Category Archives: Human oral

October 11, 2017

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Events and jobs

Microbiology Laboratory Analyst – Cork (Ringaskiddy Road, Monkstown, Co. Cork)

 

Pregnancy and early life

Effect of probiotics on perinatal outcome in patients at high risk of preterm birth. – N Kirihara – The Journal of Obstetrics and Gynaecology Research

 

 

Human oral microbiome

Quantification of carious pathogens in the interdental microbiota of young caries-free adults. – D Bourgeois – PLoS One

 

Human gut microbiome

The gut microbiome in atherosclerotic cardiovascular disease – Z Jie – Nature Communications

Review: The microbiome as a novel paradigm in studying stress and mental health. – RT Liu – The American Psychologist

Review: The mycobiome: Role in health and disease, and as a potential probiotic target in gastrointestinal disease – CL Hager – Digestive and Liver Disease

Review: Selected aspects of the human gut microbiota – M Ventura – Cellular and Molecular Life Sciences

 

Animal experiments 

Modulation of the gut microbiota by the mixture of fish oil and krill oil in high-fat diet-induced obesity mice. – C Ciu – PLoS One

Comparative characterization of bacterial communities in geese fed all-grass or high-grain diets – X Qu – PLoS One

 

Animal microbiome 

Pycnoscelus surinamensis cockroach gut microbiota respond consistently to a fungal diet without mirroring those of fungus-farming termites – C Richards – PLoS One

 

Plant, root, and soil microbiome

The impact of the omics era on the knowledge and use of Lysobacter spp. to control phytopathogenic microorganisms. – G Puopolo – Journal of Applied Microbiology

The effect of pH, electrolytes and temperature on the rhizosphere geochemistry of phytosiderophores. – M Walter – Plant and Soil

Pathogenic potential of environmental resident fungi from ornithogenic soils of Antarctica – JRP Sousa – Fungal Biology

Influences of Different Halophyte Vegetation on Soil Microbial Community at Temperate Salt Marsh – DR Chaudhary – Microbial Ecology

 

Built environment 

Unravelling the core microbiome of biofilms in cooling tower systems. – L Di Gregorio – Biofouling

 

 

Phages and viruses

Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics – S Roux – Nature Communications

Nasty Prophages and the Dynamics of Antibiotic-Tolerant Persister Cells – A Harms – bioRxiv

 

Techniques

Modified RNA-seq method for microbial community and diversity analysis using rRNA in different types of environmental samples. – YW Yan – PLoS One

A GLM-based latent variable ordination method for microbiome samples. – MB Sohn – Biometrics

Rapid enteric testing to permit targeted antimicrobial therapy, with and without Lactobacillus reuteri probiotics, for paediatric acute diarrhoeal disease in Botswana: A pilot, randomized, factorial, controlled trial – JM Pernica – PLoS One

A Tomato Spotted Wilt Virus S RNA-based Replicon System in Yeast –  K Ishibashi – Scientific Reports

Analyses Approaches for Bacteria – E Ribeiro – Exposure to Microbiological Agents in Indoor and Occupational Environments

 

Microbes in the news

Bacteria self-organize to build working sensors – EurekAlert

Effects of nutritional factors on the intestinal microbiota – Freie Universität

October 9, 2017

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Events and jobs
Postdoctoral Researcher (Experimental or Computational) – Cornell University, Ithaca, NY

The Brito Lab at Cornell University in Ithaca, NY works in the area of systems biology of the human microbiome. We are looking for talented postdocs to fill two open positions for postdoctoral researchers interested in investigating mechanistic linkages between microbes and human health outcomes.

Postdoctoral candidates can have an experimental or computational background, or both. One of the positions will be focused on engineering—any experience with synthetic biology or biomaterials is a plus. There are a range of projects in the lab relating to: clinically relevant populations (i.e. inflammatory bowel and neutropenic patients); environmental transmission of organisms and antibiotic resistance; genetic engineering of bacteria; and international research related to the microbiome. The lab strives on the diverse backgrounds of students and postdocs (e.g. microbiology, biomedical engineering, computational biology and genetics).

Start dates are flexible, but could be as early as this Fall. Interested late-stage graduate students or recently-obtained PhDs, should send Ilana Brito (ibrito (at) cornell.edu) a cover letter and CV. Promising candidates will be invited for an interview. We offer a competitive salary and benefits package.

Pregnancy and early life
Diagnosis and management of diaper dermatitis in infants with emphasis on skin microbiota in the diaper area – Maja Šikić Pogačar – International Journal of Dermatology

Human respiratory microbiome
Upregulation of bacterial-specific Th1 and Th17 responses that are enriched in CXCR5+ CD4+ T cells in non-small cell lung cancer – Qin-Yun Ma – International Immunopharmacology

Human gut microbiome
Review: Microbiome-health interactions in older people – Paul W. O’Toole – Cellular and Molecular Life Sciences

Review: Selected aspects of the human gut microbiota – Marco Ventura – Cellular and Molecular Life Sciences

Review: A comprehensive review of non-enterica subspecies of Salmonella enterica – Alexandre Lamas – Microbiological Research

Animal experiments
Effect of dietary supplements in American bullfrogs reared in low and high stocking densities – Jorgina Juliana Gradisse Freitas – Aquaculture Reports

Animal microbiome
Stenotrophomonas-like bacteria are widespread symbionts in cone snail venom ducts – Joshua P. Torres – Applied and Environmental Microbiology

Plant, root, and soil microbiome
Microbial Resistance Mechanisms to the Antibiotic and Phytotoxin Fusaric Acid – Frankie K. Crutcher – Journal of Chemical Ecology

Book: Soil Pollution: From Monitoring to Remediation – Paula Alvarenga, Christian P. Andersen (editors)

Water and extremophile microbiome
Oxic-anoxic regime shifts mediated by feedbacks between biogeochemical processes and microbial community dynamics – Timothy Bush – Nature Communications

Built environment
Impact of carbon monoxide partial pressures on methanogenesis and medium chain fatty acids production during ethanol fermentation – Sofia Esquivel-Elizondo – Biotechnology and Bioengineering

Food microbiology
Volatile Organic Compounds in Feces Associate With Response to Dietary Intervention in Patients With Irritable Bowel Syndrome – Megan Rossi – Clinical Gastroenterology and Hepatology

Tiny but mighty: bacterial membrane vesicles in food biotechnological applications – Yue Liu – Current Opinion in Biotechnology

10 – Microstructure, constituents, and their relationship with quality and functionality of dietary fibers – Naphaporn Chiewchan – Food Science, Technology and Nutrition

Targeting gut microbiota: Lactobacillus alleviated type 2 diabetes via inhibiting LPS secretion and activating GPR43 pathway – Kai-Kai Li – Journal of Functional Foods

Probiotics / prebiotics
Enhancing the viability of Lactobacillus rhamnosus GG after spray drying and during storage – Géraldine Broeckx – International Journal of Pharmaceutics

Review: Challenges and Opportunities of Nontraditional Approaches to Treating Bacterial Infections – Brian N Tse – Clinical Infectious Diseases

Probiotic intervention influences the salivary levels of Matrix Metalloproteinase (MMP)-9 and Tissue Inhibitor of metalloproteinases (TIMP)-1 in healthy adults – Heli Jäsberg – Archives of Oral Biology

Bioinformatics
Detection of complex structural variation from paired-end sequencing data – Joseph G. Arthur – bioRxiv

Codon-Dependent Translational Accuracy Controls Protein Quality in Escherichia coli but not in Saccharomyces cerevisiae – Lyne Jossé – bioRxiv

Techniques
A simple dilute and shoot approach incorporated with pentafluorophenyl (PFP) column based LC-MS/MS assay for the simultaneous determination of trimethylamine N-oxide and trimethylamine in spot urine samples with high throughput – Xiaoguang (Sunny) Li – Journal of Chromatography B

Microbes in the news
Multiple barriers to ending Madagascar’s plague outbreak – Andrew Masterson – Cosmos Magazine

A daughter’s affliction gives mother’s work ‘meaning and purpose’ – Liora Engel-Smith – The Sentinel

Antibiotic apocalypse’: doctors sound alarm over drug resistance – Robin McKie –
The Guardian

Want to cut your risk of urinary tract infection? Drink water, says study – Zee Media Bureau

Statins have power to help elderly fight off killer superbug – Sarah Westcott – Express

October 8, 2017

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General microbiome

Repurposed kinase inhibitors and β-lactams as a novel therapy for antibiotic resistant bacteria – Nathan Wlodarchak, bioRxiv

Isolation and whole genome analysis of endospore-forming bacteria from heroin – Jörn Kalinowski, Forensic Science International: Genetics

Events and jobs

DOCTORAL STUDENT / POSTDOCTORAL RESEARCHER, EARLY INTERACTIONS OF INTESTINAL MICROBIOTA AND THE IMMUNE SYSTEM – University of Helsinki

Director of the Microbiome Research Laboratory – Microbiome Research Laboratory (MRL) at UT Southwestern

Microbiology Faculty Position – University of Chicago

Human gut microbiome

Microbiome, inflammation and colorectal cancer – Ju Chen, Seminars in Immunology

The fecal microbiome of ALS patients – David Brenner, Neurobiology of Aging

Targeting gut microbiota: Lactobacillus alleviated type 2 diabetes via inhibiting LPS secretion and activating GPR43 pathway – Kai-Kai Li, Journal of Functional Foods

Volatile Organic Compounds in Feces Associate With Response to Dietary Intervention in Patients With Irritable Bowel Syndrome – Megan Rossi, Clinical Gastroenterology and Hepatology

Proteomics Dataset: The Colon Mucosa from Inflammatory Bowel Disease Patients, Gastrointestinal Asymptomic Rheumatoid Arthritis Patients, and Controls – Tue Bjerg Bennike, Data in Brief

The mycobiome: Role in health and disease, and as a potential probiotic target in gastrointestinal disease – Christopher L. Hager, Digestive and Liver Disease

Overview of paediatric IBD – David C. Wilson, Seminars in Pediatric Surgery

Improvement of Insulin Sensitivity after Lean Donor Feces in Metabolic Syndrome Is Driven by Baseline Intestinal Microbiota Composition – Ruud S. Kootte, Cell Metabolism

Fasting the Microbiota to Improve Metabolism? – Joel T. Haas, Cell Metabolism

Fecal Transplant in Inflammatory Bowel Disease – Alexander S. Browne, Gastroenterology Clinics of North America

The Brain-Gut Axis and Stress in Inflammatory Bowel Disease  – Charles N. Bernstein, Gastroenterology Clinics of North America

Human oral microbiome

The oral microbiota in colorectal cancer is distinctive and predictive – Burkhardt Flemer, Gut microbiota

Animal experiments

Interhost dispersal alters microbiome assembly and can overwhelm host innate immunity in an experimental zebrafish model – Adam R. Burns, PNAS

Ganoderma lucidum polysaccharides improve insulin sensitivity by regulating inflammatory cytokines and gut microbiota composition in mice – S. Xua, Journal of Functional Foods

Effect of enzymatically hydrolyzed scallop visceral protein powder used as a replacement of fish meal on the growth performance, immune responses, intestinal microbiota and intestinal morphology of broiler chickens – R.E. Xing, Livestock Science

Intestinal microbiota impact sepsis associated encephalopathy via the vagus nerve – Suyan Li, Neuroscience Letters

Animal microbiome

Environmental proteomics reveals taxonomic and functional changes in an enriched aquatic ecosystem – Amanda C. Northrop, Ecosphere

Plant, root, and soil microbiome

Characterization of the first rice paddy cluster I isolate, Methyloterricola oryzae gen. nov., sp. nov. and amended description of Methylomagnum ishizawai –  Katharina Frindte, International Journal of Systematic and Evolutionary Microbiology

Water and extremophile microbiome

Ultrastructural observations on prokaryotic associates of benthic foraminifera: Food, mutualistic symbionts, or parasites? – Joan M. Bernhard, Marine Micropaleontology

Food microbiology

Potentially active spoilage bacteria community during the storage of vacuum packaged beefsteaks treated with aqueous ozone and electrolyzed water – Cristian Botta, International Journal of Food Microbiology

Next generation of microbiological risk assessment: Potential of omics data for exposure assessment – Heidy M.W. den Besten, International Journal of Food Microbiology

Characterization of lactic acid bacteria recovered from atole agrio, a traditional Mexican fermented beverage – Kati Väkeväinen, LWT – Food Science and Technology

Probiotics / prebiotics

Prebiotics and Inflammatory Bowel Disease – Heather E. Rasmussen, Gastroenterology Clinics of North America

Probiotics in Inflammatory Bowel Disease – Bincy P. Abraham, Gastroenterology Clinics of North America

Enhancing the viability of Lactobacillus rhamnosus GG after spray drying and during storage – Géraldine Broeckx, International Journal of Pharmaceutics

Microbes in the news

Second grade handwashing experiment leads to big decrease in bacteria, illness – INFECTIOUS DISEASES SOCIETY OF AMERICA, EurekAlert!

UTHealth awarded $3.1 million NIH grant to study how gut bacteria relates to diabetes – UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT HOUSTON, EurekAlert!

Scientists are trying to figure out how to keep bacteria from running rampant on space missions –  Claire Maldarelli, Popular Science

“Good” Gut Bacteria Linked to Melanoma Immunotherapy Response – GEN

October 4, 2017

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Today’s digest features excellent reviews on recent advances in cryo-electron microscopy technology for understanding bacterial ribosome assembly,  and impact of gut microbiome on therapeutics. Happy reading!

General microbiome

Towards standards for human fecal sample processing in metagenomic studies – Paul I Costea – Nature Biotechnology

Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium – Rashmi Sinha – Nature Biotechnology

Editorial : Microbiome yarns: microbiome basis of memory – Kenneth Timmis – Microbial Biotechnology

Review : Cross Talk: The Microbiota and Neurodevelopmental Disorders – John R. Kelly – Frontiers in Neuroscience

Review : Gut Microbiota, Immune System, and Bone – P. D’Amelio – Calcified Tissue International

Pregnancy and early life

Meconium microbiome as a new source of information about long-term health and disease: questions and answers – P. Wilczyńska – The Journal of Maternal-Fetal & Neonatal Medicine

Evolution in fecal bacterial/viral composition in infants of two central African countries (Gabon and Republic of the Congo) during their first month of life – Lionel Brazier – Plos one

A longitudinal study of the infant nasopharyngeal microbiota: The effects of age, illness and antibiotic use in a cohort of South East Asian children – Susannah J. Salter – Plos one

Human gut microbiome

Review : Microbiota in digestive cancers: our new partner? – Anthony Lopez – Carcinogenesis

*Review : Impacts of the Human Gut Microbiome on Therapeutics – Yoshiki Vázquez-Baeza – Annual Reviews

Associations between acute gastrointestinal GvHD and the baseline gut microbiota of allogeneic hematopoietic stem cell transplant recipients and donors – C Liu – Leukemia

Natural polyreactive IgA antibodies coat the intestinal microbiota – Jeffrey J. Bunker – Science

Time of day and eating behaviors are associated with the composition and function of the human gastrointestinal microbiota – Jennifer L Kaczmarek – The American Journal of Clinical Nutrition

The Effects of an Environmentally Relevant Level of Arsenic on the Gut Microbiome and its Functional Metagenome – Liang Chi – Toxicological Sciences

Animal experiments

Probiotics modulate gut microbiota and improve insulin sensitivity in DIO mice – Renata A.Bagarolli – The Journal of Nutritional Biochemistry

Decaffeinated green and black tea polyphenols decrease weight gain and alter microbiome populations and function in diet-induced obese mice – Susanne M. Henning – European Journal of Nutritional

Microbiota-related Changes in Bile Acid & Tryptophan Metabolism are Associated with Gastrointestinal Dysfunction in a Mouse Model of Autism – Anna V. Golubeva – EBioMedicine

Repeated Oral Exposure to Nε-Carboxymethyllysine, a Maillard Reaction Product, Alleviates Gut Microbiota Dysbiosis in Colitic Mice – Nesreen ALJahdali – Digestive Disease Sciences

Comparison of the Luminal and Mucosa-Associated Microbiota in the Colon of Pigs with and without Swine Dysentery – Eric R. Burrough – Frontiers in Veterinary Science

Animal microbiome

Untangling the cecal microbiota of feral chickens by culturomic and metagenomic analyses – Chiara Ferrario – Environmental Microbiology

Bacterial community associated with worker honeybees (Apis mellifera) affected by European foulbrood – Tomas Erban – PeerJ

Comparative characterization of bacterial communities in geese fed all-grass or high-grain diets – Qi Xu – Plos One

Plant, root, and soil microbiome

Implication of graphene oxide in Cd-contaminated soil: A case study of bacterial communities – TingXiong – Journal of Environmental Management

Elucidating the microbial community associated with the protein preference of sludge degrading worms – Steef de Valk – Environmental Technology

Bacterial microbiomes of individual ectomycorrhizal Pinus sylvestris roots are shaped by soil horizon and differentially sensitive to nitrogen addition – Srisailam Marupakula – Environmental Microbiology

A comparative study of composting the solid fraction of dairy manure with or without bulking material: performance and microbial community dynamics – Xiao-ZhongZhong -Bioresource Technology

Water and extremophile microbiome

Individual-level trait diversity predicts phytoplankton community properties better than species richness or evenness – Simone Fontana – The ISME Journal

Bacterial community dynamics within an aerobic granular sludge reactor treating wastewater loaded with pharmaceuticals – Catarina L.Amorim – Ecotoxicology and Environmental Safety

Food Microbiology

Chlorogenic acid versus amaranth’s caffeoylisocitric acid – Gut microbial degradation of caffeic acid derivatives – Maren Vollmer – Food Research International

Probiotics / prebiotics

Specific signatures of the gut microbiota and increased levels of butyrate in children treated with fermented cow’s milk containing heat-killed Lactobacillus paracasei CBA L74 – Roberto Berni Canani – Applied and Environmental Microbiology

Beneficial effects of a probiotic blend on gastrointestinal side effects induced by leflunomide and amlodipine in a rat model – S.C. Song – Beneficial Microbes

Phages and viruses

Characterization of the human DNA gut virome across populations with different subsistence strategies and geographical origin – Simone Rampelli – Environmental Microbiology

Metabolomics

Identification of phenolic metabolites in human urine after the intake of a functional food made from grape extract by a high resolution LTQ-Orbitrap-MS approach – Gemma Sasot – Food Research International
http://www.sciencedirect.com/science/article/pii/S0963996917300297?via%3Dihub

Bioinformatics

A broken promise: microbiome differential abundance methods do not control the false discovery rate – Stijn Hawinkel – Briefings in Bioinformatics
https://academic.oup.com/bib/article/doi/10.1093/bib/bbx104/4091293/A-broken-promise-microbiome-differential-abundance

Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes – Nathan D. Olson – Briefings in Bioinformatics

Ananke: temporal clustering reveals ecological dynamics of microbial communities – Michael W. Hall – PeerJ

Detection of Increased Plasma Interleukin-6 Levels and Prevalence of Prevotella copri and Bacteroides vulgatus in the Feces of Type 2 Diabetes Patients – Aline Zazeri Leite – Frontiers in Immunology

k-SLAM: accurate and ultra-fast taxonomic classification and gene identification for large metagenomic data sets – David Ainsworth – Nucleic Acids Research

Techniques

* The impact of recent improvements in cryo-electron microscopy technology on the understanding of bacterial ribosome assembly – Aida Razi – Nucleic acids Research

Anitha’s non-microbiology picks

A cold, clear view of life wins chemistry Nobel

Nobel physics prize awards discovery in gravitational waves

Medicine Nobel Prize Goes to Circadian Rhythm Researchers

New portable blood analyzer could improve anemia detection worldwide

Computational study sheds doubt on latest theory of birds’ mysterious magnetic compass

 

October 3, 2017

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Review on bioinformatics software for virus sequence analysis, the wild baboon microbiome, potential health risks of spontaneous food fermentation.

Human oral microbiome

Pre-print: Novel genes required for the fitness of Streptococcus pyogenes in human saliva – Luchang Zhu – bioRxiv

Human gut microbiome

Antibiotic use and new-onset inflammatory bowel disease in Olmsted County, Minnesota: a population-based case-control study – Satimai Aniwan – Journal of Crohn’s and Colitis

The Gut Microbiota of Healthy Aged Chinese Is Similar to That of the Healthy Young – Gaorui Bian – mSphere

Animal experiments

Young Pigs Consuming Lysozyme Transgenic Goat Milk Are Protected from Clinical Symptoms of Enterotoxigenic Escherichia coli Infection – Lydia C Garas – The Journal of Nutrition

Whole-Grain Starch and Fiber Composition Modifies Ileal Flow of Nutrients and Nutrient Availability in the Hindgut, Shifting Fecal Microbial Profiles in Pigs – Janelle M Fouhse – The Journal of Nutrition

Lotus Seed Resistant Starch Regulates Gut Microbiota and Increases SCFAs Production and Mineral Absorption in Mice – Hongliang Zeng – Journal of Agricultural and Food Chemistry

Animal microbiome

Microbiota Diversity Within and Between the Tissues of Two Wild Interbreeding Species – Emmanuel Guivier – Microbial Ecology

Group Living and Male Dispersal Predict the Core Gut Microbiome in Wild Baboons – Laura E Grieneisen – Integrative and Comparative Biology

Plant, root, and soil microbiome

Pre-print: Rice paddy Nitrospirae encode and express genes related to sulfate respiration: proposal of the new genus Candidatus Sulfobium – Sarah Zecchin – bioRxiv

Effects of Grazing and Fire Frequency on Floristic Quality and its Relationship to Indicators of Soil Quality in Tallgrass Prairie – George C Manning – Environmental Management

Pre-print: Hunters or gardeners? Linking community structure and function of trap-associated microbes to the nutrient acquisition strategy of a carnivorous plant – Dagmara Sirová – bioRxiv

Multitrophic interactions in the rhizosphere of a temperate forest tree affect plant carbon flow into the belowground food web – H R Maboreke – Soil Biology and Biochemistry

Water and extremophile microbiome

Rhabdanaerobium thermarum gen. nov., sp. nov., a novel anaerobic bacterium isolated from a hot spring – Lan Liu – International Journal of Systematic and Evolutionary Microbiology

Food microbiology

Review: Spontaneous Food Fermentations and Potential Risks for Human Health – Vittorio Capozzi – Fermentation

Phages and viruses

Review: Software Dedicated to Virus Sequence Analysis “Bioinformatics Goes Viral” – Martin Hölzer – Advances in Virus Research

Bioinformatics

Nephele: A cloud platform for simplified, standardized, and reproducible microbiome data analysis – Nick Weber – Bioinformatics

More microbes

Pre-print: A LaeA- and BrlA-dependent cellular network governs tissue-specific secondary metabolism in the human pathogen Aspergillus fumigatus – Abigail L Lind – bioRxiv

Pre-print: Dual RNAseq shows the human mucosal immunity protein, MUC13, is a hallmark of Plasmodium exoerythrocytic infection – Gregory M LaMonte – bioRxiv

September 29, 2017

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General microbiome

Metabolic and process engineering for biodesulfurization in Gram-negative bacteria – I. Martínez, Journal of Biotechnology

Biofilms: Survival and defense strategy for pathogens – Ashutosh Kumar, International Journal of Medical Microbiology

Effect of Substrate Conversion on Performance of Microbial Fuel Cells and Anodic Microbial Communities – Zhao Yang-Guo, Environmental Engineering Science

Comparison of the impacts of zinc ions and zinc nanoparticles on nitrifying microbial community – Qiang Wu, Journal of Hazardous Materials

Models of microbiome evolution incorporating host and microbial selection – Qinglong Zeng, Microbiome

Pregnancy and early life

Impact of delivery mode on the colostrum microbiota composition – Marco Toscano, BMC Microbiology

Multi-site human microbiome

Human Microbiome in Brazil – Luciana Campos Paulino, The Brazilian Microbiome

Forensic genetics and genomics: Much more than just a human affair – Miguel Arenas, PLoS Genetics

South Asian Health: Inflammation, Infection, Exposure, and the Human Microbiome – Jennifer Leng, Journal of Immigrant and Minority Health

Natural Products as Platforms To Overcome Antibiotic Resistance – Sean E. Rossiter, Chemical Reviews

Intestinal Dysbiosis and Rheumatoid Arthritis: A Link between Gut Microbiota and the Pathogenesis of Rheumatoid Arthritis – Gabriel Horta-Baas, Journal of Immunology Research

Human respiratory microbiome

Individual Patterns of Complexity in Cystic Fibrosis Lung Microbiota, Including Predator Bacteria, over a 1-Year Period – Juan de Dios Caballero, mBio

Sputum microbiota in severe asthma patients: Relationship to eosinophilic inflammation – Naijian Li, Respiratory Medicine

Human skin microbiome

Culture characterization of the skin microbiome in type 2 diabetes mellitus: a focus on the role of innate immunity – Akshay Thimmappaiah Jagadeesh, Diabetes Research and Clinical Practice

Human vaginal microbiome

Lactobacillus iners-dominated vaginal microbiota is associated with increased susceptibility to Chlamydia trachomatis infection in Dutch women: a case–control study – Robin van Houdt, Epidemiology

Human gut microbiome

Bacterial chat: intestinal metabolites and signals in host -microbiota -pathogen interactions – Bruna C. Lustri, Infection and Immunity

Gut inflammation and dysbiosis in human motor neuron disease – Julie Rowin, Physiological Reports

Molecular basis of gut microbiome-associated colorectal cancer: A synthetic perspective – Alan R. Healy, Journal of American Chemical Society

Metagenomic Paleomicrobiology Characterizes Fecal Microbiomes and Viromes of Pre-Columbian Cultures from Vieques, Puerto Rico – Jessica I. Rivera-Perez, ProQuest

A randomised trial of the effect of omega-3 polyunsaturated fatty acid supplements on the human intestinal microbiota – Henry Watson, BMJ Journals

Functional Changes in the Gut Microbiome Contribute to Transforming Growth Factor β-Deficient Colon Cancer – Scott G. Daniel, mSystems

The Induction of Oxalate Metabolism In Vivo Is More Effective with Functional Microbial Communities than with Functional Microbial Species – Aaron W. Miller, mSystems

Thiamine Acquisition Strategies Impact Metabolism and Competition in the Gut Microbe Bacteroides thetaiotaomicron – Zachary A. Costliow, mSystems

Human oral microbiome

Host Genetic and Environemental Associations and the Human Salivary Microbiome – Brittany Ann Demmitt, ProQuest

Animal microbiome

Pathogenesis of oral FIV infection – Craig Miller, PLoS ONE

Photosynthetic epibionts and endobionts of Pacific oyster shells from oyster reefs in rocky versus mudflat shores – Laurent Barillé, PLoS ONE

Free-living and captive turtles and tortoises as carriers of new Chlamydia spp. – Agata Mitura, PLoS ONE

Microbiomes Associated with Animals: Implications for Livestock and Animal Production – Hilario Cuquetto Mantovani, The Brazilian Microbiome

Maintenance of distal intestinal structure in the face of prolonged fasting: A comparative examination of species from five vertebrate classes – Marshall D. McCue, The Anatomical Record

Plant, root, and soil microbiome

Assessment of derelict soil quality: Abiotic, biotic and functional approaches – Quentin Vincent, Science of The Total Environment

Endophytic fungal communities of Polygonum acuminatum and Aeschynomene fluminensis are influenced by soil mercury contamination – William Pietro-Souza, PLoS ONE

Shifts in the bacterial community composition along deep soil profiles in monospecific and mixed stands of Eucalyptus grandis and Acacia mangium – Arthur Prudêncio de Araujo Pereira, PLoS ONE

Temporal dynamics in microbial soil communities at anthrax carcass sites – Karoline Valseth, BMC Microbiology

Pyrosequencing reveals soil enzyme activities and bacterial communities impacted by graphene and its oxides – Yan Rong, Journal of Agriculture and Food Chemistry

Alterations in soil fungal community composition and network assemblage structure by different long-term fertilization regimes are correlated to the soil ionome – Chao Xue, Biology and Fertility of Soils

The Brazilian Soil Microbiome – Fernando Dini Andreote, The Brazilian Microbiome

Lechevalieria rhizosphaerae sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.) and emended description of the genus Lechevalieria – Junwei Zhao, International Journal of Systematic and Evolutionary Microbiology

Carbon nanomaterials alter plant physiology and soil bacterial community composition in a rice-soil-bacterial ecosystem – Yi Hao, Environmental Pollution

Potential sources of microbial colonizers in an initial soil ecosystem after retreat of an alpine glacier – Thomas Rime, ISME

Jaminaea pallidilutea sp. nov. (Microstromatales), a basidiomycetous yeast isolated from plant material of mangrove forests in Iran – Shaghayegh Nasr, International Journal of Systematic and Evolutionary Microbiology

Klebsiella sp. confers enhanced tolerance to salinity and plant growth promotion in oat seedlings (Avena sativa) – Swapnil Sapre, Microbiological Research

Bacterial traits and quality contribute to the diet choice and survival of bacterial-feeding nematodes – Ting Liu, Soil Biology and Biochemistry

A novel Burkholderia ambifaria strain able to degrade the mycotoxin fusaric acid and to inhibit Fusarium spp. growth – Ester Simonetti, Microbiological Research

Impact of herbicide application on Beneficial soil microbial community, Nodulation and Yield parameters of chickpea (Cicer arietinum L.) – Raghavendra, K. S, Bulletin of Environment, Pharmacology and Life Sciences

Isolation And Characterization of Phosphate Solubilizing Microorganisms From Maize Rhizosperic Soils – S. Vinod Babu, Bulletin of Environment, Pharmacology and Life Sciences

Aerobic deterioration of corn stalk silage and its effect on methane production and microbial community dynamics in anaerobic digestion – Huan Zhang, Bioresource Technology

Plant Microbiome: Composition and Functions in Plant Compartments – Maike Rossmann, The Brazilian Microbiome

Changing soil legacies to direct restoration of plant communities – E Pernilla Brinkman, AoB Plants

Water and extremophile microbiome

Change in Emiliania huxleyi Virus Assemblage Diversity but Not in Host Genetic Composition during an Ocean Acidification Mesocosm Experiment – Andrea Highfield, Viruses

Shifts in diversity and function of lake bacterial communities upon glacier retreat – Hannes Peter, ISME

Expression and characterization of a new heat-stable endo-type alginate lyase from deep-sea bacterium Flammeovirga sp. NJ-04 – Benwei Zhu, Extremophiles

Wastewater treatment plant effluent introduces recoverable shifts in microbial community composition in receiving streams – Jacob R. Price, Science of The Total Environment

Insight into the microbial community and its succession of a coupling anaerobic-aerobic biofilm on semi-suspended bio-carriers – Bing Tang, Bioresource Technology

Acclimation to extremely high ammonia levels in continuous biomethanation process and the associated microbial community dynamics – Hailin Tian, Bioresource Technology

Effect of hydraulic retention time on microbial community in biochemical passive reactors during treatment of acid mine drainage – Yaneth Vasquez, Bioresource Technology

Microbial megacities fueled by methane oxidation in a mineral spring cave – Clemens Karwautz, ISME

Built environment

Microbes and associated soluble and volatile chemicals on periodically wet household surfaces – Rachel I. Adams, Microbiome

Food microbiology

Traditional Norwegian Kveik Yeasts: Underexplored Domesticated Saccharomyces cerevisiae Yeasts – Richard Preiss, bioRxiv

Probiotics / prebiotics

Prebiotic Oligosaccharides: Special Focus on Fructooligosaccharides, Its Biosynthesis and Bioactivity – Sudhir P. Singh, Applied Biochemistry and Biotechnology

Single-strain vs multi-strain probiotic supplementation strategy against rheumatoid arthritis – Giancarlo Ceccarelli, Arthritis and Rheumatology

The Genomic Basis of Lactobacilli as Health-Promoting Organisms –  Elisa Salvetti, Microbiology Spectrum

Phages and viruses

Phage mobility is a core determinant of phage-bacteria coexistence in biofilms – Matthew Simmons, bioRxiv

Bioinformatics

Bioinformatics for Microbiome Research: Concepts, Strategies, and Advances – Leandro Nascimento Lemos, The Brazilian Microbiome

Techniques

A universal, genome-wide guide finder for CRISPR/Cas9 targeting in microbial genomes – Michelle Spoto, bioRxiv

Direct PCR offers a fast and reliable alternative to conventional DNA isolation methods for animal gut microbiomes – Elin Videvall, bioRxiv

Microbes in the news

Artwork brings ‘echoes of DNA’ to UB’s new medical school building – ELLEN GOLDBAUM, UBNow

JooMo launches new body wash with skin bacteria tech – Lucy Whitehouse, Cosmetics Design Europe

September 27, 2017

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Human oral microbiome

Complex Intratissue Microbiota Forms Biofilms in Periodontal Lesions – Baek K – Journal of Dental Research

Human vaginal microbiome

Lactobacillus iners-dominated vaginal microbiota is associated with increased susceptibility to Chlamydia trachomatis infection in Dutch women: a case–control study – Robin van Houdt – Sexually Transmitted Infections

Human gut microbiome

[Review] Modulation of Type 1 Diabetes Risk by the Intestinal Microbiome – Knip M – Current Diabetes Reports

[Review] The Relationship Between the Human Genome and Microbiome Comes into View – Julia K. Goodrich – Annual Review of Genetics

Animal microbiome

[pre-print] The virome of Drosophila suzukii, an invasive pest of soft fruit – Nathan C. Medd – bioRxiv

Characterisation of North American Brucella isolates from marine mammals – Adrian M. Whatmore – PLOS ONE

Denitrification potential of the eastern oyster microbiome using a 16S rRNA gene based metabolic inference approach – Ann Arfken – PLOS ONE

Effects of Eimeria tenella infection on chicken caecal microbiome diversity, exploring variation associated with severity of pathology – Sarah E. Macdonald – PLOS ONE

Microbial characterization of bee pollen from the Vesuvius area collected by using three different traps – Gianluigi Mauriello – PLOS ONE

Plant, root, and soil microbiome

Multiscale Investigation on Biofilm Distribution and its Impact on Macroscopic Biogeochemical Reaction Rates – Zhifeng Yan – Water Resources Research

Comparative metagenomics approaches to characterize the soil fungal communities of western coastal region, Saudi Arabia – Tarek A. A. Moussa – PLOS ONE

Bacterial and diazotrophic diversities of endophytes in Dendrobium catenatum determined through barcoded pyrosequencing – Ou Li – PLOS ONE

A secreted antibacterial neuropeptide shapes the microbiome of Hydra – René Augustin – Nature Communications

Probiotics / prebiotics

Methanobrevibacter attenuation via probiotic intervention reduces flatulence in adult human: A non-randomised paired-design clinical trial of efficacy – Minseok Seo – PLOS ONE

Bioinformatics

Predicting metabolic adaptation from networks of mutational paths – Christos Josephides & Peter S. Swain – Nature Communications

Microbes in the news 

Florida Seawater Bacteria Death Toll Rises – Patch

Researchers Find New Microbial Communities in Human Body

Microbes on the market

Paris-based Eligo Bioscience secures $20 million to bring Precision Medicine to the Microbiome – EU-Startups

Science, publishing, and career

New open-access journal Metabarcoding & Metagenomics joins the lines of publisher Pensoft – EurekAlert!

Ed’s non-microbiology picks

Infants make more attempts to achieve a goal when they see adults persist – Julia A. Leonard – Science

University of Tokyo pair invent loop-based quantum computing technique

Cancer immunotherapy with recombinant poliovirus induces IFN-dominant activation of dendritic cells and tumor antigen–specific CTLs – Michael C. Brown – Science Translational Medicine

Stereodivergent synthesis with a programmable molecular machine – Salma Kassem, – Nature

Trispecific broadly neutralizing HIV antibodies mediate potent SHIV protection in macaques – Ling Xu – Science

September 26, 2017

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Today’s digest is a delight for dog lovers – an interesting look at the nasal microbiome of dogs and two interesting studies on freshwater phages. Lastly, researchers in South Korea establish a human stool bank.

Human Gut Microbiome

REVIEW: A review of the relationship between the gut microbiota and amino acid metabolism

Lin R.Amino Acids

Advanced glycation end products dietary restriction effects on bacterial gut microbiota in peritoneal dialysis patients; a randomized open label controlled trial

Yacoub R. PloS one

Oral Microbiome

Exploring the salivary microbiome of children stratified by the oral hygiene index

Mashima I. PLoS ONE

Animal experiments and microbiome

Ground Juniperus pinchotii and urea in supplements fed to Rambouillet ewe lambs Part 2: Ewe lamb rumen microbial communities

Ishaq SL. Journal of Animal Science

Characterization of the nasal and oral microbiota of detection dogs

Isaiah A. PLoS one

Marine and Inland Water microbiome 

Biodiversity and species competition regulate the resilience of microbial biofilm community

Feng K. Molecular Ecology

Plant and soil microbiome

The Fructan Syndrome: Evolutionary Aspects and Common Themes Among Plants and Microbes

Versluys M. Plant, Cell & Environment

Agricultural land use determines functional genetic diversity of soil microbial communities

Manoharan L. Soil Biology and Biochemistry

Synergetic suppression of soybean cyst nematodes by chitosan and Hirsutella minnesotensis via the assembly of the soybean rhizosphere microbial communities

Mwaheb MAMA .Biological Control

Patterns and mechanisms of responses by soil microbial communities to nitrogen addition

Zhou Z. Soil Biology and Biochemistry

Links between plant and fungal diversity in habitat fragments of coastal shrubland.

Maltz MR. PloS one

The response of soil bacterial communities to mining subsidence in the west China aeolian sand area

Shi P. Applied Soil Ecology

Comparative metagenomics approaches to characterize the soil fungal communities of western coastal region, Saudi Arabia

Moussa TAA. PLoS one

Disentangling environmental and host sources of fungal endophyte communities in an experimental beachgrass study

David AS. Molecular Ecology

Virome

Metaproteomics of marine viral concentrates reveals key viral populations and abundant periplasmic proteins in the oligotrophic deep chlorophyll maximum of the deep chlorophyll maximum of the South China Sea

Xie ZX. Environmental Microbiology

Genome characteristics and environmental distribution of the first phage that infects the LD28 clade, a freshwater methylotrophic bacterial group

Moon K. Environmental Microbiology

Protocol

Assessment of molecular detection of anaerobic ammonium-oxidizing (anammox) bacteria in different environmental samples using PCR primers based on 16S rRNA …

Han P. Applied Microbiology and Biotechnology

Use of RNALater® Preservation for Virome Sequencing in Outbreak settings

Kohl C.Frontiers in Microbiology

DESMAN: a new tool for de novo extraction of strains from metagenomes

Quince C. Genome Biology

Microbiome News

Korea’s first stool bank gets down to business

-Korean Biomedical Review

September 25, 2017

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General microbiome

Comprehensive analysis of central carbon metabolism reveals multiple connections between nutrients, biosynthetic capacity, and cell morphology in Escherichia coli – CS Westfall – bioRxiv

 

 

Human oral microbiome

Periodontal Pathogen Colonization in Young Children by PCR Quantification – A Longitudinal Survey. – K Takahashi – The Journal of Clinical Pediatric Dentistry

 

 

Human nearly-sterile sites 

The Gut Microbial Metabolite Trimethylamine-N-Oxide Is Present in Human Cerebrospinal Fluid. – D Del Rio – Nutrients

 

Human gut microbiome

Obesity increases the risk of small intestinal bacterial overgrowth (SIBO). – BC Roland – Neurogastroenterology & Motility

Consumption of Two Healthy Dietary Patterns Restored Microbiota Dysbiosis in Obese Patients With Metabolic Dysfunction. –  C Haro – Molecular nutrition & Food Research

The Gut Microbiota and Pediatric Multiple Sclerosis: Recent Findings. – H Tremlett – Neurotherapeutics

Review: Role of the intestinal microbiota in the immunomodulation of influenza virus infection. – CJ Chen – Microbes and Infection

Effect of vitamin A supplementation on gut microbiota in children with autism spectrum disorders – a pilot study. – J Liu – BMC Microbiology

Modulation of the gut microbiota: a focus on treatments for irritable bowel syndrome. – LA Harris – Postgraduate Medicine

Gut Microbiome-based Therapeutics in Liver Cirrhosis: Basic Consideration for the Next Step. – H Fukui – Journal of Clinical and Translational Hepatology

 

Animal experiments 

Effects of dietary threonine supplementation on intestinal barrier function and gut microbiota of laying hens. – XY Dong – Poultry Science

Lack of NLRP3-inflammasome leads to gut-liver axis derangement, gut dysbiosis and a worsened phenotype in a mouse model of NAFLD. – P Irene – Scientific Reports

RNA-Seq Profiling of Intestinal Expression of Xenobiotic Processing Genes in Germ-Free Mice. – ZD Fu – Drug Metabolism and Disposition

Differential effects of rice bran cultivars to limit Salmonella Typhimurium in chicken cecal in vitro incubations and impact on the cecal microbiome and metabolome. – PM Rubinelli – PLoS One

Houttuynia cordata Facilitates Metformin on Ameliorating Insulin Resistance Associated with Gut Microbiota Alteration in OLETF Rats. – JH Wang – Genes (Basel)

Lack of Effect of Murine Astrovirus Infection on Dextran Sulfate-induced Colitis in NLRP3-deficient Mice. – SR Compton – Comparative Medicine

 

Animal microbiome 

A distinctive and host-restricted gut microbiota in populations of a cactophilic Drosophila species. – VG Martinson – Applied and Environmental Microbiology

Gastrointestinal microbial population of turkey (Meleagris gallopavo) affected by hemorrhagic enteritis virus. – S D’Andreano – Poultry Science

 

Plant, root, and soil microbiome

Colonization of Paracoccus sp. QCT6 and Enhancement of Metribuzin Degradation in Maize Rhizosphere Soil. – X Huang – Current Microbiology

Verrucosispora rhizosphaerae sp. nov., isolated from mangrove rhizosphere soil. – QY Xie – Antonie van Leeuwenhoek

Oomycete Communities Associated with Reed Die-Back Syndrome. – M Cerri – Frontiers in Plant Science

 

Water and extremophile microbiome 

Depth distribution and assembly of sulfate-reducing microbial communities in marine sediments of Aarhus Bay. – LM Jochum – Applied and Environmental Microbiology

Bottled aqua incognita: microbiota assembly and dissolved organic matter diversity in natural mineral waters. – CC Lesaulnier – Microbiome

 

Built environment 

Metagenomic characterization of ambulances across the USA. – NB O’ Hara – Microbiome

 

Food microbiology

Comparative analysis of the microbial communities in raw milk produced in different regions of Korea. – IS Kim – Asian-Australasian Journal of Animal Sciences

 

 

Techniques

DNA microarray assay and real-time PCR as useful tools for studying the respiratory tract Mycoplasma populations in young dairy calves. – M Bottinelli – Journal of Medical Microbiology

 

Microbes in the news

London Underground covered in vomit and diarrhoea-inducing bacteria found in human POO – Daily Star

BioArt and Bacteria Exhibition is Coming to Oxford – Labiotech.eu

Drug-resistant bacteria emerge from drug companies’ untreated effluents – The Hindu

Vivid green bacteria bloom in the river running through Toledo – Michigan Radio

Kingwood woman dies from flesh-eating bacteria after cutting elbow in flooded home, officials say  – Click2Houston

Microbiome-Derived Immune Modulators (Pediatric) – Puretech Health

September 22, 2017

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Human Microbiome

Microbiome profile of the amniotic fluid as a predictive biomarker of perinatal outcome – Daichi Urushiyama – Scientific Reports

Role of gut microbiota on cardio-metabolic parameters and immunity in coronary artery disease patients with and without type-2 diabetes mellitus – Lidia Sanchez-Alcoholado – Frontiers in Microbiology

Perspective: Linking the gut microbial ecosystem with the environment: does gut health depend on where we live? – Nishat Tasnim – Frontiers in Microbiology

Effect of caloric restriction on gut permeability, inflammation markers, and fecal microbiota in obese women – Beate Ott – Scientific Reports

Perspective: The immunology of the allergy epidemic and the hygiene hypothesis – Bart N Lambrecht – Nature Immunology

Pearls: The microbiome and the hallmarks of cancer – Laura E. Fulbright – PLoS Pathogens

Exploring the salivary microbiome of children stratified by the oral hygiene index – Izumi Mashima – PLoS ONE

 

Built Site Microbiome

Metagenomic characterization of ambulances across the USA – Niamh B. O’Hara – Microbiome (BMC)

 

Food Microbiome

Review: A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies – Yu Cao – Frontiers in Microbiology

Bottled aqua incognita: microbiota assembly and dissolved organic matter diversity in natural mineral waters – Celine C. Lesaulnier – Microbiome (BMC)

 

Pathogen Research

An engineered bispecific DNA-encoded IgG antibody protects against Pseudomonas aeruginosa in a pneumonia challenge model – Ami Patel – Nature Communications

Illusions regarding Helicobacter pylori clinical trials and treatment guidelines – David Y Graham – Gut (BMJ)

 

Beneficial Microbes

Akkermansia muciniphila May Determine the Ameliorating or Aggravating Effects of Chondroitin Sulfate on Osteoarthritis – Qing-Ping Zeng – Frontiers in Microbiology

Minireview: Next-Generation Beneficial Microbes: The Case of Akkermansia muciniphila – Patrice D. Cani – Frontiers in Microbiology

The PGPR Stenotrophomonas maltophilia SBP-9 augments resistance against biotic and abiotic stress in wheat plants – Prabhat N. Jha – Frontiers in Microbiology

 

Beneficial Molecules

pH-dependant antifungal activity of valproic acid against the human fungal pathogen Candida albicans – Julien Chaillot – Frontiers in Microbiology

Dietary teasaponin ameliorates alteration of gut microbiota and cognitive decline in diet-induced obese mice – Sen Wang – Scientific Reports

Mulberry leaf alleviates streptozotocin-induced diabetic rats by attenuating NEFA signaling and modulating intestinal microflora – Yao Sheng – Scientific Reports

 

Microbial Evolution

New Insights into the Diversity of the Genus Faecalibacterium – Leandro Benevides – Frontiers in Microbiology

 

Environmental Microbiology

Insights into microalga and bacteria interactions of selected phycosphere biofilms using metagenomic, transcriptomic and proteomic approaches – Ines Krohn-Molt – Frontiers in Microbiology

 

Bioinformatics, Genomics and Methodologies

Genomic GC-content affects the accuracy of 16S rRNA gene sequencing based microbial profiling due to PCR bias – Martin I. Bahl – Frontiers in Microbiology

Preprint: Optimizing scoring function of dynamic programming of pairwise profile alignment using derivative free neural network – Kazunori D. Yamada – BioRxiv

Improving contig binning of metagenomic data using dS2 oligonucleotide frequency dissimilarity – Ying Wang – BMC Bioinformatics

A Laboratory Methodology for Dual RNA-Sequencing of Bacteria and their Host Cells In Vitro – James W. Marsh – Frontiers in Microbiology

 

Other

Review: A review of the relationship between the gut microbiota and amino acid metabolism – Rui Lin – Amino Acids (Springer)