Category Archives: General Microbiome

April 6, 2017

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Jobs

Microbial genomics expert : Basel, Switzerland via Nature Jobs

University Lecturer/University Senior Lecturer in Microbiology : Cambridge, United Kingdom via Nature Jobs

 

Microbiome Research

Review: Gut Microbiota Modulation and Its Relationship with Obesity Using Prebiotic Fibers and Probiotics: A Review  – Dinesh K. Dahiya – Frontiers in Microbiology

Mini-Review: Linking Diet to Colorectal Cancer: The Emerging Role of MicroRNA in the Communication between Plant and Animal Kingdoms – Manuela Del Cornò –  Frontiers in Microbiology

Comparative Analysis of the Gut Microbial Communities in Forest and Alpine Musk Deer Using High-Throughput Sequencing – Xiaolong Hu – Frontiers in Microbiology

Complex pectin metabolism by gut bacteria reveals novel catalytic functions – Didier Ndeh – Nature

State of the Art: The association of the skin microbiota with health, immunity and disease – Markus Egert – Clinical Pharmacology and Therapeutics

Human milk oligosaccharide composition predicts risk of necrotising enterocolitis in preterm infants – Chloe A Autran – Gut (BMJ)

Targeting the gut microbiota with inulin-type fructans: preclinical demonstration of a novel approach in the management of endothelial dysfunction  – Emilie Catry – Gut (BMJ)

Exposure to household furry pets influences the gut microbiota of infant at 3–4 months following various birth scenarios – Hein M. Tun – Microbiome (BMC)

 

Probiotics – Prebiotics

Antimicrobial Compounds Produced by Vaginal Lactobacillus crispatus Are Able to Strongly Inhibit Candida albicans Growth, Hyphal Formation and Regulate Virulence-related Gene Expressions – Shuai Wang – Frontiers in Microbiology

Oral administration of Lactobacillus gasseri SBT2055 is effective in preventing Porphyromonas gingivalis-accelerated periodontal disease – R. Kobayashi  – Scientific Reports

Commentary: Inulin prebiotic: is it all about bifidobacteria? – Sandrine Paule Claus – Gut (BMJ)

 

Extremophiles

Relative importance of chemoautotrophy for primary production in a light exposed marine shallow hydrothermal system – Gonzalo V. Gomez-Saez – Frontiers in Microbiology

The ecology of acidophilic microorganisms in the corroding concrete sewer environment – Xuan Li  – Frontiers in Microbiology

 

Pathogen Research

A geographically widespread outbreak investigation and development of a rapid screening method using whole genome sequences of enterohemorrhagic Escherichia coli O121 – Ken-Ichi Lee – Frontiers in Microbiology

Comprehensive Diagnosis of Bacterial Infection Associated with Acute Cholecystitis using Metagenomic Approach – Manabu Kujiraoka – Frontiers in Microbiology

In vitro transfer of methicillin resistance determinants mecA from methicillin resistant Staphylococcus aureus (MRSA) to methicillin susceptible Staphylococcus aureus (MSSA) – Asinamai Athliamai Bitrus – BMC Microbiology

Effects of Pseudomonas aeruginosa and Streptococcus mitis mixed infection on TLR4-mediated immune response in acute pneumonia mouse model – Chao Song – BMC Microbiology

Mosquito Microbiome Dynamics, a Background for Prevalence and Seasonality of West Nile Virus – Eva Novakova – Frontiers in Microbiology

Supplemental invasion of Salmonella from the perspective of Salmonella enterica serovars Kentucky and Typhimurium – Kevin Howe – BMC Microbiology

Whole-genome comparative analysis of Salmonella enterica serovar Newport strains reveals lineage-specific divergence – Jie Zheng  – Genome Biology and Evolution

 

Evolution

Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.) – David W. Waite – Frontiers in Microbiology

Evolutionary dynamics of CRISPR gene drives – Charleston Noble – Science Advances

 

Methods

Novel micelle PCR-based method for accurate, sensitive and quantitative microbiota profiling – Stefan A. Boers – Scientific Reports

A Novel Ultra High-Throughput 16S rRNA Amplicon Sequencing Library Preparation Method On The Illumina HiSeq Platform – Eric J. de Muinck – BioRxiv

Improving ancient DNA genome assembly – Alexander Seitz  – PeerJ (peer-reviewed)

 

Bioinformatic Tools

ATLAS (Automatic Tool for Local Assembly Structures) – a comprehensive infrastructure for assembly, annotation, and genomic binning of metagenomic and metatranscriptomic data – Richard Allen White III – PeerJ Preprints

 

News

Science Article Post: Ph.D. students face significant mental health challenges –  Elisabeth Pain

News: A deep dive into the genomes of penicillin fungi reveals a trove of potential drugs via Cosmos Magazine

 

April 5, 2017

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Today’s digest features interesting research on the dynamic microbiome evolution in social bees and the alteration in quorum Sensing, cell motility, stress Response, and carbohydrate metabolism  of gut microbiome by the organophosphate pesticide Diazinon. Low dose penicillin in early life can induce long term changes in mice gut microbiota, brain cytokines and behavior. Interesting reviews on the microbiome and human biology, and role of gut microbiota in the development of hypertension, including that associated with obstructive sleep apnea.

General microbiome

*Review: The Microbiome and Human Biology – Rob Knight – Annual Review of Genomics and Human Genetics

*Dynamic microbiome evolution in social bees – Waldan K. Kwong – Science Advances

Anaerobic Bacterial Fermentation Products Increase Tuberculosis Risk in Antiretroviral-Drug-Treated HIV – Leopoldo N. Segal – Cell Host & Microbe

Pregnancy and early life

Vancomycin treatment is a risk factor for vancomycin-nonsusceptible Staphylococcus capitis sepsis in preterm neonates – Marine Butin – Clinical Microbiology and Infection

Human oral microbiome

Relative abundance of total subgingival plaque-specific bacteria in salivary microbiota reflects the overall periodontal condition in patients with periodontitis – Shinya Kageyama – Plos One

Review: Biofilm over teeth and restorations: What do we need to know? – Nancy J. Lin – Dental Materials

Human skin microbiome

Cutaneous Burn Injury Promotes Shifts in the Bacterial Microbiome in Autologous Donor Skin: Implications for Skin Grafting Outcomes – Jennifer K. Plichta – Shock

Human gut microbiome

Review : The gut microbiota: a possible factor influencing systemic lupus erythematosus – Hadar Neuman – Current Opinion in Rheumatology

*Organophosphate Diazinon Altered Quorum Sensing, Cell Motility, Stress Response, and Carbohydrate Metabolism of Gut Microbiome – Bei Gao -Toxicological Sciences

Baseline gut microbiota predicts clinical response and colitis in metastatic melanoma patients treated with ipilimumab – N. Chaput – Oncology

*Review: Obstructive Sleep Apnea-Induced Hypertension: Role of the Gut Microbiota – David J. Durgan – Current Hypertension Reports

Review: The Gut Microbiota and Alzheimer’s Disease – Chunmei Jiang – Journal of Alzheimer’s Disease

Fecal Microbiota Transplantation

Fecal Microbiota Transplantation in Patients with Blood Disorders Inhibits Gut Colonization with Antibiotic-Resistant Bacteria: Results of a Prospective, Single-Center Study – Jaroslaw Bilinski – Clinical Infectious Diseases

Animal microbiome

Multi-Omics Analysis Reveals a Correlation between the Host Phylogeny, Gut Microbiota and Metabolite Profiles in Cyprinid Fishes – Tongtong Li – Frontiers in Microbiology

Diurnal Dynamics of Gaseous and Dissolved Metabolites and Microbiota Composition in the Bovine Rumen – Henk J. van Lingen – Frontiers in Microbiology

Microbial Biogeography and Core Microbiota of the Rat Digestive Tract – Dongyao Li – Scientific Reports

Animal experiments

Bifidobacterium in the gut microbiota confer resilience to chronic social defeat stress in mice – Chun Yang – Scientific Reports

Lack of Evidence That Selenium-Yeast Improves Chicken Health and Modulates the Caecal Microbiota in the Context of Colonization by Campylobacter jejuni – Alexandre Thibodeau – Frontiers in Microbiology

Review : Outstanding animal studies in allergy II: from atopic barrier and microbiome to allergen-specific immunotherapy – Erika Jensen-Jarolim – Current Opinion in Allergy & Clinical Immunology

Faecalibacterium prausnitzii treatment improves hepatic health and reduces adipose tissue inflammation in high-fat fed mice – Eveliina Munukka – ISME Journal

*Low-dose penicillin in early life induces long-term changes in murine gut microbiota, brain cytokines and behavior –  Sophie Leclercq – Nature Communications

Nod2 and Nod2-regulated microbiota protect BALB/c mice from diet-induced obesity and metabolic dysfunction – Ivan Rodriguez-Nunez – Scientific Reports

Plant, root, and soil microbiome

Aluminum-tolerant bacteria improve the plant growth and phosphorus content in ryegrass grown in a volcanic soil amended with cattle dung manure – María de la Luz Mora- Applied Soil Ecology

Invisible but consequential: root endophytic fungi have variable effects on belowground plant–insect interactions – Huyijuie Gan – Ecosphere

Land-use types and soil chemical properties influence soil microbial communities in the semiarid Loess Plateau region in China – Qin Tian – Scientific Reports

Phylogenetic conservation of substrate use specialization in leaf litter bacteria – Kristin L. Dolan – Plos ONE

Root biomass and exudates link plant diversity with soil bacterial and fungal biomass – Nico Eisenhauer – Scientific Reports

Water and extremophile microbiome

Discrimination of Four Marine Biofilm-Forming Bacteria by LC-MS Metabolomics and Influence of Culture Parameters – Laurie Favre – Journal of Proteome Research

Iron assimilation and utilization in anaerobic ammonium oxidizing bacteria – Christina Ferousi – Current Opinion in Chemical Biology

*Potential sources of bacteria colonizing the cryoconite of an Alpine glacier – Andrea Franzetti – PLOS ONE

Spatio-Temporal Variations of Marine Biofilm Communities Colonizing Artificial Substrata Including Antifouling Coatings in Contrasted French Coastal Environments – Jean-François Briand – Microbial Ecology

Metabolomics

Review: Metabolomics: Strategies to Define the Role of Metabolism in Virus Infection and Pathogenesis – Marianne Manchester – Advances in Virus Research

Effect of Major Royal Jelly Proteins on Spatial Memory in Aged Rats: Metabolomics Analysis in Urine – Di Chen -Journal of Agricultural and Food Chemistry

Food microbiology

Sourdough authentication: quantitative PCR to detect the lactic acid bacterial microbiota in breads – Erica Pontonio – Scientific Reports

Probiotics / prebiotics

Evaluation of Potential Probiotics Isolated from Human Milk and Colostrum – Quésia S. Damaceno – Probiotics and Antimicrobial Proteins

Bioinformatics

SLIMM: species level identification of microorganisms from metagenomes – Temesgen Hailemariam Dadi – PeerJ

Techniques

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area – Kazuma Nakano – Human Cell

High-pressure microscopy for tracking dynamic properties of molecular machines – Masayoshi Nishiyama – Biophysical Chemistry

Gut Microbiome Standardization in Control and Experimental Mice – Kathy D. McCoy – Current Protocols in Immunology

Diastereomer-specific Quantification of Bioactive Hexosylceramides from Bacteria and Mammals – Johanna von Gerichten – Journal of Lipid Research

Microbes in the news

Genetically engineered microbes make their own fertilizer, could feed the world’s poorest

The Next Plague (5) Bacteria: The Coming And Going And Coming Again Of Bacterial Plagues

Latest Helicobacter pylori breakthrough could lead to eradication of bacteria

Science, publishing, and career

Journal editor calls for ‘culture change’ around clinical trial data

Anitha’s non-microbiology picks

In the quest of Planet 9

April 4, 2017

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General microbiome

Diversity of fungus-growing termites (Macrotermes) and their fungal symbionts (Termitomyces) in the semiarid Tsavo Ecosystem, Kenya – R Vesala – Biotropica

Indole signalling and (micro)algal auxins decrease the virulence of Vibrio campbellii, a major pathogen of aquatic organisms – Q Yang – Environmental Microbiology

Large population study shows that adolescents with celiac disease have an increased risk of multiple autoimmune and nonautoimmune comorbidities –  A Assa – Acta Paediatrica

In vitro fermentation of oat β-glucan and hydrolysates by fecal microbiota and selected probiotic strains – JL Dong – Journal of the Science of Food and Agriculture

 

Human gut microbiome

Gastric microbiota features associated with cancer risk factors and clinical outcomes: A pilot study in gastric cardia cancer patients from Shanxi, China – G Yu – International Journal of Cancer

 

Animal microbiome

Host species shapes the co-occurrence patterns rather than diversity of stomach bacterial communities in pikas – H Li – Applied Microbiology and Biotechnology

 

Plant, root and soil microbiome

Phylloplane bacteria increase the negative impact of food limitation on insect fitness – GL Olson – Ecological Entomology

Bodyguards: Pathogen-Derived Decoys That Protect Virulence Factors – JK Paulus – Trends in Plant Science

Response of the rhizosphere prokaryotic community of barley (Hordeum vulgare L.) to elevated atmospheric CO2 concentration in open-top chambers – M Szoboszlay – Microbiology Open

Draft Genome Sequence of Pseudomonas putida Strain GM4FR, an Endophytic Bacterium Isolated from Festuca rubra L. – F Wemheuer – Genome Announcements

Phytoremediation of Petroleum-Contaminated Soil in Association with Soil Bacteria – P Pokethitiyook – Phytoremediation

Phytoremediation of Salt-Impacted Soils and Use of Plant Growth-Promoting Rhizobacteria (PGPR) to Enhance Phytoremediation – KE Gerhardt – Phytoremediation

Genomic identification and characterization of the elite strains Bradyrhizobium yuanmingense BR 3267 and Bradyrhizobium pachyrhizi BR 3262 recommended for cowpea inoculation in Brazil – J Leite – Brazilian Journal of Microbiology

Effect of elevated nitrate on biodegradation of pentabromodiphenyl ether (BDE-99) and change in microbial communities during groundwater recharge with tertiary-treated municipal wastewater – Y Yan – International Biodeterioration & Biodegradation

The tale of a neglected energy source: Elevated hydrogen exposure affects both microbial diversity and function in soil – M Khdhiri – Applied and Environmental Microbiology

 

Water and extremophile microbiome

Production and persistence of bacterial and labile organic matter at the hypoxic water–sediment interface of the St. Lawrence Estuary – M Hébert – Limnology and Oceanography

Comparative proteomics reveals signature metabolisms of exponentially growing and stationary phase marine bacteria – S Muthusamy – Environmental Microbiology

Spatiotemporal dynamics of bacterial community composition in large shallow eutrophic Lake Taihu: High overlap between free-living and particle-attached assemblages – X Tang – Limnology and Oceanography

 

Built environment

Coarse-graining bacteria colonies for modelling critical solute distributions in picolitre bioreactors for bacterial studies on single-cell level – C Westerwalbesloh – Microbial Biotechnology

 

Phages and Virus

Short-Sighted Virus Evolution and a Germline Hypothesis for Chronic Viral Infections – KA Lythgoe – Trends in Microbiology

Conflicting selection alters the trajectory of molecular evolution in a tripartite bacteria–plasmid–phage interaction – E Harrison – Molecular Ecology

 

Techniques

*Review: Bioelectrochemical Systems for Measuring Microbial Cellular Functions – HMM Selim – Electroanalysis

Engineering bacterial thiosulfate and tetrathionate sensors for detecting gut inflammation – KNM Daeffler – Molecular Systems Biology

Impact of Contaminating DNA in Whole Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis – M Thoendel – Journal of Clinical Microbiology

Genomics and Metagenomics in Microbial Ecology: Recent Advances and Challenges  – T Narihiro – Microbes and Environments

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

Optimization of a bioassay to evaluate Escherichia coli stress responses – B Cunha – IEEE

 

More microbes

*Review: Shapeshifting to Survive: Shape Determination and Regulation in Caulobacter crescentus – SA Woldemeskel – Trends in Microbiology

 

Microbes in news

Antibiotic Resistant Bacteria Common in Diabetic Foot Ulcers – S Gupta – Endocrinology Advisor

Fighting Antibiotic-Resistant Bacteria in Food Animals – J Bartel – Veterinary Medicine News

Vets warn dog owners about potentially deadly bacteria lurking in water – A Lasker – Lifestyle

Magnetic brain stimulation causes weight loss by making gut bacteria healthier – The Endocrine Society – Science Daily

Vapour droplets from threatened orcas show pneumonia bacteria – Waterloo Region Record – TheRecord.com

Hitchhiking Earth bacteria could evolve to live on Mars – M Irving – New Atlas

Bionic leaf turns air, water, sunlight and bacteria into fertilizer – B Hays – UPI

Nicholls sophomore researches antibiotic-resistant bacteria – G Ohlmeyer – Houmatoday.com

What the Bacteria in Your Mouth May Reveal About Your Cancer Risk – SG Miller – Live Science

April 1, 2017

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Events and jobs

Asst/Assoc Collegiate-Track Clinical Microbiology Faculty – Virginia Tech

General microbiome

Salivary inflammatory markers and microbiome in normoglycemic lean and obese children compared to obese children with type 2 diabetes – Waleed F. Janem – PLOS ONE

Microbiome study finds children with type 2 diabetes more likely to have poor oral health – Ellen Goldbaum – Medical Xpress

Cross-talk among metabolic parameters, esophageal microbiota, and host gene expression following chronic exposure to an obesogenic diet – Nadeem O. Kaakoush – Scientific Reports

Review: Microbiome Tools for Forensic Science – Jessica L. Metcalf – Trends in Biotechnology

Book: Forensic Microbiology – David O. Carter

Review: The legacy of the past: effects of historical processes on microbial metacommunities – Máté Vass – Aquatic Microbial Ecology

Human respiratory microbiome

The microbiome and secondary lung disease in neuromuscular patients: Is it time to change our clinical practice? – Reply – Florian Stehling – Respirology

Human skin microbiome

Patterns in the skin microbiota differ in children and teenagers between rural and urban environments – Jenni Lehtimäki – Scientific Reports

Human vaginal microbiome

Transient microbiota exposures activate dormant Escherichia coli infection in the bladder and drive severe outcomes of recurrent disease – Nicole M. Gilbert – PLOS Pathogens

Vaginal bacteria can trigger recurrent UTIs, study shows – Science Daily

Human gut microbiome

Review: Diet and microbiota in inflammatory bowel disease: The gut in disharmony – Davy CM Rapozo – World Journal of Gastroenterology

The microbiome of professional athletes differs from that of more sedentary subjects in composition and particularly at the functional metabolic level – Wiley Barton – Gut

Animal experiments

NLRP12 regulates gut microbiota to suppress intestinal inflammation – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

Community structure of the gut microbiota in sympatric species of wild Drosophila – Vincent G. Martinson – Ecology Letters

Defining Brugia malayi and Wolbachia symbiosis by stage-specific dual RNA-seq – Alexandra Grote – PLOS Neglected Tropical Diseases

Researchers profile symbiotic relationship between bacteria and filarial nematodes – Medical Xpress

The Bacterial Community Found on the surface Purple Martin (Progne subis) Eggs – Beth A. Potter – The Open Ornithology Journal

Stable mucus-associated bacterial communities in bleached and healthy corals of Porites lobata from the Arabian Seas – Ghaida Hadaidi – Scientific Reports

Plant, root, and soil microbiome

Relationship of microbial communities and suppressiveness of Trichoderma fortified composts for pepper seedlings infected by Phytophthora nicotianae – Margarita Ros – PLOS ONE

Two-year field monitoring shows little evidence that transgenic potato containing ABF3 significantly alters its rhizosphere microbial community structure – Ki Jung Nam – Journal of Ecology and Environment

Members of Gammaproteobacteria as indicator species of healthy banana plants on Fusarium wilt-infested fields in Central America – Martina Köberl – Scientific Reports

Review: From yogurt to yield: Potential applications of lactic acid bacteria in plant production – John R. Lamont – Soil Biology and Biochemistry

Changes in soil bacterial community structure as a result of incorporation of Brassica plants compared with continuous planting eggplant and chemical disinfection in greenhouses – Tianzhu Li – PLOS ONE

Water and extremophile microbiome

Impact of selectively enriched microbial communities on long-term fermentative hydrogen production – R.K. Goud – Bioresource Technology

Co-invasion hypothesis explains microbial community structure changes in upland streams affected by riparian invader – Paul J. McInerney – Freshwater Science

Silver nanoparticles uptake by salt marsh plants – Implications for phytoremediation processes and effects in microbial community dynamics – Joana P. Fernandes – Marine Pollution Bulletin

Food microbiology

Identification of Microbial Profile of Koji Using Single Molecule, Real-Time Sequencing Technology – Wenyan Hui – Journal of Food Science

Probiotics / prebiotics

Roles of Probiotic Lactobacilli Inclusion in Helping Piglets Establish Healthy Intestinal Inter-environment for Pathogen Defense – Jiajun Yang – Probiotics and Antimicrobial Proteins

Phages and viruses

Review: Intriguing interaction of bacteriophage-host association: An understanding in the era of omics – Krupa M. Parmar – Frontiers in Microbiology

Bioinformatics

Review: Are Next-Generation Sequencing Tools Ready for the Cloud? – Antonio Celesti – Trends in Biotechnology

Techniques

Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP) – Scott Tighe – Journal of Biomolecular Technology

In vitro gene expression-coupled bacterial cell chip for screening species-specific antimicrobial enzymes – Seok-Joon Kwon – Journal of Biotechnology and Bioengineering

Review: International Standards for Genomes, Transcriptomes, and Metagenomes – Christopher E. Mason – Journal of Biomolecular Technology

A comparison of sampling methods for examining the laryngeal microbiome – Alissa S. Hanshew – PLOS ONE

Microbes in the news

Probiotics For Babies: Why Your Baby’s Gut Health Is So Important –  Joy D’Souza – The Huffington Post Canada

NIH Wants to Test New Bacteria Therapy for Eczema – Maggie Fox – NBC News

Microbes on the market

Regulator OKs bacteria’s spread – Martin Cash – Winnipeg Free Press

March 31, 2017

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Microbiome research

Potential role of fecal microbiota from patients with slow transit constipation in the regulation of gastrointestinal motility – Xiaolong Ge, Scientific Reports

Opinion: Gut microbiome as a clinical tool in gastrointestinal disease management: are we there yet? – Eamonn M. M. Quigley – Nature Reviews Gastroenterology & Hepatology

Relevance of secretor status genotype and microbiota composition in susceptibility to rotavirus and norovirus infections in humans  – Jesús Rodríguez-Díaz – Scientific Reports

Milk Fat Globule Membrane Supplementation in Formula Modulates the Neonatal Gut Microbiome and Normalizes Intestinal Development – Ganive Bhinder – Scientific Reports

Critical Review: Microbiota-Gut-Brain Axis: Modulator of Host Metabolism and Appetite – Marcel van de Wouw – The Journal of Nutrition

Comparison of stool versus rectal swab samples and storage conditions on bacterial community profiles – Christine M. Bassis – BMC Microbiology

Ethnic and diet-related differences in the healthy infant microbiome – Jennifer C. Stearns – Genome Medicine (BMC)

Intestinal Barrier Function and the Gut Microbiome Are Differentially Affected in Mice Fed a Western-Style Diet or Drinking Water Supplemented with Fructose – Valentina Volynets – The Journal of Nutrition

The gut microbiota of insecticide-resistant insects houses insecticide-degrading bacteria: A potential source for biotechnological exploitation – Luis Gustavo de Almeida – PLOS One

Probiotics / Synbiotics

A comparative characterization of different host-sourced Lactobacillus ruminis strains and their adhesive, inhibitory, and immunomodulating functions – Xia Yu – Frontiers in Microbiology

Rice bran and Probiotics Alter the Porcine Large Intestine and Serum Metabolomes for Protection Against Human Rotavirus Diarrhea  – Nora Jean Nealon – Frontiers in Microbiology

Development of a synbiotic beverage enriched with bifidobacteria strains and fortified with whey proteins – Federico Baruzzi – Frontiers in Microbiology

Inferring Microbial Interactions in the Gut of the Hong Kong Whipping Frog (Polypedates megacephalus) and a Validation Using Probiotics – Francis Cheng-Hsuan Weng – Frontiers in Microbiology

The effects of probiotic and synbiotic supplementation on metabolic syndrome indices in adults at risk of type 2 diabetes: study protocol for a randomized controlled trial – Nazila Kassaian – Trials (BMC)

Good Bugs vs Bad Bugs: Evaluation of Inhibitory Effect of Selected Probiotics against Enterococcus faecalis – Aarti A Bohora – The Journal of Contemporary Dental Practice (PDF here)

Probiotic bacteria prevent Salmonella – induced suppression of lymphoproliferation in mice by an immunomodulatory mechanism – R. Doug Wagner – BMC Microbiology

Exogenous lactobacilli mitigate microbial changes associated with grain fermentation (corn, oats, and wheat) by equine fecal microflora ex vivo – Brittany E. Harlow – PLOS One

 

Pathogens

Methicillin resistant Staphylococcus aureus emerged long before the introduction of methicillin in to clinical practice – Catriona Harkins – BioRxiv

Azathioprine, Mercaptopurine, and 5-Aminosalicylic Acid Affect the Growth of IBD-Associated Campylobacter Species and Other Enteric Microbes – Fang Liu –  Frontiers in Microbiology

Untargeted metabolomics analysis reveals key pathways responsible for the synergistic killing of colistin and doripenem combination against Acinetobacter baumannii – Mohd Hafidz Mahamad Maifiah – Scientific Reports

 

Other Genomics / Metagenomics

Untangling Genomes of Novel Planctomycetal and Verrucomicrobial Species from Monterey Bay Kelp Forest Metagenomes by Refined Binning – John Vollmers – Frontiers in Microbiology

Genome-Scale Reconstruction of the Metabolic Network in Oenococcus oeni to Assess Wine Malolactic Fermentation – Sebastián N. Mendoza – Frontiers in Microbiology

Comparative genomics of transport proteins in probiotic and pathogenic Escherichia coli and Salmonella enterica strains – Jimmy Do – Microbial Pathogenesis (Elsevier)

 

Bioinformatics

STITCHER 2.0: primer design for overlapping PCR applications  – Damien M. O’Halloran – Scientific Reports

 

Evolution

Phylogenomic evolutionary surveys of subtilase superfamily genes in fungi – Juan Li – Scientific Reports

Evolutionary dynamics on any population structure – Benjamin Allen – Nature

On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria – Rochelle M. Soo – Science

A perspective article about the latter paper here: How Cyanobacteria went green by Robert E. Blankenship

Structural reconstruction of protein ancestry – Romain Rouet – PNAS

 

March 30, 2017

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Midgut microbiome of a vector for leishmaniasis, reviews on the human oral microbiome, using microfluidics to visualize live root-bacteria interactions, new open-access publishing project from the Gates Foundation.

General microbiome

Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions – Babak Moment – eLIFE

Human oral microbiome

Review: Oral Microbiome and Nitric Oxide: the Missing Link in the Management of Blood Pressure – Nathan S. Bryan – Current Hypertension Reports

Review: Microbiota, Immune Subversion, and Chronic Inflammation – Carolyn D Kramer – Frontiers in Microbiology

Human gut microbiome

Highlight: Shaping the gut microbiome from the pancreas – Wei Wong – Science Signaling

Review: Mechanisms and consequences of intestinal dysbiosis – G. Adrienne Weiss – Cellular and Molecular Life Sciences

Animal experiments

Metaproteogenomics Reveals Taxonomic and Functional Changes between Cecal and Fecal Microbiota in Mouse – Alessandro Tanca – Frontiers in Microbiology

Helminth-induced alterations of the gut microbiota exacerbate bacterial colitis – C Su – Mucosal Immunology

Sex-related alterations of gut microbiota composition in the BTBR mouse model of autism spectrum disorder – Lorena Coretti – Scientific Reports

Milk Fat Globule Membrane Supplementation in Formula Modulates the Neonatal Gut Microbiome and Normalizes Intestinal Development – Ganive Bhinder – Scientific Reports

Gut metagenomic analysis reveals prominent roles of Lactobacillus and cecal microbiota in chicken feed efficiency – Wei Yan – Scientific Reports

Animal microbiome

An integrated overview of the midgut bacterial flora composition of Phlebotomus perniciosus, a vector of zoonotic visceral leishmaniasis in the Western Mediterranean Basin – Wael Fraihi – PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

* Live imaging of root–bacteria interactions in a microfluidics setup – Hassan Massalha – PNAS

Mechanisms of nitrogen deposition effects on temperate forest lichens and trees – Therese S. Carter – Ecosphere

Research priorities for harnessing plant microbiomes in sustainable agriculture – Posy E Busby – PLOS Biology

Fe plaque-related aquatic uranium retention via rhizofiltration along a redox-state gradient in a natural Phragmites australis Trin ex Steud. wetland – Weqing Wang – Environmental Science and Pollution Research

Functional and phylogenetic diversity of cultivable rhizobacterial endophytes of sorghum [Sorghum bicolor (L.) Moench] – Venkadasamy Govindasamy – Antonie van Leeuwenhoek

Enhanced growth of halophyte plants in biochar-amended coastal soil: roles of nutrient availability and rhizosphere microbial modulation – Hao Zheng – Plant, Cell & Environment

Water and extremophile microbiome

Metagenomic Analysis of a Complex Community Present in Pond Sediment – Vivek Negi – Journal of Genomics

Probiotics/prebiotics

The preliminary study of prebiotic potential of Polish wild mushroom polysaccharides: the stimulation effect on Lactobacillus strains growth – Renata Nowak – European Journal of Nutrition

Probiotics may delay the progression of nonalcoholic fatty liver disease by restoring the gut microbiota structure and improving intestinal endotoxemia – Li Xue – Scientific Reports

Bioinformatics

MIPE: A metagenome-based community structure explorer and SSU primer evaluation tool – Bin Zou – PLOS One

Metabolomics

Gas chromatography/mass spectrometry metabolomics of urine and serum from nonhuman primates exposed to ionizing radiation: Impacts on the tricarboxylic acid cycle and protein metabolism – Evan L Pannkuk – Journal of Proteome Research

Techniques

Review: Pretreatment methods of lignocellulosic biomass for anaerobic digestion – Farrukh Raza Amin – AMB Express

Comparison of Standard Culture-Based Method to Culture-Independent Method for Evaluation of Hygiene Effects on the Hand Microbiome – C Zapka – mBio

More microbes

Depleting Mycobacterium tuberculosis of the transcription termination factor Rho causes pervasive transcription and rapid death – Laure Botella – Nature Communications

A Pseudomonas T6SS effector recruits PQS-containing outer membrane vesicles for iron acquisition – Jinshui Lin – Nature Communications

Indole-Induced Activities of β-Lactamase and Efflux Pump Confer Ampicillin Resistance in Pseudomonas putida KT2440 – Jisun Kim – Frontiers in Microbiology

Microbes in the news

Microbiome: Puppy power – Sujata Gupta – Nature (Outlook section)

Biological underpinnings of chronic fatigue syndrome begin to emerge – Amy Maxmen – Nature (News section)

Bacteria from sewage are infecting coral reefs – Elena Motivans – ZME Science

Key research priorities for agricultural microbiomes identified – Phys Org

Viral Bacterial Parasites Called Phages Drive Co-Evolution of Gut Microbiome – MedicalResearch.com

MSU, Shedd Aquarium partnering to create healthier aquatic homes – EurekAlert

Painting with bacteria is a thing and BUGSS will show you how – Stephen Babcock – Technical.ly Baltimore

Microbes on the market

Marrone Bio Innovations and Evogene Advance Novel Bacteria and Related Proteins Beyond Discovery into Insecticidal Product Development Phase – GlobeNewswire – Yahoo!Finance

Science, publishing, and career

* Gates Foundation announces open-access publishing venture – Declan Butler – Nature (News section)

The readability of scientific texts is decreasing over time – Pontus Plavén-Sigray – bioRxiv

Amy’s non-microbiology picks

Iron minerals within specific microfossil morphospecies of the 1.88 Ga Gunflint Formation – Kevin Lepot – Nature Communications

March 28, 2017

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A brief digest today, but with several interesting news pieces, including one about 3D-printing bacteria and one about ammonia-digesting bacteria in urinals. Also worth reading are the relationship between human papillomavirus, cancers and the impact of land-based pollution on coral reefs and how clean do you think your home is?

General microbiology

Preprint: Primary souring: a novel bacteria-free method for sour beer production – Kara Osburn – bioRxiv

Human gut microbiome

Low FODMAP in 2017: Lessons learned from clinical trials and mechanistic studies – S. Eswaran – Neurogastroenterology and Motility

Animal experiments

Mouse: Alterations to the Gut Microbiome Impair Bone Strength and Tissue Material Properties – Jason D Guss – Journal of Bone and Mineral Research

Water and extremophile microbiome

Review: New insights into a hot environment for early life – Jianhong Dai – Environmental Microbiology Reports

*A Next-Generation Sequencing Approach to Characterize the Impacts of Land-based Sources of Pollution on the Microbiota of Southeast Florida Coral Reefs – Christopher Staley – Applied and Environmental Microbiology

Effect of salinity on the microbial community and performance on anaerobic digestion of marine macroalgae – Yi Zhang – Journal of Chemical Technology and Biotechnology

Phages and viruses

*Human papillomavirus in cervical cancer and oropharyngeal cancer: One cause, two diseases – Tara A. Berman and John T. Schiller – Cancer

Microbes in the news

On World Tuberculosis Day, Doctors Warn Of New Drug-Resistant Bacteria – Henry Ridgwell – VOA News
Bad breath: Study find array of bacteria when orcas exhale – Phuong Le – ABC News

*Creating materials in a novel way by 3-D printing bacteria – Bob Yirka – Phys.org

Mumbai airport goes green: replaces water in urinals with ammonia-breaking bacteria – DNA web team – DNA India

Gonad-chomping bacteria to be unleashed on dengue virus – Anusha Venkat – Asia Times

Gut bacteria new weapon in fight against asthma – Thoracic Society for Australia and New Zealand Annual Scientific Meeting

*The Dirtiest Things In The Home Don’t Include The Toilet – Zye Angiwan – Immortal News

March 27, 2017

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Exploring life within the biofilm and how free-living microbes thrive, and focus on life history patterns of symbionts. Finally, big dairy (Parmalat- South Africa)  was found guilty of repeatedly hiding serious infections (Salmonella and Listeria,)from their consumers.

General microbiome

Biofilm formation enables free-living nitrogen-fixing rhizobacteria to fix nitrogen under aerobic conditions.

Wang D. ISME Journal

Symbiont Acquisition and Replacement as a Source of Ecological Innovation.

Sudakaran S. Trends in Microbiology

Distinct succession patterns of abundant and rare bacteria in temporal microcosms with pollutants.

Jiao S. Environmental Pollution

Similar articles

Human gut microbiome

Early-life origin of intestinal inflammatory disorders.

Ley D. Nutrition Reviews

From mystery to mechanism: Can proteomics build systems-level understanding of our gut microbes?

Gonzalez CG. Expert Reviews of Proteomics

Human oral microbiome

Circadian oscillations of microbial and functional composition in the human salivary microbiome.

Takayasu L. DNA Research

Comparison of Boiling and Robotics Automation Method in DNA Extraction for Metagenomic Sequencing of Human Oral Microbes.

Yamagishi J.PLoS One.

Water, estuarine and marine microbiome

Integrated metabolism in sponge-microbe symbiosis revealed by genome-centered metatranscriptomics.

Moitinho-Silva L. ISME Journal

Are Oligotypes Meaningful Ecological and Phylogenetic Units? A Case Study of Microcystis in Freshwater Lakes.

Berry MA. Frontiers in Microbiology

Shotgun metagenomic sequencing reveals freshwater beach sands as reservoir of bacterial pathogens.

Mohiuddin MM. Water Research

Symbiosis and microbiome flexibility in calcifying benthic foraminifera of the Great Barrier Reef.

Prazeres M. Microbiome

Farm animal microbiome

Effects of dietary rapeseed meal supplementation on cecal microbiota in laying hens with different flavin-containing monooxygenase 3 genotypes.

Long C. Poultry Science

A distinct bacterial dysbiosis associated skin inflammation in ovine footrot.

Maboni G. Scientific Reports

Pasture flock chicken cecal microbiome responses to prebiotics and plum fiber feed amendments.

Park SH. Poultry Science

Respiratory system microbiome

Dendritic cell expression of the signaling molecule TRAF6 is required for immune tolerance in the lung.

Han D. International Immunology

Eukaryote microbiome

UniEuk: Time to Speak a Common Language in Protistology!

Berney C. The Journal of Eukaryotic Microbiology

Animal microbiome

Colonization by non-pathogenic bacteria alters mRNA expression of cytochromes P450 in originally germ-free mice.

Jourová L. Folia Microbiologica

Gut microbiome-related metabolic changes in plasma of antibiotic-treated rats.

Behr C. Archives of Toxicology

Indoor microbiome

Hospital microbial surface colonization revealed during monitoring of Klebsiella spp., Pseudomonas aeruginosa, and non-tuberculous mycobacteria.

Geadas Farias P. Antonie Van Leeuwenhoek

Microbes in the news

Parmalat hides bacteria infections

-News24

Indians find a new bacterial target for drug development

-The Hindu

March 22, 2017

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Today’s digest features interesting review articles on the role of microbiome in health and disease, heart failure, and how the respiratory tract microbiota act as gatekeepers to respiratory health. Also, we have original research articles on the response of bacterial communities in oil-contaminated marine waters to addition of chemical and biological dispersants. Also, a very fascinating article in Harvard Business review on the gender bias against junior female scientists. Not surprising!! Enjoy.

General microbiome

*Review: The role of the microbiome in human health and disease: an introduction for clinicians – Vincent B Young – British Medical Journal

*Review: Targeting the Microbiome in Heart Failure – Allyson Zabell – Current Treatment Options in Cardiovascular Medicine

Gastric microbiota features associated with cancer risk factors and clinical outcomes: A pilot study in gastric cardia cancer patients from Shanxi, China – Guoqin Yu – international Journal of Cancer

Pregnancy and early life

Late preterm birth has direct and indirect effects on infant gut microbiota development during the first six months of life – M Forsgren – Acta Pediatrica

Vaginal microbiome

Characterization of vaginal Lactobacillus species by rplK -based multiplex qPCR in Russian women – Vladimir V. Demkin – Anaerobe

Human oral microbiome

Changes in salivary microbiota increase volatile sulfur compounds production in healthy male subjects with academic-related chronic stress – Bruno Dias Nani – Plos One

Candida albicans biofilm heterogeneity does not influence denture stomatitis but strongly influences denture cleansing capacity – Lindsay E. O’Donnell – Journal of Medical Microbiology

Oral Bacterial Infections : Diagnosis and Management – Glendee Reynolds-Campbell – Dental Clinics of North America

Human respiratory microbiome

*The microbiota of the respiratory tract: gatekeeper to respiratory health – Wing Ho Man – Nature Reviews Microbiology

Human gut microbiome

Editorial : Infant colic is still a mysterious disorder of the microbiota–gut–brain axis – Anna Pärtty – Acta Pediatrica

Review: More Flavor for Flavonoid-Based Interventions? – Nadeem O. Kaakoush – Trends in Molecular Medicine

Perspectives : New Frontiers in Fibers: Innovative and Emerging Research on the Gut Microbiome and Bone Health – Taylor C. Wallace – Journal of the American College of Nutrition

Does the Gut Microbiota Influence Immunity and Inflammation in Multiple Sclerosis Pathophysiology? – Monika Adamczyk-Sowa – Journal of Immunology Research

The Role of Intestinal Alkaline Phosphatase in Inflammatory Disorders of Gastrointestinal Tract – Jan Bilski – Mediators of Inflammation

The Gut Microbiome, Energy Homeostasis, and Implications for Hypertension – Ruth A. Riedl – Current Hypertension Reports

Fecal Microbiota Transplantation

Commentary: A proposed definition of microbiota transplantation for regulatory purposes – Diane E. Hoffmann – Gut Microbes

Review: Novel Indications for Fecal Microbial Transplantation: Update and Review of the Literature – Nathaniel Aviv Cohen – Digestive Diseases and Sciences

Animal microbiome

Review: Role of the microbiome in swine respiratory disease – Megan C. Niederwerder – Veterinary Microbiology

Comparative composition, diversity, and abundance of oligosaccharides in early lactation milk from commercial dairy and beef cows – William M. Sischo – Journal of Dairy Science

Comparative analysis of fecal microbial communities in cattle and Bactrian camels – Liang Ming – Plos One

Sheep fed with banana leaf hay reduce ruminal protozoa population – Cláudio Eduardo Silva Freitas – Tropical Animal Health and Production

Metabolomics

Review: Metabolomic-guided discovery of Alzheimer’s disease biomarkers from body fluid – Che Nor Adlia Enche Ady – Journal of Neuroscience Research

Animal experiments

The farming environment protects mice from allergen-induced skin contact hypersensitivity – C. P. Frossard – Clinical and Experimental Allergy

Metabolomics insights into diabetes nephropathy and protective effects of Radix Scutellariae on rats using ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry – Lihui Men – RSC Advances

Plant, root, and soil microbiome

Root plant growth promoting rhizobacteria inoculations increase ferric chelate reductase (FC-R) activity and Fe nutrition in pear under calcareous soil conditions – Muzaffer İpek – Scientia Horticulturae

Bacterial diversity of the rhizosphere and nearby surface soil of rice (Oryza sativa) growing in the Camargue (France) – Jorge R. Osman – Rhizosphere

Structure and function of the bacterial communities during rhizoremediation of hexachlorobenzene in constructed wetlands – Cuiping Zhang – Environmental Science and Pollution Research

Water and extremophile microbiome
Characterization of spatial distribution of the bacterial community in the South Sea of Korea – Ji-Hui Seo – Plos One

Diversity and community structure of cyanobacteria and other microbes in recycling irrigation reservoirs – Ping Kong – Plos One

*Response of the bacterial community in oil-contaminated marine water to the addition of chemical and biological dispersants – Camila Rattes de Almeida Couto – Journal of Environmental Management

Probiotics / prebiotics

Lactobacillus johnsonii supplementation attenuates respiratory viral infection via metabolic reprogramming and immune cell modulation – W. Fonseca- Mucosal Immunology

Identification of the key excreted molecule by Lactobacillus fermentum related to host iron absorption – Ana González – Food Chemistry

Effect of 8-weeks prebiotics/probiotics supplementation on alcohol metabolism and blood biomarkers of healthy adults: a pilot study – Christopher Irwin – European Journal of Nutrition

Bioinformatics

Making big data smart—how to use metagenomics to understand soil quality – Gisle Vestergaard – Biology and Fertility of Soils

Techniques

SILVA, RDP, Greengenes, NCBI and OTT — how do these taxonomies compare? – Monika Balvočiūtė – BMC Genomics

Comparative evaluation of four bacteria-specific primer pairs for 16S rRNA gene surveys – Sofie Thijs – Frontiers in Microbiology

Microbes in the news

Asthma: Researchers discover how exposure to microbes protects against asthma

Rainy Day? Microbes May Be at Play

Building A Brewery, Chapter 4: For the Love of Microbes

Science, publishing, and career 

*Junior Female Scientists Aren’t Getting the Credit They Deserve “despite evidence that women on average, may perform better than men in early stage of their careers”

Anitha’s non-microbiology picks

How Pluto’s haze could explain its red spots

Cancer cells cast a sweet spell on the immune system

Actinide chemistry expands to new oxidation states

March 21, 2017

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Events and jobs

Microbiology Department Manager – Medlab Pathology – Sydney

General microbiome

The ecology of human microbiota: dynamics and diversity in health and disease – A Karkman – Annals of the New York Academy of Sciences

Human gut microbiome

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

Shaping the Metabolism of Intestinal Bacteroides Population through Diet to Improve Human Health – DR Covian – Frontiers in Microbiology

Animal microbiome

Effects of a protected inclusion of organic acids and essential oils as antibiotic growth promoter alternative on growth performance, intestinal morphology and gut microflora in broilers – Y Liu – Animal Science Journal

Extreme drought, host density, sex, and bullfrogs influence fungal pathogen infection in a declining lotic amphibian – AJ Adams – Ecosphere

Neoagarotetraose protects mice against intense exercise-induced fatigue damage by modulating gut microbial composition and function – N Zhang – Molecular Nutrition and Food Research

Effects of Gliadin consumption on the Intestinal Microbiota and Metabolic Homeostasis in Mice Fed a High-fat Die –  L Zhang – Scientific Reports

Plant, root and soil microbiome

*Review: Rhizogenic agrobacteria in hydroponic crops: epidemics, diagnostics and control – L Bosmans – Plant Pathology

Mn accumulation in a submerged plant Egeria densa (Hydrocharitaceae) is mediated by epiphytic bacteria – K Tsuji – Plant, Cell and Environment

Water microbiome and extremophiles

Microbial players and processes involved in phytoplankton bloom utilization in the water column of a fast-flowing, river-dominated estuary – MW Smith – Microbiology Open

Metagenomics of Hyperthermophilic Environments: Biodiversity and Biotechnology – A Strazzulli – Microbial Ecology of Extreme Environments

Sediment depth and habitat as predictors of the diversity and composition of sediment bacterial communities in an inter-tidal estuarine environment – DFR Cleary – Marine Ecology

Crenarchaeal Viruses of Hot Springs: Diversity, Ecology and Co-evolution –  AC Ortmann – Microbial Ecology of Extreme Environments

*Review: Marine Prasinoviruses and Their Tiny Plankton Hosts: A Review – KD Weynberg – Viruses

Microbial Electron Transport in the Deep Subsurface – J Hinks – Microbial Ecology of Extreme Environments

New Insights into the Microbial Diversity of Polar Desert Soils: A Biotechnological Perspective – J v Dorst – Microbial Ecology of Extreme Environments

Transcriptomics

Mechanism for microbial population collapse in a fluctuating resource environment – S Turkarslan – Molecular Systems Biology

Techniques

SILVA, RDP, Greengenes, NCBI and OTT — how do these taxonomies compare? – M Balvociute – BMC Genomics

Prediction of virus-host infectious association by supervised learning methods – M Zhang – BMC Bioinformatics

Comparison of methods for identification of microbial communities in book collections: Culture-dependent (sequencing and MALDI-TOF MS) and culture-independent (Illumina MiSeq) – L Krakova – International Biodeterioration & Biodegradation

More microbes

*Review: The role of bacillithiol in Gram-positive Firmicutes – P Chandrangsu – Antioxidants & Redox Signaling

The effect of antibiotics and diet on enterolactone concentration and metabolome studied by targeted and non-targeted LC-MS metabolomics – AK Bolviq – Journal of Proteome Research

Exploring the Viral Ecology of High Latitude Aquatic Systems – C Chenard – Microbial Ecology of Extreme Environments

The Nature and Relevance of Solvent Stress in Microbes and Mechanisms of Tolerance – M Manefield – Microbial Ecology of Extreme Environments

Surveillance of Exhibit Associated Aquatic Viruses Using Next Generation Sequencing Technologies – WV Bonn – IAAAM 2016

Microbes in the news

Before you consume billions of live bacteria … – E Cauthorn – Las Vegas Sun

Bacteria between humans and pets? Could improve global health: researchers – M Shah – Toronto Sun

There is a reason dogs like meat – NZ Herald

ANTIBIOTIC APOCALYPSE: Harvard reveals doomsday scenario that could KILL 10 million a year – O Smith – Express

THE ALTERATION OF THE INTESTINAL MICROBIOTA COULD PROTECT METABOLIC DISEASES – Zoe – The Quebec Times