Category Archives: Resistome

December 14, 2017

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Two interesting articles on pregnancy and early life: the placentobiome, and the cervical microbiome, as well as articles on the circadian rhythms of the saliva microbiome, the microbiome of exposed rock,  and new techniques to sequence single bacterial and archaeal cells.

Events and jobs

Postdoctoral Research Scientist – Genomics and Metagenomics – Quadram Institute Bioscience – Norwich UK

Assistant Professor, Cell Biology, Molecular Biology or Microbiology – Albany College of Pharmacy and Health Sciences

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Pregnancy and early life

*Mother-to-newborn transmission of mycobacterial L-forms and Vδ2 T-cell response in placentobiome of BCG-vaccinated pregnant women – T. Dimova – Scientific Reports*

*Analysis of the cervical microbiome and potential biomarkers from postpartum HIV-positive women displaying cervical intraepithelial lesions – Gislaine Curty – Scientific Reports

Multi-site human microbiome

Microbiome in PTEN hamartoma tumor syndrome – Victoria Byrd – Society for Endrocrinology

Human respiratory microbiome

The Alteration of Nasopharyngeal and Oropharyngeal Microbiota in Children with MPP and Non-MPP – Zhiwei Lu – Genes

Human skin microbiome

Review: Staphylococcus aureus and Atopic Dermatitis: A Complex and Evolving Relationship – Joan A. Geoghegan – Trends in Microbiology

Human oral microbiome

*Timing of food intake impacts daily rhythms of human salivary microbiota: a randomized, crossover study – María Carmen Collado – The FASEB Journal

Human vaginal microbiome

Influence of Orally Administered Probiotic Lactobacillus Strains on Vaginal Microbiota in Women with Breast Cancer during Chemotherapy: A Randomized Placebo-Controlled Double-Blinded Pilot Study – J Marschalek – Breast Care

Human gut microbiome

A Metagenomic and in Silico Functional Prediction of Gut Microbiota Profiles May Concur in Discovering New Cystic Fibrosis Patient-Targeted Probiotics – Pamela Vernocchi – Nutrients

Entamoeba Species in South Africa: Correlations With the Host Microbiome, Parasite Burdens, and First Description of Entamoeba bangladeshi Outside of Asia – Renay Ngobeni – Journal of Infectious Diseases

Mutual interaction of phenolic compounds and microbiota: Metabolism of complex phenolic apigenin C- and kaempferol O-derivatives by human fecal samples – Maren Vollmer – Journal of Agricultural and Food Chemistry

Estimation of the bioaccessibility and bioavailability of Fe, Mn, Cu, and Zn in Chinese vegetables using the in vitro digestion/Caco-2 cell model: the influence of gut microbiota – Xiaolin Cai – Food and Function

Food-Associated Lactobacillus plantarum and Yeasts Inhibit the Genotoxic Effect of 4-Nitroquinoline-1-Oxide – Roberta Prete – Frontiers in Microbiology

Butyrate suppresses motility of colorectal cancer cells via deactivating Akt/ERK signaling in histone deacetylase dependent manner – Qingran Li – Journal of Pharmacological Sciences

Review: Exercise has the guts: How physical activity may positively modulate gut microbiota in chronic and immune-based diseases – Roberto Codella – Digestive and Liver Disease

Review: Alzheimer’s disease and gut microbiota modifications: The long way between preclinical studies and clinical evidence – Cesare Mancuso – Pharmacological Research

Adjuvant Probiotics and the Intestinal Microbiome: Enhancing Vaccines and Immunotherapy Outcomes – Luis Vitetta – Vaccines

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Animal experiments

Fecal short-chain fatty acids at different time points after ceftriaxone administration in rats – Yu. V. Holota – The Ukrainian Biochemical Journal

1H NMR-Based Metabonomic Study of Functional Dyspepsia in Stressed Rats Treated with Chinese Medicine Weikangning – Yu Guo – Evidence-Based Complementary and Alternative Medicine

A Novel Prebiotic Blend Product Prevents Irritable Bowel Syndrome in Mice by Improving Gut Microbiota and Modulating Immune Response – Qian Chen – Nutrients

Animal microbiome

Diversification of Type VI Secretion System Toxins Reveals Ancient Antagonism among Bee Gut Microbes – Margaret I. Steele – mBio

Differential Microbial Diversity in Drosophila melanogaster: Are Fruit Flies Potential Vectors of Opportunistic Pathogens? – Luis A. Ramírez-Camejo – International Journal of Microbiology

Archaeal community structure and underlying ecological processes in swine manure slurry – Priyanka Kumari – bioRxiv

Genetic adaptation of microbial populations present in high-intensity catfish production systems with therapeutic oxytetracycline treatment – Qifan Zeng – Scientific Reports

Altered Gut Microbiota Profiles in Sows and Neonatal Piglets Associated with Porcine Epidemic Diarrhea Virus Infection – Deping Song – Scientific Reports

Plant, root, and soil microbiome

*Tales from the tomb: the microbial ecology of exposed rock surfaces
Authors – Tess E Brewer – Environmental Microbiology

Long-term nitrogen addition affects the phylogenetic turnover of soil microbial community responding to moisture pulse – Chi Liu – Scientific Reports

Impact of Glyphosate on the Rhizosphere Microbial Communities of An EPSPS-Transgenic Soybean Line ZUTS31 by Metagenome Sequencing – Gui-Hua Lu – Current Genomics

Microbial communities in natural rubber coagula during maturation: impacts on technological properties of dry natural rubber – Mélanie Salomez – Journal of Applied Microbiology

Manure and mineral fertilization change enzyme activity and bacterial community in millet rhizosphere soils – Lixia Xu – World Journal of Microbiology and Biotechnology

Resistome

Drivers of dissolved organic carbon export in a subarctic catchment: Importance of microbial decomposition, sorption-desorption, peatland and lateral flow – Itziar Lekunberri – Environmental Pollution

Food microbiology

Conference Proceedings: The microbial community and free amino acid composition in salted and fermented squid products – Daisuke Ouchi- The JSFS 85th Anniversary-Commemorative International Symposium

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Waste and Pollution

Anaerobic Baffled Reactor in Treatment of Natural Rubber Processing Wastewater: Reactor Performance and Analysis of Microbial Community – Phuong Thao Tran – Journal of Water and Environment Technology

Microbial Community Structure and Enumeration of Bacillus species in Activated Sludge – Masashi Hatamoto – Journal of Water and Environment Technology

Techniques

Sampling, Extraction, and High-Throughput Sequencing Methods for Environmental Microbial and Viral Communities – Pedro J. Torres – In: Next Generation Sequencing. Methods in Molecular Biology, vol 1712. Humana Press

*Sequencing of Genomes from Environmental Single Cells – Robert Bowers – In: Methods in Molecular Biology, vol 1712. Humana Press

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Microbes in the news

Why Probiotic Skin Care Is (Actually) Worth It, According to Experts – Lauren Valenti – – Vogue

Celebrating a decade of interdisciplinary microbiology – Raleigh McElvery – MIT News

Plant pathologists discover unusual evolutionary transition in common bacteria – Chris Branam – Phys.org

Efforts of bacteria to defend against predators is so great that few resources left for offspring – Science Daily

Specially designed protein fights several species of bacteria – EurekaAlert

Reprogramming bacteria instead of killing them could be the answer to antibiotic resistance – Yu-Hsuan Tsai – Phys.org

Bacteria and Art

Shout Out: Hunter Cole, biology lecturer and artist – Genevieve Bookwalter- Chicago Tribune

Kathy High with Sadie R. Starnes, Gut Love: You are my future – Esther Klein – The Brooklyn Rail

 

 

December 13, 2017

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Many interesting articles today: Probiotics can inhibit human colonic smooth muscle contraction in vitro in a dose dependent manner, arsenic exposure early in life alters the gut microbiome and can increase E.coli resistance genes, oral administration of two probiotics in mice has specific effects on gene expression in the small intestine, a detailed investigation of the impacts of T. congolense infection in the tsetse fly, and multiple articles on plant and rhizosphere microbiome volatiles.

Events and jobs

Visiting Professor (Part Time) Microbiology  – Chamberlain College of Nursing, Jacksonville, FL Campus

Seminar: The “Bedside to Bench and Back Again” Paradigm in Gut Microbiome Research – Gary D. Wu – University of Chicago

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General microbiome

Review: Hygiene Hypothesis in Asthma Development: Is Hygiene to Blame? – Erik van Tilburg Bernardes – Archives of Medical Research

Human respiratory microbiome

Composition and variation of respiratory microbiota in healthy military personnel – Jun Hang – PLOS One

Human oral microbiome

Periodontitis is associated with significant hepatic fibrosis in patients with non-alcoholic fatty liver disease – William Alazawi – PLOS One

Human gut microbiome

Hypoxia and inactivity related physiological changes precede or take place in absence of significant rearrangements in bacterial community structure: The PlanHab randomized trial pilot study – Robert Šket – PLOS One

*Arsenic exposure and intestinal microbiota in children from Sirajdikhan, Bangladesh – Xiaoxi Dong – PLOS One

Editorial overview: Gastrointestinal: New frontiers in therapeutics for GI diseases and disorders — from microRNAs to novel pharmaceutics, to low FODMAP diets and microbiome – Fievos L Christofi – Current Opinion in Pharmacology

*Inhibition effect of Bifidobacterium longum, Lactobacillus acidophilus, Streptococcus thermophilus and Enterococcus faecalis and their related products on human colonic smooth muscle in vitro – Jing Gong – PLOS One

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Animal experiments

*The distinct effects of orally administered Lactobacillus rhamnosus GG and Lactococcus lactis subsp. lactis C59 on gene expression in the murine small intestine – Chise Suzuki – PLOS One

Diversity of intestinal bacterial lactase gene in antibiotics-induced diarrhea mice treated with Chinese herbs compound Qi Wei Bai Zhu San – Lu He – 3 Biotech

The Impact of Long-Term Intake of Phenolic Compounds-Rich Grape Pomace on Rat Gut Microbiota – Stéphanie Chacar – Journal of Food Science

Preprint: High-dimensional microbiome interactions shape host fitness – Alison L Gould – bioRxiv

Animal microbiome

Comparison of the intestinal mucosal microbiota in dogs siagnosed with idiopathic inflammatory bowel disease and dogs with food-responsive diarrhea before and after treatment – K. Kalenyak – FEMS Microbiology Ecology

*Molecular characterization of tsetse’s proboscis and its response to Trypanosoma congolense infection – Erick O. Awuoche – PLOS Neglected Tropical Diseases

Preprint: Who is the host of the host-associated microbiome? Colony-level dynamics overshadow individual-level characteristics in the fur microbiome of a social mammal, the Egyptian fruit-bat – oren kolodny – BioRxiv

Plant, root, and soil microbiome

Pontibacter brevis sp. nov., isolated from rhizosphere soil of Tamarix ramosissima – Ghenijan Osman – International Journal of Systemic and Evolutionary Microbiology

*Volatiles in the Rhizosphere: Bioprospecting for Sustainable Agriculture and Food Security – Shyamalina Haldar – In: Volatiles and Food Security. Springer

*Characterization of Bacterial Volatiles and Their Impact on Plant Health Under Abiotic Stress – Anukool Vaishnav – In: Volatiles and Food Security. Springer

Dissertation: Plant growth-promoting rhizobacteria (PGPR) mediate interactions between abiotic and biotic stresses in cool- and warm-season grasses – Richard Coy – Auburn University

Endophytic Microorganisms: Promising Candidate as Biofertilizer – Manish Kumar – In: Microorganisms for Green Revolution. Microorganisms for Sustainability, vol 6. Springer

*Bacterial Volatiles in Promotion of Plant Under Biotic Stress – Shekhar Jain – In: Volatiles and Food Security. Springer

*Microbial Volatiles in Defense – Monika – In: Volatiles and Food Security. Springer

*Microbial Volatiles and Plant Defense – Kalaivani K. Nadarajah – In: Volatiles and Food Security. Springer

Wonders of Microbes in Agriculture for Productivity and Sustainability – Rajababu V. Vyas – In: Microorganisms for Green Revolution. Microorganisms for Sustainability, vol 6. Springer

Water and extremophile microbiome

Review: Marine microbiology: Illuminating the importance of nitrite oxidation – Ursual Hofer – Nature Reviews Microbiology

Microbial Ecology

Robustness of a model microbial community emerges from population structure among single cells of a clonal population – Anne W. Thompson – Environmental Microbiology

Resource availability modulates biodiversity-invasion relationships by altering competitive interactions – Tianjie Yang – Environmental Microbiology

Resistome

Action mechanism of naphthofuranquinones against fluconazole-resistant Candida tropicalis strains evidenced by proteomic analysis: The role of increased endogenous ROS – João Batista de Andrade Neto – Microbial Pathogenesis

Evolution of virulence in Enterococcus faecium, a hospital-adapted opportunistic pathogen – Wei Gao – Current Opinion in Microbiology

Surveillance of antibiotic resistance among common Clostridium difficile ribotypes in Hong Kong – Viola C. Y. Chow – Scientific Reports

Food microbiology

Preprint: Copy number variation in fungi and its implications for wine yeast genetic diversity and adaptation – Jacob Steenwyk – bioRxiv

More Microbes

Draft genome sequence of Actinotignum schaalii DSM 15541T: Genetic insights into the lifestyle, cell fitness and virulence – Atteyet F. Yassin – PLOS one

PsrA controls the synthesis of the Pseudomonas aeruginosa quinolone signal via repression of the FadE homolog, PA0506 – Greg Wells – PLOS one

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Phages and viruses

Dissertation: Uncovering the Biological Features of Unknown Viruses Using Shotgun Metagenomic Sequence Data – Daniel Joseph Nasko – University of Delaware

Bioinformatics

MPA Portable: a Stand-alone Software Package for Analyzing Metaproteome Samples on the Go – Thilo Muth – Analytical Chemistry

Dissertation: Revealing Microbial Responses to Environmental Dynamics: Developing Methods for Analysis and Visualization of Complex Sequence Datasets – Matthew Kellom – Arizona State University

Preprint: Rarefaction, alpha diversity, and statistics – Amy Willis – bioRxiv

Biotechnology

Review: Electron transport phenomena of electroactive bacteria in microbial fuel cells: a review of Proteus hauseri – I-Son Ng – Bioresources and Bioprocessing

Dissertation: From Biofuels to Natural Products: Microbial Metabolic Engineering for Chemical Production – Nicole E Nozzi -University of California, Davis

Waste and Pollution

Assessment of a novel anti-biofouling microorganism (Bacillus sp. T5) for control of membrane biofouling and its effect on bacterial community structure in membrane bioreactors – Bahar Yavuztürk Gül – Water Science and Technology

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Microbes in the news

New Data: 2 Million Puerto Ricans Risk Water Contamination – Mekela Panditharatne – NRDC

Bacteria development marks new era in cellular design – Phys.org

Feeding Overcrowded Bacteria Increases Antibiotic Susceptibility – Genetic Engineering and Biotechnology News

A Bacterial Role In High Blood Pressure – The Microbiome Speaks – Chuck Dinerstein – American Council on Science and Health

New Microbiome Analysis Tool Resolves Individual Species, Strains – Rachel Lutz – MD Magazine

How honey bee gut bacteria help to digest their pollen-rich diet – EurekaAlert

Microbes on the market

Bio-Rad Inks Supply and Distribution Agreement for Microbiome MDx – genomeweb

Dannon, as a part of DanoneWave Public Benefit Corporation, Announces $50K in Grants for Graduate Studies – Markets Insider

 

November 30, 2017

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A wide variety of interesting articles: Antibiotics administrated during labour impact  infant gut microbiome development, altered gut microbiome is related to liver function in individuals with Hep B, specific pathogens can alter social signaling in drosophila, a comphrensive study of the impact of diet on the lemur gut microbiome, a survey of antibiotic resistence genes in the drinking water across multiple continents, the impact of the hospital microbiome on the gut microbiome of preterm infants, the first evidence of a gut archeae impact on the host immune system, and two popular news articles refuting yesterday’s report of possible alien bacteria on the international space station.

Events and jobs

Web Developer, Microbiome Core – Harvard T.H. Chan School of Public Health

Account Manager – Microbiology –  South East England

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General microbiome

  • Health Economics and Regulations 

Faecal microbiota transplantation: a regulatory hurdle? – Frederick Verbeke – BMC Gastroenterology

Cost-effectiveness analysis of fecal microbiota transplantation for inflammatory bowel disease – Ting Zhang – Oncotarget

Pregnancy and early life

*Intrapartum antibiotics for GBS prophylaxis alter colonization patterns in the early infant gut microbiome of low risk infants – Jennifer C. Stearns – Scientific Reports

Human skin microbiome

Skin Immune Landscape: Inside and Outside the Organism – Florence Abdallah – Mediators of Inflammation

Human gut microbiome
*Gut Microbial Dysbiosis Is Associated with Altered Hepatic Functions and Serum Metabolites in Chronic Hepatitis B Patients – Jing Wang – Frontiers in Microbiology

Faecal bacterial microbiota in patients with cirrhosis and the effect of lactulose administration – Aditya Narayan Sarangi – BMC Gastroenterology

Delivered Fecal Microbiota Transplantation on Recurrent Clostridium difficile Infection – Dina Kao – JAMA

Capsules for Fecal Microbiota Transplantation in Recurrent Clostridium difficile Infection – Krishna Rao – JAMA

Review: Antibiotic therapy in neonates and impact on gut microbiota and antibiotic resistance development: a systematic review – Jon Widding Fjalstad – Journal of Antimicrobial Chemotherapy

Long-term proton pump inhibitor therapy leads to small bowel bacterial overgrowth as determined by breath hydrogen and methane excretion – Agnieszka Sieczkowska – Journal of Breath Research

Review: Impact of gut microbiota on drug metabolism: an update for safe and effective use of drugs – Keumhan Noh – Archives of Pharmacal Research

Evaluating the effect of Clostridium difficile conditioned medium on fecal microbiota community structure – Sabina Horvat – Scientific Reports

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Animal experiments

Preprint: The Vibrio cholerae Type VI Secretion System Can Modulate Host Intestinal Mechanics to Displace Commensal Gut Bacteria – Savannah L Logan – bioRxiv

Genes and Gut Bacteria Involved in Luminal Butyrate Reduction Caused by Diet and Loperamide – Nakwon Hwang – Genes

Simultaneous delivery of antibiotics neomycin and ampicillin in drinking water inhibits fermentation of resistant starch in rats – Diana G. Carvajal-Aldaz – Molecular Nutrition and Food Research

Animal microbiome

*Pathogenic bacteria enhance dispersal through alteration of Drosophila social communication – Ian W. Keesey – Nature Communications

*Feeding strategy shapes gut metagenomic enrichment and functional specialization in captive lemurs – E. A. McKenney – Gut Microbes

Impact of Dietary Galacto-Oligosaccharide (GOS) on Chicken’s Gut Microbiota, Mucosal Gene Expression, and Salmonella Colonization – Rebecca-Ayme Hughes – Frontiers in Veterinary Science

Dietary energy drives the dynamic response of bovine rumen viral communities – Christopher L. Anderson – Microbiome

Effect of microalgae on intestinal inflammation triggered by soybean meal and bacterial infection in zebrafish – Karina Bravo-Tello – PLOS ONE

In vivo effects of Allium cepa L. on the selected gut microflora and intestinal histomorphology in broiler – Sajidur Rahman – Acta Histochemica

Enteric Pathogens and Their Toxin-Induced Disruption of the Intestinal Barrier through Alteration of Tight Junctions in Chickens – Wageha A. Awad – Toxins

Plant, root, and soil microbiome

The Ecological Role of Volatile and Soluble Secondary Metabolites Produced by Soil Bacteria – Olaf Tyc – Trends in Microbiology

Impact of peat mining, and restoration on methane turnover potentials and methane-cycling microorganisms in a northern bog – Max Reumer – Applied and Environmental Microbiology

Burkholderia humptydooensis sp. nov., a New Species Related to Burkholderia thailandensis and the Fifth Member of the Burkholderia pseudomallei Complex – Apichai Tuanyok – Applied and Environment Microbiology

Water and extremophile microbiome
Functional Characterization of Probiotic Potential of Novel Pigmented Bacterial Strains for Aquaculture Applications – Sekar Jinendiran – Probiotics and Antimicrobial Proteins

Resistome

Preprint: Increased usage of antiseptics is associated with reduced susceptibility in clinical isolates of S. aureus – Katherine Hardy – bioRxiv

*Catalogue of antibiotic resistome and host-tracking in drinking water deciphered by a large scale survey – Liping Ma – Microbiome

Review: Assessing the Risk of Antibiotic Resistance Transmission from the Environment to Humans: Non-Direct Proportionality between Abundance and Risk – Célia M. Manaia – Trends in Microbiology

Built environment

*Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome – Brandon Brooks – Nature Communications

Predominance and Metabolic Potential of Halanaerobium spp. in Produced Water from Hydraulically Fractured Marcellus Shale Wells – Daniel Lipus – Applied and Environment Microbiology

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Microbial Ecology

Effect of Antimicrobial and Physical Treatments on Growth of Multispecies Staphylococcal Biofilms – Elizabeth J. Stewart – Applied and Environment Microbiology

More Microbes

  • Archaea

*Associated Archaeon Methanosphaera stadtmanae Is Recognized through Its RNA and Induces – Tim Vierbuchen – Frontiers in Immunology

  • Synthetic Microbes

Analysis and Implementation of a Multicellular Feedback Control Strategy in a Synthetic Bacterial Consortium – Gianfranco Fiore – ACS Synthetic Biology

Techniques

Diazotroph community characterization via a high-throughput nifH amplicon sequencing and analysis pipeline – John Christian Gaby – Applied and Environmental Microbiology

Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes – Elin Videvall – mSystems

Generation of bacteriophage-insensitive mutants of Streptococcus thermophilus using an antisense RNA CRISPR-Cas silencing approach – Brian McDonnell – Applied and Environmental Microbiology

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Microbes in the news

*Bacteria on Space Station Likely From Germy Humans, Not Aliens – Elaina Zachos – National Geographic

*We are basically positive that the Russians did not find alien bacteria in space – Mary Beth Griggs – Popular Science

Custom Bacteria Make New Molecules On Demand – Sam Lemonick – Forbes

Toilet art sheds light on gut health – Newshub

September 13,2017

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Our midweek digest is a treat for wine drinkers- two studies looking at vineyard microbiomes and news of how Nestlé is moving into microbiome research. Lastly, read about an exciting workflow that makes it easier to map the resistome.

General Microbiome

Microbial communities in placentas from term normal pregnancy exhibit spatially variable profiles.

Parnell LA .Scientific Reports

Human gut microbiome

Host-microbe interaction in the gastrointestinal tract.

Parker A.Environmental Microbiology Report

Gut microbiota composition is associated with polypharmacy in elderly hospitalized patients.

Ticinesi A.Scientific Reports

Microbes in Infant Gut Development: Placing Abundance Within Environmental, Clinical and Growth Parameters.

Obermajer T.Scientific Reports

Animal experiments and microbiome

Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models.

Cekanaviciute E, PNAS

The microbiota influences cell death and microglial colonization in the perinatal mouse brain.

Castillo-Ruiz A. Brain, Behaviour, and Immunity

Microbial colonization is required for normal neurobehavioral development in zebrafish.

Phelps D,.Scientific Reports

Biotechnology 

Ozone-cathode microbial desalination cell; An innovative option to bioelectricity generation and water desalination.

Gholizadeh A. Chemosphere.

Plant and soil microbiome

Grape microbiome as a reliable and persistent signature of field origin and environmental conditions in Cannonau wine production.

Mezzasalma V. PLoS One.

Is microbial terroir related to geographic distance between vineyards?

Miura T. Environmental Microbiology Reports

Bacteria utilising plant-derived carbon in the rhizosphere of Triticum aestivum change in different depths of an arable soil.

Uksa M. Environmental Microbiology Reports

Mining the Volatilomes of Plant-Associated Microbiota for New Biocontrol Solutions.

Bailly A. Frontiers in Microbiology

More than 2500 years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis.

Michas A. Microbiome

Lung Microbiome

Functional characterization of the Mycobacterium abscessus genome coupled with condition specific transcriptomics reveals conserved molecular strategies for host adaptation and persistence.

Miranda-CasoLuengo AA.BMC Genomics

Mechanistic insight into the function of the microbiome in lung diseases.

Ubags NDJ. European Respiratory Journal

Antibiotics

A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity.

Ruiz VE.Nature Communications

Resistome

The recent emergence in hospitals of multidrug-resistant community-associated sequence type 1 and spa type t127 methicillin-resistant Staphylococcus aureus investigated by whole-genome sequencing: Implications for screening.

Earls MR. PLoS One

Rapid resistome mapping using nanopore sequencing.

van der Helm E.Nucleic Acids Research  

Network of microbial and antibiotic interactions drive colonization and infection with multidrug-resistant organisms

Wang J. PNAS

News

Nestlé moves into gut microbiome tests.

News- Nature Biotechnology

Protocol

Shotgun metagenomics, from sampling to analysis.

Quince C,Nature Biotechnology

Erratum 

Erratum to: Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey Species.

Hale VL. Microbial Ecology

July 23, 2017

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General microbiome

Systems biology of lactic acid bacteria: For food and thought – Bas Teusink, Current Opinion in Systems Biology

Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta) – Susan H. Brawley, PNAS

Parasite Microbiome Project: Systematic Investigation of Microbiome Dynamics within and across Parasite-Host Interactions – Nolwenn M. Dheilly, mSystems

Human respiratory microbiome

Airway microbiota signals anabolic and catabolic remodeling in the transplanted lung – Stéphane Mouraux, Journal of Allergy and Clinical Immunology

Human skin microbiome

The Skin Microbiome of Cohabiting Couples – Ashley A. Ross, mSystems

Human oral microbiome

Metabolic Fingerprints from the Human Oral Microbiome Reveal a Vast Knowledge Gap of Secreted Small Peptidic Molecules – Anna Edlund, mSystems

Human gut microbiome

Sequencing the gut metagenome as a non-invasive diagnosis for advanced nonalcoholic steatohepatitis – Lixin Zhu, Hepatology

Molecular Characterization of the Human Stomach Microbiota in Gastric Cancer Patients – Guoqin Yu, Frontiers in Microbiology

Inulin-type fructans and whey protein both modulate appetite but only fructans alter gut microbiota in adults with overweight/obesity: a randomized controlled trial – Raylene A. Reimer, Molecular Research and Food Research

Incomplete metabolism of phytoestrogens by gut microbiota from children under the age of three – Pilar Gaya, International Journal of Food Sciences and Nutrition

Animal experiments

An In Vitro Chicken Gut Model Demonstrates Transfer of a Multidrug Resistance Plasmid from Salmonella to Commensal Escherichia coli – Roderick M. Card, mBio

Maternally-transmitted microbiota affects odor emission and preference in Drosophila larva – Jean-Pierre Farine, Scientific Reports

Burn Injury Leads to Increase in Relative Abundance of Opportunistic Pathogens in the Rat Gastrointestinal Microbiome – Guangtao Huang, Scientific Reports

Linking Sex Differences in Non-Alcoholic Fatty Liver Disease to Bile Acid Signaling, Gut Microbiota, and High Fat Diet  – John Y.L. Chiang, The American Journal of Pathology

Early-life disruption of amphibian microbiota decreases later-life resistance to parasites – Sarah A. Knutie, Nature Communication

In vitro characteristics of an Atlantic salmon (Salmo salar L.) hind gut microbial community in relation to different dietary treatments – Kamarul Zaman Zarkasia,  Research in Microbiology

Effects of coconut oil on glycemia, inflammation, and urogenital microbial parameters in female Ossabaw mini-pigs – Annie E. Newell-Fugate, PLoS ONE

Effect of acute ozone exposure on the lung metabolomes of obese and lean mice – Joel Andrew Mathews, PLoS ONE

Animal microbiome

Skin Bacterial Community Reorganization Following Metamorphosis of the Fire-Bellied Toad (Bombina orientalis) – Arnaud Bataille, Microbial Ecology

Inferring microbial interactions in thermophilic and mesophilic anaerobic digestion of hog waste – Grace Tzun-Wen Shaw, PLoS ONE

Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation – Olov Svartström, ISME

Genome Sequences of Two Shewanella spp. Isolated from the Gut of the Sea Cucumber Apostichopus japonicus (Selenka, 1867) – Hyun-Hee Hong, Genome Anouncements

Feather-Degrading Bacteria: Their Biochemical and Genetic Characteristics – Paweł Kowalczyk, Arabian Journal for Science and Engineering

Plant, root, and soil microbiome

The tree species matters: Belowground carbon input and utilization in the myco-rhizosphere – Janine Sommera, European Journal of Soil Biology

Soil bacterial community response to vegetation succession after fencing in the grassland of China – Quanchao Zeng, Science of The Total Environment

Drought Stress Results in a Compartment-Specific Restructuring of the Rice Root-Associated Microbiomes – Christian Santos-Medellín, mBio

Improved grain yield of cowpea (Vigna unguiculata) under water deficit after inoculation with Bradyrhizobium elkaniiand Rhizophagus irregularis – Rui S. Oliveira, Crop and Pasture Science

Understanding the holobiont: the interdependence of plants and their microbiome – Carmen Sánchez-Cañizares, Current Opinion in Microbiology

Pseudomonas fluorescens R68 assisted enhancement in growth and fertilizer utilization of Amaranthus tricolor (L.) – C. Jimtha John, 3Biotech

Ecological guild and enzyme activities of rhizosphere soil microbial communities associated with Bt-maize cultivation under field conditions in North West Province of South Africa – Deidré A. B. van Wyk, Journal of Basic Microbiology

A genomic perspective on stoichiometric regulation of soil carbon cycling – Wyatt H Hartman, ISME

The rhizosphere microbiome of burned holm-oak: potential role of the genus Arthrobacter in the recovery of burned soils – Antonio J. Fernández-González, Scientific Reports

Biological control of potential antagonistic bacteria isolates to restrict Magnaporthe grisea infection on rice – David P. Tokpah, African Journal of Microbiology Research

Bacteria associated to plants naturally selected in a historical PCB polluted soil show potential to sustain natural attenuation – Lorenzo Vergani, Frontiers in Microbiology

Water and extremophile microbiome

Unraveling the Microbial Interactions and Metabolic Potentials in Pre- and Post-treated Sludge from a Wastewater Treatment Plant Using Metagenomic Studies – Chandni Sidhu, Frontiers in Microbiology

Metagenomics of urban sewage identifies an extensively shared antibiotic resistome in China – Jian-Qiang Su, Microbiome

Microbial Community Structure and Function Decoupling Across a Phosphorus Gradient in Streams – Erick S. LeBrun, Microbial Ecology

Microbial communities and their predicted metabolic functions in growth laminae of a unique large conical mat from Lake Untersee, East Antarctica – Hyunmin Koo, Frontiers in Microbiology

Draft genome sequence of Exiguobacterium aurantiacumstrain PN47 isolate from saline ponds, known as “Salar del Huasco”, located in the Altiplano in the North of Chile – Erwin Strahsburger, Brazilian Journal of Microbiology

Diversity of culturable filamentous Ascomycetes in the eastern South Pacific Ocean off Chile – Jeanett Vera, World Journal of Microbiology and Biotechnology

Salinity Drives the Virioplankton Abundance but Not Production in Tropical Coastal Lagoons – Pedro C. Junger, Microbial Ecology

Characterization of a cold-adapted DNA photolyase from C. psychrerythraea 34H – Sudipto Munshi, Extremophiles

Marine archaeal dynamics and interactions with the microbial community over 5 years from surface to seafloor – Alma E Parada, ISME

Unusual metabolic diversity of hyperalkaliphilic microbial communities associated with subterranean serpentinization at The Cedars – Shino Suzuki, ISME

Comparative Omics and Trait Analyses of Marine Pseudoalteromonas Phages Advance the Phage OTU Concept – Melissa B. Duhaime, Frontier in Microbiology

Effects of Physiochemical Factors on Prokaryotic Biodiversity in Malaysian Circumneutral Hot Springs – Chia S. Chan, Frontiers in Microbiology

Climate oscillations reflected within the microbiome of Arabian Sea sediments – William D. Orsi, Scientific Reports

Microbiome of Trichodesmium Colonies from the North Pacific Subtropical Gyre – Mary R. Gradoville, Frontiers in Microbiology

Antarctic sea ice region as a source of biogenic organic nitrogen in aerosols – Manuel Dall’Osto, Scientific Reports

Built environment

A role for microbial selection in frescoes’ deterioration in Tomba degli Scudi in Tarquinia, Italy – Maria Cristina Tomassetti, Scientific Reports

Food microbiology

An Exploration into the Bacterial Community under Different Pasteurization Conditions during Substrate Preparation (Composting–Phase II) for Agaricus bisporus Cultivation – Fabricio Rocha Vieira, Microbial Ecology

Metagenome-based surveillance and diagnostic approaches to studying the microbial ecology of food production and processing environments – Conor J Doyle, Environmental Microbiology

Draft Genome Sequences of Three Lactobacillusparacasei Strains, Members of the Nonstarter Microbiota of Mature Cheddar Cheese – Ewelina Stefanovic, Genome Anouncements

Bioinformatics

Cohesion: a method for quantifying the connectivity of microbial communities – Cristina M Herren, ISME

Developing integrative systematics in the informatics and genomic era, and calling for a global Biodiversity Cyberbank – Jun Wen, Journal of Systematics and Evolution

Techniques

Rapid differentiation of bacterial communities using high resolution melting analysis – Steven Everman, Journal of Microbiological Methods

Proteomics in Inflammatory Bowel Disease: Approach Using Animal Models – Fadi H. Mourad, Digestive Diseases and Sciences

July 5, 2017

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General microbiome

Letter to the editor: Introducing the sporobiota and sporobiome – George Tetz – Gut Pathogens

Human oral microbiome

Oropharyngeal and Sputum Microbiomes Are Similar Following Exacerbation of Chronic Obstructive Pulmonary Disease – Hai-Yue Liu – Frontiers in Microbiology

Human respiratory microbiome

Review: Respiratory microbiota and lower respiratory tract disease – Miguel Lanaspa – Expert Review of Anti-infective Therapy

Human gut microbiome

Review: Feeding the microbiota: transducer of nutrient signals for the host – Fergus Shanahan – Gut

Animal microbiome

Early Postnatal Diets Affect the Bioregional Small Intestine Microbiome and Ileal Metabolome in Neonatal Pigs – Brian D Piccolo – The Journal of Nutrition

Variation between the oral and faecal microbiota in a free-living passerine bird, the great tit (Parus major) – Lucie Kropáčková – Plos One

Temperature variation, bacterial diversity, and fungal infection dynamics in the amphibian skin – Ana V. Longo – Molecular Ecology

Early-Life Diet Affects Host Microbiota and Later-Life Defenses Against Parasites in Frogs – Sarah A. Knutie – Integrative & Comparitive Biology

Animal experiments

Relative variations of gut microbiota in disordered cholesterol metabolism caused by high-cholesterol diet and host genetics – Tao Bo – Microbiology Open

Plant, root, and soil microbiome

Nutrient and Rainfall Additions Shift Phylogenetically Estimated Traits of Soil Microbial Communities – Kelly Gravuer – Frontiers in Microbiology

Long-term rock phosphate fertilization impacts the microbial communities of maize rhizosphere – Ubiana C. Silva – Frontiers in Microbiology

Global change and the soil microbiome: A human-health perspective – Raúl Ochoa-Hueso – Frontiers in Ecology and Evolution

The Impact of Hydration and Temperature on Bacterial Diversity in Arid Soil Mesocosms – Adam Št’ovíček – Frontiers in Microbiology

Contrasting bacterial communities in two indigenous Chionochloa (Poaceae) grassland soils in New Zealand – Jocelyn C. Griffith – Plos One

Water and extremophile microbiome

Bacterial diversity and population shifts driven by spotlight wastewater micropollutants in low-temperature highly nitrifying activated sludge – Antonina Kruglova – JScience of The Total Environment

Probiotics / prebiotics

The potential synergistic behaviour of inter- and intra-genus probiotic combinations in the pattern and rate of short chain fatty acids formation during fibre fermentation – Warnakulasuriya M. A. D. B. Fernando – International Journal of Food Sciences and Nutrition

Review: Structural features underlying prebiotic activity of conventional and potential prebiotic oligosaccharides in food and health – Subin R. C. K. Rajendran – Journal of Food Biochemistry

Phages and viruses

Case control comparison of enteric viromes in captive rhesus macaques with acute or idiopathic chronic diarrhea – Beatrix Kapusinszky – Journal of Virology

A viral metagenomic approach on a non-metagenomic experiment: Mining next generation sequencing datasets from pig DNA identified several porcine parvoviruses for a retrospective evaluation of viral infections – Samuele Bovo – Plos One

Bioinformatics

Does colorectal cancer significantly influence the assembly of gut microbial communities? – Lin Dai – PeerJ

Review: Using metagenomics to investigate human and environmental resistomes – Johan Bengtsson-Palme – Journal of Antimicrobial Chemotherapy

RRmix: A method for simultaneous batch effect correction and analysis of metabolomics data in the absence of internal standards – Stephen Salerno Jr – Plos One

Predicting the ecological quality status of marine environments from eDNA metabarcoding data using supervised machine learning – Tristan Cordier – Environmental Science and Technology

Anitha’s non-microbiology picks

AI is changing how we do science. Get a glimpse

Scientists explain ancient Rome’s long-lasting concrete

May 7, 2017

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A short digest for Sunday morning. Few interesting gut microbiome articles and Time magazine cover story about the next pandemic and novel detection technologies.

General microbiome

Antibiotics in a general population: Relations with gender, body mass index (BMI) and age and their human health risks – Sisi Liu -Science of the Total Environment

Human gut microbiome

A Clostridium difficile-Specific, Gel-Forming Protein Required for Optimal Spore Germination – ML Donnelly – MBio

The intestinal microbiome and paediatric liver disease – Daniel H Leung, MD – The Lancet

Plant, root, and soil microbiome

Review: Communication in the Phytobiome – Jan E. Leach – Cell

Food microbiology

The impact of nutrition on intestinal bacterial communities – Harry J Flint – Current opinion in Microbiology

Large-scale targeted metagenomics analysis of bacterial ecological changes in 88 kimchi samples during fermentation – Moeun Lee – Food microbiology

Probiotics / prebiotics

Designer probiotics for the prevention and treatment of human diseases – Koon Jiew Chua – Current opinion in chemical biology

Microbes in the news

Time magazine: The world is not ready for the next pandemic

Researchers find link between gut microbiome, osteoarthritis pain

March 24, 2017

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Complex glycan degradation in the gut; role of LPS-binding protein in NAFLD; contribution of environmental factors to arbuscular mycorrhizal fungi community composition and structure; and ResistoMap, a new web-based bioinformatic tool for visualizing the human gut resistome.

 

Events and jobs
Visiting Professor (Part Time) Microbiology – Chamberlain College of Nursing – Arlington, VA

Scientific Officer (Full Time) Microbiology – Australian Clinical Labs – Sydney, AU

Human respiratory microbiome
Understanding the Lung Abscess Microbiome: Outcomes of Percutaneous Lung Parenchymal Abscess Drainage with Microbiologic Correlation – Christopher Duncan – Cardiovascular and Interventional Radiology

Human oral microbiome
Subgingival microbiota dysbiosis in systemic lupus erythematosus: association with periodontal status – Joice Dias Correa – Microbiome

Candida albicans alters the bacterial microbiome of early in vitro oral biofilms – M. M. Janus – Journal of Oral Microbiology

Human skin microbiome
Injections through skin colonized with Staphylococcus aureus biofilm introduce contamination despite standard antimicrobial preparation procedures – Yi Wang – Scientific Reports

Compartmentalized Control of Skin Immunity by Resident Commensals – Shruti Naik – Science

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

Protective Factors in the Intestinal Microbiome Against Clostridium difficile infection in Recipients of Allogeneic Hematopoietic Stem Cell Transplantation – Yeon Joo Lee – The Journal of Infectious Diseases

Dysbiosis and compositional alterations with aging in the gut microbiota of patients with heart failure – Takehiro Kamo – PLoS One

Alterations in Gastric Microbiota After H. Pylori Eradication and in Different Histological Stages of Gastric Carcinogenesis – Tung Hiu Li – Scientific Reports

Dietary emulsifiers directly alter human microbiota composition and gene expression ex vivo potentiating intestinal inflammation – Benoit Chassaing – Gut

Review: Gut microbiota: Neonatal gut microbiota induces lung immunity against pneumonia – Sabrina Tamburini & Jose C. Clemente – Nature Reviews Gastroenterology & Hepatology

Proteobacteria explain significant functional variability in the human gut microbiome – Patrick S. Bradley & Katherine S. Pollard – Microbiome

Antigen-Presenting Human γδ T Cells Promote Intestinal CD4+ T Cell Expression of IL-22 and Mucosal Release of Calprotectin – Christopher J. Tyler – Journal of Immunology

Odd Chain Fatty Acids; New Insights of the Relationship Between the Gut Microbiota, Dietary Intake, Biosynthesis and Glucose Intolerance – Benjamin J. Jenkins – Scientific Reports

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

Animal experiments
Loss of lipopolysaccharide-binding protein attenuates the development of diet-induced non-alcoholic fatty liver disease in mice – Cheng Jun Jin – Journal of Gastroenterology and Hepatology

Animal microbiome
Transcriptional characterization of Vibrio fischeri during colonization of juvenile Euprymna scolopes – Luke R. Thompson – Environmental Microbiology

Plant, root, and soil microbiome
The influence of environmental factors on communities of arbuscular mycorrhizal fungi associated with Chenopodium ambrosioides revealed by MiSeq sequencing investigation – Xihui Xu – Scientific Reports

Intercropping maize and common bean enhances microbial carbon and nitrogen availability in low phosphorus soil under Mediterranean conditions – Mourad Latati – European Journal of Soil Biology

The effects of plant nutritional strategy on soil microbial denitrification activity through rhizosphere primary metabolites – Julien P. Guyonnet – FEMS Microbiology Ecology

Water and extremophile microbiome
Geographic distribution of cadmium and its interaction with the microbial community in the Longjiang River: risk evaluation after a shocking pollution accident – Ming Jiang Zhang – Scientific Reports

Beneficial Microorganisms for Corals (BMC): Proposed Mechanisms for Coral Health and Resilience – Raquel S. Peixoto – Frontiers in Microbiology

Small Molecules Belowground: The Role of Specialized Metabolites in the Rhizosphere – Massalha H – The Plant Journal

Food microbiology
Rice- or pork-based diets with similar calorie and content result in different rat gut microbiota – Xiaozhe Qi – International Journal of Food Sciences and Nutrition

Bioinformatics
ResistoMap – online visualization of human gut microbiota antibiotic resistome – Konstantin Yarygin – bioRxiv

February 25, 2017

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Insight into the role of gut microbiome lipid metabolites in central nervous system diseases. A role of invasive plants in altering the soil microbiome. Evidence that microbiome alterations in Crohn’s disease are not genetically based.

Events and jobs

Post-Doctoral Research Associate in immunology, microbiology, virology, and/or biochemistry – MRIGlobal, Gaithersburg, Maryland, USA

Research Scientist – Department of Microbiology – University of Illinois at Urbana-Champaign, USA

Part-Time Microbiology Instructor – Foothill-De Anza Community College District, California, USA

First Stage Researcher with background in environmental microbiology – Faculty of Biology, University of Warsaw, Poland

General microbiome

Altered antibiotic tolerance in anaerobic digesters acclimated to triclosan or triclocarban – Daniel E. Carey – Chemosphere

Antimicrobial Resistance and Molecular Characterization of Extended-Spectrum β-Lactamases and Other Escherichia coli Isolated from Food of Animal Origin and Human Intestinal Isolates – Krizman M – Journal of Food Protection

Human oral microbiome

Prospective, randomised, controlled study evaluating early modification of oral microbiota following admission to the intensive care unit and oral hygiene with chlorhexidine – Felipe Francisco Tuon – Journal of Global Antimicrobial Resistance

The potential effect of oral microbiota in the prediction of mucositis during radiotherapy for nasopharyngeal carcinoma -Xiao-Xia Zhu – EBioMedicine

Human urinary microbiome

*Special Issue Preface: Preface to the human microbiome in urologic health and disease – Daniel A. Shoskes – Annals of Translational Medicine

*Review: The mycobiome of the human urinary tract: potential roles for fungi in urology – A. Lenore Ackerman – Annals of Translational Medicine

Human vaginal microbiome

Longitudinal analysis of vaginal microbiota in women with recurrent vulvovaginal candidiasis – Ma X – Journal of Southern Medical University (Nan Fang Yi Ke Da Xue Xue Bao)

Human gut microbiome

The distinct features of microbial ‘dysbiosis’ of Crohn’s disease do not occur to the same extent in their unaffected, genetically-linked kindred – Umer Zeeshan Ijaz – PLOS

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

Gut-brain axis: Role of lipids in the regulation of inflammation, pain and CNS diseases – Russo R – Current Medicinal Chemistry

What roles do colon stem cells and gap junctions play in the left and right location of origin of colorectal cancers? – James E. Trosko – Journal of Cell Communication and Signaling

Contributions of the Interaction between Dietary Protein and Gut Microbiota to Intestinal Health – Ma N – Current Protein and Peptide Science

*Review: Dietary Fiber Gap and Host Gut Microbiota – Han M – Protein Peptide Letters

Structural Modulation of Gut Microbiota during Alleviation of Antibiotic-Associated Diarrhea with Herbal Formula – Weijie Lv – International Journal of Biological Macromolecules

Association of diverse bacterial communities in human bile samples with biliary tract disorders: a survey using culture and polymerase chain reaction-denaturing gradient gel electrophoresis methods – E. Tajeddin – European Journal of Clinical Microbiology & Infectious Disease

Immunomodulatory Effects of Lactobacillus plantarumLp62 on Intestinal Epithelial and Mononuclear Cells – Thalis Ferreira dos Santos – BioMed Research International

How to modulate gut microbiota: diet, pre-probiotics or antibiotics? – Ponziani FR – Minerva Gastroenterologica E Dietologica

* Review: AISF position paper on nonalcoholic fatty liver disease (NAFLD): Updates and future directions – Italian Association for the Study of the Liver (AISF), Lonardo A – Digestive and Liver Disease

Clostridium difficile infection in acute flares of inflammatory bowel disease: A prospective study -Harry Sokol – Digestive and Liver Disease

 Multi-site human microbiome

Porphyromonas gingivalis lipopolysaccharide induces pro-inflammatory adipokine secretion and oxidative stress by regulating Toll-like receptor-mediated signaling pathways and redox enzymes in adipocytes – Fanny Le Sage – Molecular and Cellular Endocrinology

Animal experiments

Impact of TIGECYCLINE versus other antibiotics on the fecal metabolome and on colonization resistance to CLOSTRIDIUM DIFFICILE in mice – Robin L.P. Jump – Pathological Immunology

Animal microbiome

Temporal Stability and the Effect of Transgenerational Transfer on Fecal Microbiota Structure in a Long Distance Migratory Bird – Jakub Kreisinger – Frontiers in Microbology

Convergent patterns in the evolution of mealybug symbioses involving different intrabacterial symbionts – Gitta Szabó – The ISME Journal

New roles in hemicellulosic sugar fermentation for the uncultivated Bacteroidetes family BS11 – Lindsey M Solden – The ISME Journal

Changes in rumen microbiota composition and in situ degradation kinetics during the dry period and early lactation as affected by rate of increase of concentrate allowance – K. Dieho – Journal of Dairy Science

Plant, root, and soil microbiome

Response of rhizosphere soil microbial to Deyeuxia angustifolia encroaching in two different vegetation communities in alpine tundra – Lin Li – Scientific Reports

Influence of phylogenetic conservatism and trait convergence on the interactions between fungal root endophytes and plants – Sevda Haghi Kia – The ISME Journal

Comparative fibre-degrading capacity in foals at immediate and late post-weaning periods – C. Faubladier – Cambridge Core

The effect of the source of microorganisms on adaptation of hydrolytic consortia dedicated to anaerobic digestion of maize silage – Krzysztof Poszytek – Anaerobe

Water and extremophile microbiome

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

Direct single-cell biomass estimates for marine bacteria via Archimedes’ principle – Nathan Cermak – The ISME Journal

Evidence for a role of viruses in the thermal sensitivity of coral photosymbionts – Rachel Ashley Levin – The ISME Journal

Use of plankton-derived vitamin B1 precursors, especially thiazole-related precursor, by key marine picoeukaryotic phytoplankton – Ryan W Paerl – The ISME Journal

Elevated temperature increases carbon and nitrogen fluxes between phytoplankton and heterotrophic bacteria through physical attachment – Nestor Arandia-Gorostidi – The ISME Journal

Warming and nutrient enrichment in combination increase stochasticity and beta diversity of bacterioplankton assemblages across freshwater mesocosms – Lijuan Ren – The ISME Journal

Integration of Metagenomic and Stable Carbon Isotope Evidence Reveals the Extent and Mechanisms of Carbon Dioxide Fixation in High-Temperature Microbial Communities – Ryan de Montmollin Jennings – Frontiers in Microbiology

Seasonal Variation in Abundance and Diversity of Bacterial Methanotrophs in Five Temperate Lakes – Md Sainur Samad – Frontiers in Microbiology

Predominance of Viable Spore-Forming Piezophilic Bacteria in High-Pressure Enrichment Cultures from ~1.5 to 2.4 km-Deep Coal-Bearing Sediments below the Ocean Floor – Jiasong Fang – Frontiers in Microbiology

Metagenomics and resistome

Co-occurrence of antibiotic and metal resistance genes revealed in complete genome collection – Li-Guan Li – The ISME

Metabolomics

Assessment of the bimodality in the distribution of bacterial genome sizes – Hyun S Gweon – The ISME Journal

Genome of ‘Ca. Desulfovibrio trichonymphae’, an H2-oxidizing bacterium in a tripartite symbiotic system within a protist cell in the termite gut – Hirokazu Kuwahara – The ISME Journal

A family of interaction-adjusted indices of community similarity – Thomas Sebastian Benedikt Schmidt – The ISME Journal

Refined experimental annotation reveals conserved corrinoid autotrophy in chloroform-respiring Dehalobacter isolates – Po-Hsiang Wang – The ISME Journal

Phylogenetic relationships among Staphylococcus aureus isolated from clinical samples in Mashhad, Iran – Farzad Khadem – Journal of Infection and Public Health

Closed-reference metatranscriptomics enables in planta profiling of putative virulence activities in the grapevine trunk-disease complex – Abraham Morales-Cruz – Molecular Plant Pathology

More microbes

Redox potential as a master variable controlling pathways of metal reduction by Geobacter sulfurreducens – Caleb E Levar – The ISME Journal

Coupled molecular and isotopic evidence for denitrifier controls over terrestrial nitrogen availability – Erin F E Lennon – The ISME Journal

Enhanced microbial electrosynthesis by using defined co-cultures – Jörg S Deutzmann – The ISME Journal

Temperature is a key factor in Micromonas–virus interactions – David Demory – The ISME Journal

Evolutionary convergence in experimental Pseudomonas populations – Peter A Lind – The ISME Journal

Microbes in the news

Are There Health Benefits To Exposing Our Immune Systems To Bacteria? – Forbes
Nutrition: Trust your gut instincts — whole grains are good for you – Los Angeles Daily News

There could be a surprising link between how people respond to a new cancer treatment and their microbiome – Lydia Ramsey – Business Insider

December 9, 2016

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Human oral microbiome

Chapter Four – The Oral Microbiome in Health and Its Implication in Oral and Systemic Diseases – B. Sampaio-Maia – Advances in Applied Microbiology

Protocol: Methods to Study Antagonistic Activities Among Oral Bacteria – Fengxia Qi – Oral Biology

Protocol: The Oral Microbiota in Health and Disease: An Overview of Molecular Findings – José F. Siqueira Jr. – Oral Biology

Human skin microbiome

The protective effect of microbiota on S. aureus skin colonization depends on the integrity of the epithelial barrier – Marc Burian – Journal of Investigative Dermatology

Human respiratory microbiome (also Early Life)

Differences in the Nasopharyngeal Microbiome During Acute Respiratory Tract Infection With Human Rhinovirus and Respiratory Syncytial Virus in Infancy – Christian Rosas-Salazar – The Journal of Infectious Diseases

Reemergence of Lower-Airway Microbiota in Lung Transplant Patients with Cystic Fibrosis – Saad A. Syed – Annals of the American Thoracic Society

Editorial: Changes in the Cystic Fibrosis Airway Microbiome after Lung Transplant: The More Things Change, the More They Stay the Same – Shawn D. Aaron – Annals of the American Thoracic Society

Human gut microbiome

Blautia massiliensis sp. nov., isolated from a fresh human fecal sample and emended description of the genus Blautia – Guillaume A. Durand – Anaerobe

Review: Formation of propionate and butyrate by the human colonic microbiota – Petra Louis – Environmental Microbiology

Review: Exercise-induced stress behavior, gut-microbiota-brain axis and diet: a systematic review for athletes – Allison Clark – Journal of the International Society of Sports Nutrition

Animal experiments

Analysis of the intestinal microbial community and inferred functional capacities during the host response to Pneumocystis pneumonia – Derrick R. Samuelson – Experimental Lung Research

Plant, root, and soil microbiome

The prey’s scent – Volatile organic compound mediated interactions between soil bacteria and their protist predators – Kristin Schulz-Bohm – The ISME Journal

How miniature predators get their favorite soil bacteria. Sniffing out your dinner in the dark – Science Daily

Food microbiology

Dynamics of microbial community during the extremely long-term fermentation process of a traditional soy sauce – Yang Yang – Journal of the Science of Food and Agriculture

Water microbiology

Diversity and Abundance of the Denitrifying Microbiota in the Sediment of Eastern China Marginal Seas and the Impact of Environmental Factors – Minghong Gao – Microbial Ecology

Phages and viruses

Exploring the contribution of bacteriophages to antibiotic resistance – Itziar Lekunberri – Environmental Pollution

Bioinformatics and metagenomics

K-shuff: A Novel Algorithm for Characterizing Structural and Compositional Diversity in Gene Libraries – Kamlesh Jangid – PLOS ONE

More microbiology

17th Century Variola Virus Reveals the Recent History of Smallpox – Ana T. Duggan – Current Biology

A Mummy’s DNA May Help Solve The Mystery Of The Origins Of Smallpox – Nell Greenfieldboyce – NPR

Drug resistant pathogens and travel: No road map but a new initiative from Travel Medicine and Infectious Disease – Patricia Schlagenhauf – Travel Medicine and Infectious Disease

Microbes in the news

uBiome Joins Google, SpaceX, and Oculus as 2016 World Technology Award Finalist – PR Web

Paul Schreckenberger, microbiology lab director at Loyola, dies at 69 – Chicago Tribune

Antibacterial products may help bacteria beat antibiotics – Bob Holmes

Corticosteroid Success Linked to Differences in Bronchial Microbiome – Kenneth Bender – HCP live

Guest Post — The Emergent Microbiome: A Revolution for the Life Sciences — Part IX, The Microbiome and Immunotherapy II – David Puelo – JDSupra

Scientist Studies the Infant Resistome to Combat Superbugs – Infection Control Today

The Microbiome and Risk for HIV: Research in South Africa shows how the balance of bacteria in a woman’s vagina can raise or lower her risk for HIV – Columbia