest features a roundworm as a new model of host-microbiota interactions, a new theory on apple replant disease, and a double-blinded, placebo-controlled, crossover-designed probiotic trial on Japanese medical students. Also, an interesting study on how an active lifestyle promotes growth of Faecalibacterium prausnitzii, Roseburia hominis and Akkermansia muciniphila commensals in women when compared to a sedentary lifestyle. Stay active!

General microbiome

C. elegans and its bacterial diet as a model for systems-level understanding of host–microbiota interactions – Jingyan Zhang – Current Opinion in Biotechnology

Microbial Respiration and Formate Oxidation as Metabolic Signatures of Inflammation-Associated Dysbiosis – Elizabeth R. Hughes – Cell Host & Microbe

Metagenomic and metatranscriptomic analyses reveal structure and dynamics of a dechlorinating community containing Dehalococcoides mccartyi and corrinoid-providing microorganisms under cobalamin-limited condition – Yujie Men – Applied and Environmental Microbiology

Human respiratory microbiome

Sputum DNA sequencing in cystic fibrosis: non-invasive access to the lung microbiome and to pathogen details – Rounak Feigelman – Microbiome

Human gut microbiome

Review: Role of the Gut Microbiome in the Pathogenesis of Obesity and Obesity-Related Metabolic Dysfunction – Kristien E. Bouter – Gastroenterology

*Differences in gut microbiota profile between women with active lifestyle and sedentary women. – Carlo Bressa – PLoS One

Animal experiments

Secondary bile acid-induced dysbiosis promotes intestinal carcinogenesis – Hailong Cao – International Journal of Cancer

Enteric helminth-induced type-I interferon signalling protects against pulmonary virus infection through interaction with the microbiota – Amanda J. McFarlane – Journal of Allergy and Clinical Immunology

Berberine-induced bioactive metabolites of the gut microbiota improve energy metabolism – Yan Wang – Metabolism

Plant, root, and soil microbiome

Use of endophytic and rhizosphere bacteria to improve phytoremediation of arsenic-contaminated industrial soils by autochthonous Betula celtiberica. – Victoria Mesa – Applied and Environmental Microbiology

Fumigation with dazomet modifies soil microbiota in apple orchards affected by replant disease – Lidia Nicola – Applied Soil Ecology

Food microbiology

Review: Non-dairy Based Probiotics: A Healthy Treat for Intestine. – Sangita Bansal –
Critical Reviews in Food Science and Nutrition

Probiotics / prebiotics

Daily intake of Lactobacillus gasseri CP2305 improves mental, physical, and sleep quality among Japanese medical students enrolled in a cadaver dissection course – Daisuke Sawada – Journal of Functional Foods

Bioinformatics

Recovery of genomes from metagenomes via a dereplication, aggregation, and scoring strategy – Christian M.K. Sieber – bioRxiv

February 12, 2017

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Being Sunday there aren’t that many publications to talk about. However the study by Zheng and colleagues makes up for it and is a must read! A bit like BCG for bladder cancer they engineered bacteria to induce an effective antitumor immune response, successfully treating tumors in several different mouse models with no evidence of toxicity. In another interesting study, Harach et al demonstrate microbial involvement in the development of Abeta amyloid pathology, and suggest that microbiota may contribute to the development of neurodegenerative diseases.

General microbiome

*Two-step enhanced cancer immunotherapy with engineered Salmonella typhimurium secreting heterologous flagellin – Jin Hai Zheng – Science Translational Medicine

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

A target-specific assay for rapid and quantitative detection of Mycobacterium chimaera DNA in environmental and clinical specimens – Enrique Zozaya-Valdes – bioRxiv

Human gut microbiome

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

Gut bacteria may play a role in Alzheimer’s disease –  Science Daily

Water and extremophile microbiome 

A survey of microparasites present in adult migrating Chinook salmon (Oncorhynchus tshawytscha) in south-western British Columbia determined by high-throughput quantitative polymerase chain reaction – A L Bass – Journal of Fish Disease

Distinct Biogeographic Patterns for Archaea, Bacteria, and Fungi along the Vegetation Gradient at the Continental Scale in Eastern China – B Ma – mSystems

Bioinformatics

OptiClust: Improved method for assigning amplicon-based sequence data to operational taxonomic units – Sarah L Westcott – bioRxiv

 Microbes in the news 

Gut Microbiota Improved when Eating Whole Grains – Council Chronicle

Feeding probiotics to rats before stressing them out reduces disruption of gut microbiota – The Indian Express

Researchers develop new method that can rapidly profile resistome of gut microbial communities – News Medical

February 11, 2017

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Changes in the gut microbiota during aging is associated with increased gut permeability and peripheral inflammation and may mediate cognitive decline. An overview of the gut microbiome in Crohn’s Disease and insight into how extremophiles might maintain protein folding. 

General microbiome

Whole genome sequence of lactic acid bacterium Pediococcus acidilactici strain S1 – Gun-Seok Park – Brazilian Journal of Microbiology

‘Pygmaiobacter massiliensis’ sp. nov., a new bacterium isolated from the human gut of a Pygmy woman – M. Bilen – NMNI

Human and rat gut microbiome composition is maintained following sleep restriction – Zhang SL – PNAS

Palaeogeographic variation in the Permian−Triassic boundary microbialites: A discussion of microbial and ocean processes after the end-Permian mass extinction – Stephen Kershaw – Journal of Palaeogeography

Assessment of bacterial profiles in aged, home-made Sichuan paocai brine with varying titratable acidity by PacBio SMRT sequencing technology – Jialu Cao – Food Control

 

Human gut microbiome

A microbial signature for Crohn’s disease – Victoria Pascal – Gut

Differences in Gut Metabolites and Microbial Composition and Functions between Egyptian and U.S. Children Are Consistent with Their Diets  – V. Shankar – mSystems

*PrePrint:  Postmortem succession of gut microbial communities in human cadavers – Jennifer M DeBruyn – PeerJ Preprints

Substituting whole grains for refined grains in a 6-wk randomized trial has a modest effect on gut microbiota and immune and inflammatory markers of healthy adults – Vanegas SM – American Journal of Clinical Nutrition

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 experiments 

Revisiting Metchnikoff: Age-related Alterations in Microbiota-Gut-Brain Axis in the Mouse – Karen A. Scott – Brain, Behavior, and Immunity

Animal microbiome 

Immune system stimulation by the native gut microbiota of honey bees – Waldan K. Kwong – Royal Society for Open Science

Deep Sequencing Reveals Highly Variable Gut Microbial Composition of Invasive Fish Mossambicus Tilapia (Oreochromis mossambicus) Collected from Two Different Habitats – Swapnil Sopan Gaikwad – Indian Journal of Microbiology

The gastrointestinal tract microbiota of the Japanese quail, Coturnix japonica –  Ngare Wilkinson – Environmental Biotechnology

Bacterial community diversity associated with different levels of dietary nutrition in the rumen of sheep – Yaoyue Wang – Applied Microbiology and Biotechnology

Plant, root, and soil microbiome

Hydrogen Peroxide and Strigolactones Signaling Are Involved in Alleviation of Salt Stress Induced by Arbuscular Mycorrhizal Fungus in Sesbania cannabina Seedlings – Cun-Cui Kong – Journal of Plant Growth Regulation

Potential Role of Plant-Associated Bacteria in Plant Metal Uptake and Implications in Phytotechnologies – Petra S. Kidd – Advances in Botanical Research

Application of bacteria from non-cultivated plants to promote growth, alter root architecture and alleviate salt stress of cotton – Ivelisse Irizarry – Journal of Applied Microbiology

*Reference:  Phytomyxea – Simon Bulman – Springer Reference – Handbook of the Protists

Water and extremophile microbiome 

Molecular determinant of the effects of hydrostatic pressure on protein folding stability – Calvin R. Chen – Nature Communications

Microarray analysis of the benthic bacterium Shewanella piezotolerans WP3 at low temperature – Huahua Jian – Marine Genomics

Metagenomic exploration of microbial community in mine tailings of Malanjkhand copper project, India – Abhishek Gupta – Genomics Data

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

Variations in airborne bacterial communities at high altitudes over the Noto Peninsula (Japan) in response to Asian dust events – Teruya Maki – Atmospheric Chemistry and Physics Discussions

Phages and viruses

Viruses comprise an extensive pool of mobile genetic elements in eukaryote cell cultures and human clinical samples – Thannesberger J – The FASEB Journal

Techniques

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

Cultivation-Free Raman Spectroscopic Investigations of Bacteria – Björn Lorenz – Trends in Microbiology

*Review:  Proteomics Tracing the Footsteps of Infectious Disease – Todd M Greco – Molecular and Cellular Proteomics

Metabolomics as a Challenging Approach for Medicinal Chemistry and Personalized Medicine – Michel Fredérich – Journal of Medical Chemistry

An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data – Wadsworth WD – BMC Bioinformatics

Microbes on the market 

Lipid accumulation in prokaryotic microorganisms from arid habitat – Philippa Hauschild – Applied Microbiology and Biotechnology

 

 

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 7, 2017

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General microbiome

*Review: Gut microbiota and acute coronary syndromes: ready for use in the emergency room? – Trøseid M. – Eur Heart J

Review: Fecal Microbiota Transplant versus Oral Vancomycin Taper: Important Undiscussed Limitations. – Jansen JW – Clin Infect Dis

Review: Fecal Microbiota Transplantation: do we need harmonization? – Galpérine T – Clin Infect Dis

Fecal microbiota transplantation in patients with slow-transit constipation: A randomized, clinical trial. – Tian H – PLoS One

Listeriolysin S: a bacteriocin from epidemic Listeria monocytogenes strains that targets the microbiota. – Quereda-Torres JJ – Gut Microbes

*Possible Alternative Predictors of Failure of Fecal Microbiota Transplant for Therapy of Recurrent C difficile Infection. – Bodiwala V – Am J Gastroenterol

Repeated fecal microbiota transplantations attenuate diarrhea and lead to sustained changes in the fecal microbiota in acute, refractory gastrointestinal graft-versus-host-disease. – Spindelboeck W – Haematologica

Review: Gastrointestinal Immune and Microbiome Changes During Parenteral Nutrition. – Pierre JF –  Am J Physiol Gastrointest Liver Physiol.

Microbiome sharing between children, livestock and household surfaces in western Kenya. – Mosites E – PLoS One

 

Pregnancy and early life

Oral yeast colonization throughout pregnancy. – Rio R – Med Oral Patol Oral Cir Bucal

Review: Human Milk Oligosaccharides and the Preterm Infant: A Journey in Sickness and in Health. – Moukarzel S – Clin Perinatol

Loss of cutaneous microbial diversity during first three weeks of life in very low birth weight infants. – Salava A – Exp Dermatol

The Fecal Microbial Community of Breast-fed Infants from Armenia and Georgia. – Lewis ZT – Sci Rep

Antibiotic resistance potential of the healthy preterm infant gut microbiome. – Rose G – PeerJ

 

Multi-site human microbiome

Review: From Evolutionary Advantage to Disease Agents: Forensic Reevaluation of Host-Microbe Interactions and Pathogenicity. – Rivera-Pérez JI – Microbiol Spectr

 

Human respiratory microbiome

*Microbes Associate with Host Innate Immune Response in Idiopathic Pulmonary Fibrosis. – Huang Y – Am J Respir Crit Care Med

 

 

Human gut microbiome

Review: The Enigmatic Gut in Cystic Fibrosis: Linking Inflammation, Dysbiosis, and the Increased Risk of Malignancy. – Garg M – Curr Gastroenterol Rep

Involvement of gut microbiota in the association between GLP-1/GLP-1 receptor expression and gastrointestinal motility. – Yang M – Am J Physiol Gastrointest Liver Physiol

*Novel insight into the role of microbiota in colorectal surgery. – Bachmann R – Gut

*Race-dependent association of sulfidogenic bacteria with colorectal cancer. –  Yazici C – Gut

Review: The “gut microbiota” hypothesis in primary sclerosing cholangitis. – Pontecorvi V – Ann Transl Med

Review: The development and role of microbial-host interactions in gut mucosal immune development. – Stokes CR – J Anim Sci Biotechnol

Yogurt Containing Lactobacillus gasseri Mitigates Aspirin-Induced Small Bowel Injuries: A Prospective, Randomized, Double-Blind, Placebo-Controlled Trial. – Suzuki T – Digestion

 

Animal experiments 

Dietary fibres modulate the composition and activity of butyrate-producing bacteria in the large intestine of suckling piglets – Mu C – Antonie Van Leeuwenhoek

Drunk Bugs: Chronic Vapour Alcohol Exposure Induces Marked Changes in the Gut Microbiome in Mice. – Peterson VL – Behav Brain Res

Microscopic Evaluation of the Effect of Oral Microbiota on the Development of Bisphosphonate-Related Osteonecrosis of the Jaws in Rats. – Silveira FM – J Oral Maxillofac Res

 

Animal microbiome

The bovine colostrum microbiome and its association with clinical mastitis. – Lima SF – J Dairy Sci

Bacterial bile salt hydrolase: an intestinal microbiome target for enhanced animal health. – Geng W – Anim Health Res Rev

Functional analysis for gut microbes of the brown tree frog (Polypedates megacephalus) in artificial hibernation. – Weng FC – BMC Genomics

 

Plant, root, and soil microbiome

Dairy propionibacteria prevent the proliferative effect of plant lectins on SW480 cells and protect the metabolic activity of the intestinal microbiota in vitro. – Zárate G – Anaerobe

 

 

Probiotics / prebiotics

Review: Potential Beneficial Effects of Probiotics on Human Migraine Headache: A Literature Review. – Dai YJ – Pain Physician

 

Bioinformatics

Robust Inference of Genetic Exchange Communities from Microbial Genomes Using TF-IDF. – Cong Y – Front Microbiol

 

Techniques

A quantitative SMRT cell sequencing method for ribosomal amplicons. – Jones BM – J Microbiol Methods

RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys. – Xie C – BMC Bioinformatics

Survey of (Meta)genomic Approaches for Understanding Microbial Community Dynamics. – Sharma A – Indian J Microbiol

 

Microbe in the news

Malin takes 33% Stake in Start-Up Microbiome Targeting Firm Artizan – Genetic Engineering & Biotechnology News (blog)

A Pilot Study Assessing Intestinal Microbiota Diversification and Changes After Travel to South(East) Asia From the US – Satellite PR News (press release)

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 1, 2017

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General Microbiome

Microbial Partnerships of Pathogenic Oomycetes-M Larousse-PLoS Pathogens

Biocontrol of Virulent Ralstonia solanacearum isolates by an Indigenous Bacillus cereus-H Mandal-Journal of Agricultural Technology

Flow Cytometric Single-Cell Identification of Populations in Synthetic Bacterial Communities-P Rubbens-PLoS ONE

Assessment of Metabolic changes in Mycobacterium smegmatis wild type and alr mutant strains: evidence for a new pathway of D-alanine biosynthesis.-DD Marshall-Journal of Proteome Research

Invasions of Host-Associated Microbiome Networks-CL Murall-Advances in Ecological Research

Review: Microbiome engineering: Current applications and its future.-JL Foo-Biotechnology Journal

Review: Microbes and Mental Health: A Review.-R Rieder-Brain, Behavior, and Immunity

Temporal dynamics of microbial communities in microcosms in response to pollutants-Shuo Jiao-Molecular Ecology

Integrated proteomics and metabolomics suggests symbiotic metabolism and multimodal regulation in a fungal-endobacterial system-Zhou Li-Environmental Microbiology

Pregnancy and Early Life

Helicobacter pylori infection is associated with an altered gastric microbiota in children-KM Brawner-Mucosal Immunology

Multi-site Human Microbiome

Inter-personal diversity and temporal dynamics of dental, tongue, and salivary microbiota in the healthy oral cavity-MW Hall-npj Biofilms and Microbiomes

Human Respiratory Microbiome

Airway Microbial Community Turnover Differs by BPD Severity in Ventilated Preterm Infants-BD Wagner-PLoS ONE

Metagenomic Analysis of Airborne Bacterial Community and Diversity in Seoul, Korea, during December 2014, Asian Dust Event-Seho Cha-PLoS ONE

Human Skin Microbiome

Review: The cutaneous ecosystem: the roles of the skin microbiome in health and its association with inflammatory skin conditions in humans and animals.-Rodrigues Hoffman A-Veterinary Dermatology

Human Nearly Sterile Sites

Impact of the Microbiota and Gastric Disease Development by Helicobacter pylori-Teresa Alarcon-Molecular Pathogenesis and Signal Transduction by Helicobacter pylori

Blood microbiota as a potential noninvasive diagnostic biomarker for liver fibrosis in severely obese patients: Choose carefully-Zongxin Ling-Heptatology

Epidemiological investigation of Candida species causing bloodstream infection in paediatric small bowel transplant recipients-Mallory J. Suhr-Mycoses

Human Gut Microbiome

Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease-Timothy R. Sampson-Cell

The Intestinal Microbiome, the Immune System and Spondyloarthropathy-ME Costello-Next-Generation Therapies and Technologies for Immune-Mediated Inflammatory Diseases

Profiling Living Bacteria Informs Preparation of Fecal Microbiota Transplantations-ND Chu-PLoS ONE

The development and role of microbial-host interactions in gut mucosal immune development-CR Stokes-Journal of Animal Science and Biotechnology

Pd-237 The Microbiome of the Colonic Mucosal-luminal Interface in Crohn’s Disease Patients in Endoscopic Remission-J Jacobs-Inflammatory Bowel Diseases

Progress with treating the microbial dysbiosis associated with irritable bowel syndrome.-JS Pearson-Current Opinion in Gastroenterology

Fecal microbiota transplantation for gastrointestinal disorders.-T Malikowski-Current Opinion in Gastroenterology

The human gut microbiome as source of innovation for health: Which physiological and therapeutic outcomes could we expect?-J Dore-Therapie

Review: Clostridium difficile colitis: A clinical review.-GK Ong-American Journal of Surgery

Biotransformation of Total Saponins in Siraitia Fructus by Human Intestinal Microbiota of Normal and Type 2 Diabetic Patients：Comprehensive Metabolites Identification and Metabolic Profile Elucidation Using LC-Q-TOF/MS.-G Zhou-Journal of Agricultural Food Chemistry

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

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

Animal Experiments

P-327 Prolonged Restraint Stressor Exposure in Outbred Cd-1 Mice Impacts Microbiota, Colonic Inflammation, and Short Chain Fatty Acids in Colonic Inflammation-R Maltz-Inflammatory Bowel Diseases

EGCG Prevents High Fat Diet-Induced Changes in Gut Microbiota, Decreases of DNA Strand Breaks, and Changes in Expression and DNA Methylation of Dnmt1 and MLH1 in C57BL/6J Male Mice.-M Remely-Oxidative Medicine and Cellular Longevity

Bovine milk oligosaccharides decrease gut permeability and improve inflammation and microbial dysbiosis in diet-induced obese mice.-G Boudry-Journal of Dairy Science

The Association of Specific Constituents of the Fecal Microbiota with Immune-Mediated Brain Disease in Dogs-Nick D. Jeffery-PLoS ONE

Animal Microbiome

Patterns in Gut Microbiota Similarity Associated with Degree of Sociality among Sex Classes of a Neotropical Primate-KR Amato-Microbial Ecology

Two biomass preparation methods provide insights into studying microbial communities of intestinal mucosa in grass carp (Ctenopharyngodon idellus)-NT Tran-Aquaculture Research

Changes in the Bacteriome of Honey Bees Associated with the Parasite Varroa destructor, and Pathogens Nosema-J Hubert-Invertebrate Microbiology

Characterization of faecal microbial communities of dairy cows fed diets containing ensiled Moringa oleifera fodder.-J Sun-Scientific Reports

Changes in bacterial community composition of Escherichia coli O157:H7 super-shedder cattle occur in the lower intestine-Rahat Zaheer-PLoS ONE

Plant, Root and Soil Microbiome

Draft Genome Sequence of Flavobacterium johnsoniae CI04, an Isolate from the Soybean Rhizosphere-JI Bravo-Genome Announcements

Draft Genome Sequence of Plant Growth–Promoting Micrococcus luteus Strain K39 Isolated from Cyperus conglomeratus in Saudi Arabia-Feras F. Lafi-Genome Announcements

Community structure, species variation, and functional characterization of rhizosphere-associated bacteria of different winter wheat (Triticum aestivum) cultivars-AK Mahoney-Frontiers in Plant Science

Draft Genome Sequence of Flavobacterium johnsoniae CI04, an Isolate from the Soybean Rhizosphere-JI Bravo-Genome Announcements

Arbuscular mycorrhizal fungi inoculation mediated changes in rhizosphere bacterial community structure while promoting revegetation in a semiarid ecosystem-G Rodriguez-Caballero-Science of the Total Environment

Plant Growth Promoting Activity of Pink Pigmented Facultative Methylotroph-Methylobacterium extorquens MM2 on Lycopersicon esculentum L.-P Subhaswaraj-Journal of Applied Biology and Biotechnology

… Genome Sequence of the Plant Growth-Promoting Rhizobacterium Pseudomonas fluorescens Strain CREA-C16 Isolated from Pea (Pisum sativum L.) Rhizosphere-N D’Agostino-Genome Announcements

Microbial species and functional diversity in rice rhizosphere of high-yield special ecological areas.-P LiYuan-Journal of Agricultural Resources and Environment

Translocation of Bacillus thuringiensis in Phaseolus vulgaris tissues and vertical transmission in Arabidopsis thaliana-R Garcia-Suarez-Journal of Applied Microbiology

Community Structures of Arbuscular Mycorrhizal Fungi in Soils and Plant Roots Inhabiting Abandoned Mines of Korea-H Park-Mycobiology

Fungal diversity in soils across a gradient of preserved Brazilian Cerrado-ASF de Araujo-Journal of Microbiology

Thesis: Potential risk factors associated with the microbiota of grass roots in the Kimberley region of Western Australia-B Achemedei

Soil Microbial Communities in Natural and Managed Cloud Montane Forests-EH Chang-Forests

Functional Genes That Distinguish Maize Phyllosphere Metagenomes in Drought and Well-Watered Conditions-Barbara A Methe-bioRxiv

Effects of jasmonic acid signalling on the wheat microbiome differ between body sites.-H Liu-Scientific Reports

Conversion from long-term cultivated wheat field to Jerusalem artichoke plantation changed soil fungal communities.-X Zhou-Scientific Reports

Water and Extremophile Microbiome

Production and Characterization of Organic Solvent-Tolerant Cellulase from Bacillus amyloliquefaciens AK9 Isolated from Hot Spring-M Irfan-Applied Biochemistry and Biotechnology

Significant seasonal variations of microbial community in an acid mine drainage lake in Anhui Province, China-C Hao-Environmental Pollution

Bacterial Community Structure and Functional Potential in the Northeastern Chukchi Sea-KM McFarlin-Continental Shelf Research

Exploring the Impacts of Anthropogenic Disturbance on Seawater and Sediment Microbial Communities in Korean Coastal Waters Using Metagenomics Analysis-NI Won-International Journal of Environmental Research and Public Health

Radiative energy budgets of phototrophic surface-associated microbial communities and their photosynthetic efficiency under diffuse and collimated light-M Lichtenberg-bioRxiv

Anaerobic Dechlorination of Tetrachlorobisphenol A in River Sediment and Associated Changes in Bacterial Communities-J Zhang-Water, Air & Soil Pollution

Microbial community changes in methanogenic granules during the transition from mesophilic to thermophilic conditions.-X Zhu-Applied Microbial Biotechnology

The Influence of Time and Plant Species on the Composition of the Decomposing Bacterial Community in a Stream Ecosystem.-AS Wymore-Microbial Ecology

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

Probiotics/Prebiotics

Toward a Personalized Approach in Prebiotics Research-M Dey-Nutrients

Phages and Viruses

Novel Temperate Phages of Salmonella enterica subsp. salamae and subsp. diarizonae and Their Activity against Pathogenic S. enterica subsp. enterica Isolates-Lenka Mikalova-PLoS ONE

Seasonal Dynamics and Metagenomic Characterization of Marine Viruses in Goseong Bay, Korea-Jinik Hwang-PLoS ONE

Bioinformatics

Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks-S Prigent-PLoS Computational Biology

P-310 Yi Characterizing Gut Metagenome Variation with Host Contamination Using Nanopore Sequencing-J Wang-Inflammatory Bowel Diseases

MetaTopics: an integration tool to analyze microbial community profile by topic model-J Yan-BMC Genomics

Discovery of C-Glycosylpyranonaphthoquinones in Streptomyces sp. MBT76 by a Combined NMR-Based Metabolomics and Bioinformatics Workflow-C Wu-Journal of Natural Products

Next-generation sequencing approaches for improvement of lactic acid bacteria-fermented plant-based beverages-Jordyn Bergsveinson-AIMS Microbiology

Microbes in the News

Seres plots path back from phase 2 microbiome blowup-FierceBiotech

 

Which foods can improve your gut bacteria?-BBC News

 

Branding BIOHM, The Tesla Of Probiotics-Forbes

 

For A Healthier Mind, Trust Your Gut-GOOD Magazine

 

Fecal Transplants May Improve Autism By Targeting Gut Bacteria-Huffington Post

 

Are prebiotics or probiotics effective against dermatitis?-EurekAlert

 

Dynamic duo could quickly identify deadly bacteria in hospitals-New Atlas
Bacteria in estuaries have genes for antibiotic resistance-Phys.Org

 

January 31, 2017

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Todays picks include nice reviews on microbiome engineering, and one on skin microbiomes in humans and animals. Biodegredation of mononitrophenol isomers by a tailor-made microbial consortium.  Quite a lot of microbiome news – from autism to inflammatory bowel disease.

 

Events and jobs

Microbiome Scientist Job – Merck – Cambridge, MA

 

General microbiome

Review: Microbiome engineering: Current applications and its future – Jee Loon Foo – Biotechnology Journal

Simultaneous biodegradation of three mononitrophenol isomers by a tailor-made microbial consortium immobilized in sequential batch reactors – H. Fu – Letters in Applied Microbiology

Human skin microbiome

Review: The cutaneous ecosystem: the roles of the skin microbiome in health and its association with inflammatory skin conditions in humans and animals – Aline Rodrigues Hoffmann – Veterinary Dermatology

 

Animal experiments

A metagenomic study of the preventive effect of Lactobacillus rhamnosus GG on intestinal polyp formation in ApcMin/+ mice – Y. Ni – Journal of Applied Microbiology

Water and extremophile microbiome

Biofilms for Monitoring Presence of Microsporidia in Environmental Water – Joseph A. Moss – Journal of Eukaryotic Microbiology

Haptophyte Diversity and Vertical Distribution Explored by 18S and 28S Ribosomal RNA Gene Metabarcoding and Scanning Electron Microscopy – Sandra Gran-Stadniczeñko – Journal of Eukaryotic Microbiology

Bioinformatics

Preprint: In-Depth Resistome Analysis by Targeted Metagenomics – Val F Lanza – bioRxiv

Microbes in the news

Could Fecal Microbiota Transplant Benefit Autistic Children? – MPR

Premature birth risk linked to bacteria in vagina and cervix – Catharine Paddock – MNT

New evidence of how gut microbes affect Inflammatory Bowel Disease – Kate Sweeney – BuisnessWeekly

Boost your immunity with foods that are alive – Rachel Yan – 9News

Rebalancing gut microbiome lengthens survival in mouse model of ALS – ScienceDaily

Carbohydrate That Promotes Biofilm May Be Key to Treating Pseudomonas Infections – Magdalena Kegel – CysticFibrosisNewsToday

 

 

January 30, 2017

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General microbiome
Commentary: The AGA’s Fecal Microbiota Transplantation National Registry: An important step toward understanding risks and benefits of microbiota therapeutics – Colleen R. Kelly – Gastroenterology

Review: Microbes and Mental Health: A Review – Ryan Rieder – Brain, Behavior, and Immunity

Review: The role of divalent metals for infectious diseases susceptibility and outcome – Guenter Weiss – Clinical Microbiology and Infection

Human gut microbiome
Effects of Acarbose on the Gut Microbiota of Prediabetic Patients: A Randomized, Double-blind, Controlled Crossover Trial – Xiuying Zhang – Diabetes Therapy

Clinical Commentary: More Than a Gut Feeling: The Implications of the Gut Microbiota in Psychiatry – Pochu Ho – Biological Psychiatry

Animal experiments
Target Intestinal Microbiota to Alleviate Disease Progression in Amyotrophic Lateral Sclerosis – Yong-guo Zhang – Clinical Therapeutics

Commensal Bacteria at the Crossroad between Cholestrol Homeostasis and Chronic Inflammation in Atherosclerosis – Kazuyuki Kasahara – Journal of Lipid Research

Bovine milk oligosaccharides decrease gut permeability and improve inflammation and microbial dysbiosis in diet-induced obese mice – Gaelle Boudry – Journal of Dairy Science

Broad spectrum antibiotic enrofloxacin modulates contact sensitivity through gut microbiota in a murine model – Anna Strzepa – Journal of Allergy and Clinical Immunology

Effects of subchronic oral toxic metal exposure on the intestinal microbiota of mice -Qixiao Zhai – Science Bulletin

In vitro fermentation of key dietary compounds with rumen fluid: A genome-centric perspective – Stefano Campanaro – Science of the Total Environment

Cow, yak, and camel milk diets differentially modulated the systemic immunity and fecal microbiota of rats – Wen Yongping – Science Bulletin

Animal microbiome
The oral microbiota of domestic cats harbors a wide variety of Staphylococcus species with zoonotic potential – Ciro Cesar Rossi – Veterinary Microbiology

Effects of daidzein on performance, serum metabolites, nutrient digestibility, and fecal bacterial community in bull calves – X.H. Zhao – Animal Feed Science and Technology

Plant microbiome
Marchantia liverworts as a proxy to plants basal microbiomes – Luis David Alcaraz – bioRxiv

Water and extremophile microbiome
Microbial succession in biofilms growing on artificial substratum in subtropical freshwater aquaculture ponds  – Zhifei Li – FEMS Microbiology Letters

Model communities hint to promiscuous metabolic linkages between ubiquitous free-living freshwater bacteria – Sarahi L Garcia – bioRxiv

Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy – William J. Brazelton – PeerJ

Food microbiology
Beneficial effects of legumes in gut health – Alfonso Clemente – Current Opinion in Food Science

Probiotics / prebiotics
Impact of ageing and a synbiotic on the immune response to seasonal influenza vaccination; a randomised controlled trial – Sumaia Enani – Clinical Nutrition

Antivirulence Properties of Probiotics in Combating Microbial Pathogenesis – M. Surendran Nair – Advances in Applied Microbiology

Bioinformatics
MetaShot: an accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data  – B Fosso – Bioinformatics

Linclust: clustering protein sequences in linear time – Martin Steinegger – bioRxiv

Techniques
Chapter 3: Best practices for germ-free derivation and gnotobiotic zebrafish husbandry – E. Melancon – Methods in Cell Biology

Chapter 10: Modeling intestinal disorders using zebrafish – X. Zhao – Methods in Cell Biology

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

Newly Isolated Strains
Actinomyces bouchesdurhonensis sp. nov. and Actinomyces mediterranea sp. nov., isolated from Human Stomach and Duodenum – Morgane Mailhe – Human Microbiome Journal

Peptoniphilus duodeni sp. nov., a new bacterial species identified in human duodenum – Morgane Mailhe – Human Microbiome Journal

Bacteroides bouchesdurhonensis sp. nov., a new bacterium isolated from the human gut – Sokhna Ndongo – Human Microbiome Journal

Microbes in the news
What Even is Kombucha, Anyway? – Anthony Rivas – BuzzFeed

Preventing Biofilm and Bacteria in Dental Operatory Tubing – Tech Featured

Non-Microbiology picks
The State of Systems Genetics in 2017 – Nitin S. Baliga – Cell Systems

Trump’s Immigration Ban Is Already Harming American Science – Ed Yong – The Atlantic

Geneticist launches bid for US Senate – Sara Reardon – Nature