Category Archives: Metagenomics & Bioinformatics

January 3, 2018

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Today we have a nice event /training in social science techniques organized by NERC in Manchester, Bristol and Edinburgh (UK), few microbiology jobs, an interesting review from Arun T. Nair in “Gut Microbiome”, quite a few papers about Synechococcus in “Water and extremophile microbiome”. Check as well “Microbes on market” where you can read about Google and Microsoft investing in medicine startup DNAnexus.

Events

Social science techniques for natural scientists training funded by NERC, UK

Jobs

Microbiologist – Kent, UK

Scientist/Sr.Scientist – Strain Development, CJM Talent Solutions, San Francisco, US

Associate/Assistant Professor : Miami, Florida, FL, US

General microbiome

Comparison of genomes and proteomes of four whole genome-sequenced Campylobacter jejuni from different phylogenetic backgrounds – Clifford G. Clark – PLOS

Phylogenetic inference of Coxiella burnetii by 16S rRNA gene sequencing – Heather P. McLaughlin -PLOS

The photosynthetic bacteria Rhodobacter capsulatus and Synechocystis sp. PCC 6803 as new hosts for cyclic plant triterpene biosynthesis – Anita Loeschcke -PLOS

Pregnancy and early life

Effect of innate antiviral glycoproteins in breast milk on seroconversion to rotavirus vaccine (Rotarix) in children in Lusaka, Zambia – Katayi Mwila-Kazimbaya – PLOS

Oral microbiome

Frequency and levels of candidate endodontic pathogens in acute apical abscesses as compared to asymptomatic apical periodontitis – Isabela N. Rôças – PLOS

Human vaginal microbiome

Combined oral and topical antimicrobial therapy for male partners of women with bacterial vaginosis: Acceptability, tolerability and impact on the genital microbiota of couples – A pilot study – Erica L. Plummer – PLOS

Candida albicans-derived mannoproteins activate NF-κB in reporter cells expressing TLR4, MD2 and CD14 – Traci Ness – PLOS

Replication-dependent size reduction precedes differentiation in Chlamydia trachomatis – Jennifer K. Lee – Nature Communications

Human gut microbiome

T6SS: The bacterial “fight club” in the host gut – Thibault G. Sana – PLOS Pathogens

Review: Gut Microbiota Dysfunction as Reliable Non-invasive Early Diagnostic Biomarkers in the Pathophysiology of Parkinson’s Disease: A Critical Review – Arun T Nair – Journal of Neurogastroenterology and Motility

Animal experiments

Effect of dietary xylooligosaccharides on intestinal characteristics, gut microbiota, cecal short-chain fatty acids, and plasma immune parameters of laying hens – X M Ding – Poultry Science

Influence of a diet enriched with virgin olive oil or butter on mouse gut microbiota and its correlation to physiological and biochemical parameters related to metabolic syndrome – Isabel Prieto – PLOS

Modulation of the diet and gastrointestinal microbiota normalizes systemic inflammation and β-cell chemokine expression associated with autoimmune diabetes susceptibility – Angela M. Henschel – PLOS

Dietary Lactobacillus acidophilus positively influences growth performance, gut morphology, and gut microbiology in rurally reared chickens  – C Forte – Poultry Science

Animal microbiome

Oral Disease and Microbiota in Free-Roaming Cats – Ana Whyte – Topics in Companion Animal Medicine

Review: Effect of Enterococcus Faecium Strain SF68 on Gastrointestinal Signs and Fecal Microbiome in Cats Administered Amoxicillin-Clavulanate – C. Torres-Henderson – Topics in Companion Animal Medicine

Water and extremophile microbiome

Clade and strain specific contributions of Synechococcus and Prochlorococcus to carbon export in the Sargasso Sea – Francesca De Martini – Limnology and Oceanography

Microbial proteins for organic material degradation in the deep ocean – David L. Kirchman – PNAS

Photosynthetic functions of Synechococcus in the ocean microbiomes of diverse salinity and seasons – Yihwan Kim – PLOS

Potential impact of global climate change on benthic deep-sea microbes – Roberto Danovaro – FEMS Microbiology Letters

Variability in the production of organic ligands, by Synechococcus PCC 7002, under different iron scenarios – Guillermo Samperio-Ramos – Journal of Oceanography

Effect of light on N2 fixation and net nitrogen release of Trichodesmium in a field study – Yangyang Lu – Biogeosciences

Microbial diversity of saline environments: searching for cytotoxic activities – Carolina Díaz-Cárdenas – AMB Express

Aerobic proteobacterial methylotrophs in Movile Cave: genomic and metagenomic analyses – Deepak Kumaresan – BMC Microbiome

Probiotics / prebiotics

Bifidobacteria or Fiber Protects against Diet-Induced Microbiota-Mediated Colonic Mucus Deterioration – Bjoern O. Schroeder – Cell Host and Microbe

Modifying progression of aging and reducing the risk of neurodegenerative diseases by probiotics and synbiotics – Huey Shi Lye – Frontiers In Bioscience

Phages and viruses

Isolation and characterization of a N4-like lytic bacteriophage infecting Vibrio splendidus, a pathogen of fish and bivalves – Pantelis Katharios – PLOS

High human papillomavirus (HPV) prevalence in South African adolescents and young women encourages expanded HPV vaccination campaigns – Zizipho Z. A. Mbulawa – PLOS

Zika virus infection modulates the bacterial diversity associated with Aedes aegypti as revealed by metagenomic analysis – Luis E. M. Villegas – PLOS

Localized Recombination Drives Diversification of Killing Spectra for Phage Derived Syringacins – David Baltrus – bioRxiv

Bioinformatics

Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing – Chao Fang – Giga Science

 

Techniques

Imaging bacteria inside their host by cryo-focused ion beam milling and electron cryotomography – João M Medeiros – Current Opinion in Microbiology

Microbes in the news

Tech company’s lights being used to kill germs in ambulances

Astronauts Identify Mystery Microbes in Space for the 1st Time

Microbes on the market

Seres Therapeutics Inc (MCRB) Holdings Increased by State Street Corp

Microsoft, Google invest in precision medicine startup DNAnexus

Tina’s non-microbiology picks

Synthetic Biology in the Driving Seat of the Bioeconomy – Yensi Flores Bueso – Trends in Biotechnology

Expect exoplanet atmospheres, organs with new functions and fewer traffic jams in 2018

January 2, 2018

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Happy New Year from the Microbiome Digest team!

General microbiome

Pre-print: Understanding How Microbiomes Influence The Systems They Inhabit: moving from a correlative to a causal research framework – E K Hall – bioRxiv

Human vaginal microbiome

A retrospective pilot study to determine whether the reproductive tract microbiota differs between women with a history of infertility and fertile women – Bryan A Wee – Australian and New Zealand Journal of Obstetrics and Gynaecology

Human gut microbiome

Rates of Gut Microbiome Divergence in Mammals – Alex H Nishida – Molecular Ecology

Animal microbiome

Processes shaping gut microbiota diversity in allopatric populations of the endemic lizard Podarcis lilfordi from Menorcan islets (Balearic Islands) – Laura Baldo – FEMS Microbiology Ecology

Individual- and Species-Specific Skin Microbiomes in Three Different Estrildid Finch Species Revealed by 16S Amplicon Sequencing – Kathrin Engel – Microbial Ecology

Plant, root, and soil microbiome

Vertical variation of a black soil’s properties in response to freeze-thaw cycles and its links to shift of microbial community structure – Ziming Han – Science of the Total Environment

Biomass, activity and structure of rhizosphere soil microbial community under different metallophytes in a mining site – Wenhao Yang – Plant and Soil

Symbiotic nitrogen fixation by rhizobia — the roots of a success story – Catherine Masson-Boivin – Current Opinion in Plant Biology

Water and extremophile microbiome

Microbial community structure and function in sediments from e-waste contaminated rivers at Guiyu area of China – Jun Liu – Environmental Pollution

Pre-print: Micro-scale ecology regulates particulate organic matter turnover in model marine microbial communities – Tim N Enke – bioRxiv

Food microbiology

Autochthonous facility-specific microbiota dominates washed-rind Austrian hard cheese surfaces and its production environment – Narciso M Quijada – International Journal of Food Microbiology

Bioinformatics

CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision – Damayanthi Herath – BMC Bioinformatics

Techniques

Serial Dilution-Based Growth Curves and Growth Curve Synchronization for High-Resolution Time Series of Bacterial Biofilm Growth – Fernando Govantes – Host-Pathogen Interactions

Microbes in the news

Fiber Is Good for You. Now Scientists May Know Why. – Carl Zimmer – The New York Times

Fast, Cheap Testing for Tuberculosis? Soon It May Be Possible – Donald G McNeil – The New York Times

How probiotics can help ward off health complications in premature babies – CTV News

Science, career, and publishing

Pre-print: Disequilibrium in Gender Ratios among Authors who Contributed Equally – Nichole A Broderick – bioRxiv

December 26, 2017

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Quite a few articles today especially in the plant/soil and water/extremophile sections. Plus: a new zebrafish model of the human gut microbiome, fiber and bifidos protect against north american diet-induced increased gut permeability in mice, prebiotics from the Morinda plant not only alter the gut microbiome but improve Alzheimers-like symptoms in a rat model, micro-eukaryotes may be an important factor in a deadly skin fungus infection in the Cascades Frog, and a new Leaf-FISH technique to visualize bacterial communities on plants. Happy Holidays!

Human oral microbiome

The oral microbiome—the relevant reservoir for acute pediatric appendicitis? – Carlotta Blod – International Journal of Colorectal Disease

Differences in carbon source usage by dental plaque in children with and without early childhood caries – Yan Zhao – International Journal of Oral Science

Review: Task Force on Design and Analysis in Oral Health Research: Host-Microbiome Interactions in Dysbiosis – T.E. Van Dyke – JDR Clinical & Translational Research

Human gut microbiome

Review: Probiotics and necrotizing enterocolitis – Ravi Mangal Patel – Seminars in Pediatric Surgery

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Animal experiments

Fusimonas intestini gen. nov., sp. nov., a novel intestinal bacterium of the family Lachnospiraceae associated with diabetes in mice – Hiroyuki Kusada – Scientific Reports

*Zebrafish Axenic Larvae Colonization with Human Intestinal Microbiota – Arias-Jayo Nerea – Zebrafish

*Bifidobacteria or Fiber Protects against Diet-Induced Microbiota-Mediated Colonic Mucus Deterioration – Bjoern O. Schroeder – Cell Host & Microbe

In Silico Analysis of the Small Molecule Content of Outer Membrane Vesicles Produced by Bacteroides thetaiotaomicron Indicates an Extensive Metabolic Link between Microbe and Host – William A. Bryant – Frontiers in Microbiology

*Prebiotic Effect of Fructooligosaccharides from Morinda officinalis on Alzheimer’s Disease in Rodent Models by Targeting the Microbiota-Gut-Brain Axis – Diling Chen – Frontiers in Aging Neuroscience

Animal microbiome

Effect of Environmental Factors and an Emerging Parasitic Disease on Gut Microbiome of Wild Salmonid Fish – Anti Vasemägi – mSphere

*Composition of Micro-eukaryotes on the Skin of the Cascades Frog (Rana cascadae) and Patterns of Correlation between Skin Microbes and Batrachochytrium dendrobatidis – Jordan G. Kueneman – Frontiers in Microbiology

Plant, root, and soil microbiome

Chemical investigation of metabolites produced by an endophytic fungi Phialemonium curvatum from the leaves of Passiflora edulis –  G. R. Nalin Rathnayake – Natural Product Research

Novel hydrocarbonoclastic metal-tolerant Acinetobacter and Pseudomonas strains from Aconcagua river oil-polluted soil – Valentina Méndez – Journal of soil science and plant nutrition

Spatial patterns of enzyme activities in the rhizosphere: Effects of root hairs and root radius – Xiaomin Ma – Soil Biology and Biochemistry

The rhizosphere microbial community response to a bio-organic fertilizer: finding the mechanisms behind the suppression of watermelon Fusarium wilt disease – Jia Zhao – Acta Physiologiae Plantarum

Efficiency of two inoculation methods of Pseudomonas putida on growth and yield of tomato plants – Luis G. Hernández-Montiel – Journal of soil science and plant nutrition

Rhizospere yeasts improve P uptake of a maize arbuscular mycorrhizal association – Marcela Sarabia – Applied Soil Ecology

Ammonia-oxidizing microorganisms: key players in the promotion of plant growth – Adenike Eunice Amoo – Journal of soil science and plant nutrition

Review: Potassium solubilizing bacteria (KSB): Mechanisms, promotion of plant growth, and future prospects ­ A review – H. Etesami – Journal of soil science and plant nutrition

Long-term phosphorus fertilization effects on arbuscular mycorrhizal fungal diversity in Uruguayan grasses – Silvina García – Journal of soil science and plant nutrition

Alcaligenes faecalisassociated with Mimosa calodendron rizhosphere assist plant survival in arsenic rich soils – Érica Barbosa Felestrino – Journal of soil science and plant nutrition

Functional land-use change effects on soil fungal communities in Chilean temperate rainforests – César Marín – Journal of soil science and plant nutrition

Probiotic strain Stenotrophomonas acidaminiphila BJ1 degrades and reduces chlorothalonil toxicity to soil enzymes, microbial communities and plant roots – Qingming Zhang – AMB Express

Low light availability alters root exudation and reduces putative beneficial microorganisms in seagrass roots –  Belinda C. Martin – Frontiers in Microbiology

Effects of biochar on nutrients and the microbial community structure of tobacco-planting soils – Gao Lin – Journal of soil science and plant nutrition

Root-associated bacterial and fungal community profiles of Arabidopsis thaliana are robust across contrasting soil P levels – Chanz Robbins – Phytobiomes

Water and extremophile microbiome

Biogeographical patterns of bacterial and archaeal communities from distant hypersaline environments – M.R. Mora-Ruiz del – Systematic and Applied Microbiology

Cloning, Over-Expression, and Purification of Carbonic Anhydrase from an Extremophilic Bacterium: An Introduction to Advanced Molecular Biology – Vijayakumar Somalinga – The American Biology Teacher

Salinivibrio kushneri sp. nov., a moderately halophilic bacterium isolated from salterns – Clara López-Hermoso – Systematic and Applied Microbiology

Genome sequencing and heterologous expression of antiporters reveal alkaline response mechanisms of Halomonas alkalicola – Lei Zhai – Extremophiles

Benthic phototrophic community from Kiran soda lake, south-eastern Siberia – Ekaterina I. Burganskaya – Extremophiles

Enhancing the adaptability of the deep-sea bacterium Shewanella piezotolerans WP3 to high pressure and low temperature by experimental evolution under H2O2 stress – Zhe Xie – Applied and Environmental Microbiology

Fungal community structure at pelagic and littoral sites in Lake Biwa determined with high-throughput sequencing – Peixue Song – Limnology

Spatiotemporal dynamics of marine bacterial and archaeal communities in surface waters off the northern Antarctic Peninsula – Camila N. Signori – Deep Sea Research Part II: Topical Studies in Oceanography

Microbial Ecology

Dissertation: The Macroecology of Microorganisms: From Pattern to Process – David Clark – University of Essex

Review: Using metabolic networks to resolve ecological properties of microbiomes – Emilie E.L. Muller – Current Opinion in Systems Biology

Microbial stress mediated intercellular nanotubes in an anaerobic microbial consortium digesting cellulose – Martina John – Scientific Reports

Built environment

Distribution of Legionella and bacterial community composition among regionally diverse US cooling towers – Anna C. Llewellyn – PLOS one

Food microbiology

Identification of natural antimicrobial peptides from bacteria through metagenomic and metatranscriptomic analysis of high-throughput transcriptome data of Taiwanese oolong teas – Kai-Yao Huang – BMC Systems Biology

Strain-Level Metagenomic Analysis of the Fermented Dairy Beverage Nunu Highlights Potential Food Safety Risks – Aaron M. Walsh – Applied and Environmental Microbiology

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Probiotics / prebiotics

Review: Recent Development of Prebiotic Research—Statement from an Expert Workshop – Giorgio La Fata – Nutrients

Effects of fermented soymilk with Lactobacillus casei Shirota on skin condition and the gut microbiota: a randomised clinical pilot trial – T. Nagino – Beneficial Microbes

Phages and viruses

Novel ssDNA viruses detected in the virome of bleached, habitat-forming kelp Ecklonia radiata –  Douglas Beattie – Frontiers in Marine Science

Bioinformatics

Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples – Jake Lin – BMC Genomics

Techniques

*Leaf-FISH: Microscale imaging of bacterial taxa on phyllosphere –  Elena L. Peredo – Frontiers in Microbiology

A new suite of plasmid vectors for fluorescence-based imaging of root colonizing pseudomonads –  Rosemarie Wilton – Frontiers in Plant Science

Synthetic microbial consortia enable rapid assembly of pure translation machinery – Fernando Villarreal – Nature Chemical Biology

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Microbes in the news

Essential science: Link between gut microbes and despair – Tim Sandle – Digital Science

Enjoy the holidays, but don’t forget your fiber – Tim Sandle – Digital Science

 

December 21, 2017

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Today’s digest features an original research article showing administration of Bifidobacterium may ameliorate toxicity of a a checkpoint blockade antibody in mice and a review on the concept of enterotypes in the human gut microbiome.

Events and jobs

Explorations in Data Analyses for Metagenomic Advances in Microbial Ecology (EDAMAME) workshop at Kellogg Biological Station 24-30 June 2018.

Human respiratory microbiome

Disordered oropharyngeal microbial communities in H7N9 patients with or without secondary bacterial lung infection – Emerging microbes & infections – Hai-feng Lu

Human gut microbiome

Review: Gut microbiota in 2017: Contribution of gut microbiota–host cooperation to drug efficacy – Nathalie M. Delzenne – Nature reviews gastroenterology & hepatology

Editorial : Are diets the answers to colon ills? Food, irritable bowel syndrome and the microbiome – Quigley Eamonn M.M.

Exposure to environmental microbiota explains persistent abdominal pain and irritable bowel syndrome after a major flood – NurFadhilah Yusof – Gut Pathogens

*Perspective : Enterotypes in the landscape of gut microbial community composition – Paul I. Costea – Nature Microbiology

Animal experiments

Evaluation of Probiotic Lactobacillus fermentum CCM 7421 Administration with Alginite in Dogs – Viola Strompfová – Probiotics and Antimicrobial Proteins

* Bifidobacterium can mitigate intestinal immunopathology in the context of CTLA-4 blockade – Feng Wang – PNAS

Plant, root, and soil microbiome

Biogeography and ecological diversity patterns of rare and abundant bacteria in oil-contaminated soils – Shuo Jiao – Molecular ecology

Water and extremophile microbiome 

Bacterial Diversity and Biogeochemistry of Two Marine Shallow-Water Hydrothermal Systems off Dominica (Lesser Antilles) – Petra Pop Ristova – Frontiers in Microbiology

Temporal Dynamics of the Microbial Community Composition with a Focus on Toxic Cyanobacteria and Toxin Presence during Harmful Algal Blooms in Two South German Lakes – Pia I. Scherer – Frontiers in Microbiology

Probiotics / prebiotics

Galactooligosaccharide supplementation provides protection against Citrobacter rodentium-induced colitis without limiting pathogen burden – Hatem Kittana – Microbiology

Bifidobacteria and Their Molecular Communication with the Immune System – Lorena Ruiz – Frontiers in Microbiology

Phages and viruses

Toward Understanding Phage:Host Interactions in the Rumen; Complete Genome Sequences of Lytic Phages Infecting Rumen Bacteria – Rosalind A. Gilbert – Frontiers in Microbiology

Resolution of habitat-associated ecogenomic signatures in bacteriophage genomes and application to microbial source tracking – Lesley A. Ogilvie – The ISME Journal

Pre-print: Temperate phages as self-replicating weapons in bacterial competition – Xiang-Yi Li – bioRxiv

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Microbes in the news

Researchers Create Bacteria-Killing Steel Nanospikes

Are phages our best bet against antibiotic-resistant bacteria?

Bacteria Art

Science and Art Join Forces to Challenge our Anthropocentric Worldviews

Loyola Biology Professor Will Display Art At ARC Gallery

Anitha’s non-microbiology picks

Scientists discover entirely new material that cannot be explained by classical physics

Smothered jet may explain weird light from neutron star crash

Study of beetle flagellum offers possible way to improve medical devices

December 20, 2017

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A long but great digest today, with lots of diversity – a few studies of poultry gut microbiome and the effects food/probiotics have, a solid showing for human gut microbiome studies – covering its implications on a range of disorders, some news about biotech companies, studies on plants and from environmental sources, a promising analysis of techniques used for sampling for human gut studies, and my normal dosage of non-microbiology science.  Happy Holidays!

Events and jobs

ON-DEMAND WEBINAR How to Harness the Microbiome: Considerations and Implications of the Microbiome in Preclinical Research with Reproducible Results

Senior Biomedical Scientist (Microbiology) – Matchtech – Essex, England

Staff Research Associate 3, UCLA Department of Microbiology, Immunology and Molecular Genetics

Assistant (10782) – Clinical chemistry, microbiology and immunology – Ghent University

Pregnancy and early life

Early-Life Human Microbiota Associated With Childhood Allergy Promotes the T Helper 17 Axis in Mice – Dagbjort H. Petursdottir – Frontiers in Immunology

[Accepted Manuscript] – The neonatal window of opportunity – early priming for life – Harald Renz -Journal of Allergy and Clinical Immunology

Human oral microbiome

The Microbiome of Potentially Malignant Oral Leukoplakia Exhibits Enrichment for Fusobacterium, Leptotrichia, Campylobacter, and Rothia Species – Abdrazak Amer – Frontiers in Microbiology

Exploring the Association between Alzheimer’s Disease, Oral Health, Microbial Endocrinology and Nutrition – Alice Harding – Frontiers in Aging Neuroscience

Admission to the Intensive Care Unit is Associated With Changes in the Oral Mycobiome – Richard R. Watkins – Journal of Intensive Care Medicine

Human nearly-sterile sites

Metagenomics in pooled plasma, with identification of potential emerging infectious pathogens – Min Xu – Transfusion

Human gut microbiome

** High-resolution profiling of the gut microbiome reveals the extent of Clostridium difficile burden – Ninalynn Daquigan – npj Biofilms and Microbiomes

Unravelling the specificity and mechanism of sialic acid recognition by the gut symbiont Ruminococcus gnavus – C. David Owen – Nature Communication

[Editorial] Is gut microbiome a predictive marker to response to immune checkpoint inhibitors? – Khalil Saleh – Immunotherapy

* Microbiota Modulate Anxiety-Like Behavior and Endocrine Abnormalities in Hypothalamic-Pituitary-Adrenal Axis – Ran Huo – Front. Cell. Infect. Microbiology

Possible role of the gut microbiota–brain axis in the antidepressant effects of (R)-ketamine in a social defeat stress model – Chun Yang – Translational Psychiatry

Microbial antigen encounter during a preweaning interval is critical for tolerance to gut bacteria – Kathryn A. Knoop – Science Immunology

* Stool Donor Body Mass Index Does Not Affect Recipient Weight After a Single Fecal Microbiota Transplantation for C. difficile Infection – Monika Fischer – Clinical Gastroenterology and Hepatology

The role of microbiota in the pathogenesis of schizophrenia and major depressive disorder and the possibility of targeting microbiota as a treatment option – Fengli Lv – Oncotarget

Characterization of the urinary microbiota of elderly women and the effects of type 2 diabetes and urinary tract infections on the microbiota – Fengping Liu – Oncotarget

Animal experiments 

* Food-grade cationic antimicrobial ε-polylysine transiently alters the gut microbial community and predicted metagenome function in CD-1 mice – Xiaomeng You – npj Science of Food

Significant improvement of intestinal microbiota of gibel carp (Carassius auratus gibelio) after traditional Chinese medicine feeding – Zhenbing Wu – Journal of Applied Microbiology

* The gastrointestinal microbiome and its association with the control of pathogens in broiler chicken production: A review – Viviana Clavijo – Poultry Science

Influence of dietary avilamycin on ileal and cecal microbiota in broiler chickens – J-H Choi – Poultry Science

Plant, root, and soil microbiome

* Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale – Pauline Bernardo – The ISME Journal

Dispersal alters bacterial diversity and composition in a natural community – Michaeline B N Albright – The ISME Journal

** Genomic features of bacterial adaptation to plants – Asaf Levy – Nature Genetics

Soil Bacterial Community Structure and Co-occurrence Pattern during Vegetation Restoration in Karst Rocky Desertification Area – Liang Xue – Frontiers in Microbiology

First insight into microbial community composition in a phosphogypsum waste heap soil – Sylwia Zielińska – ABP

* Harnessing the microbiomes of Brassica vegetables for health issues – Birgit Wassermann – Scientific Reports

Water and extremophile microbiome 

Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria – Stefan M Neuenschwander – The ISME Journal

Recurrent patterns of microdiversity in a temperate coastal marine environment – Meghan Chafee – The ISME Journal

Microcystin-LR does not induce alterations to transcriptomic or metabolomic profiles of a model heterotrophic bacterium – Robbie M. Martin – PLOS One

Pre-treatment and inoculum affect the microbial community structure and enhance the biogas reactor performance in a pilot-scale biodigestion of municipal solid waste – Valeria Ventorino – Waste Management

Food microbiology

* Inner Workings: Companies seek food safety using a microbiome approach – Carolyn Beans – PNAS

Phages and viruses

* Temporal dynamics of uncultured viruses: a new dimension in viral diversity – Ksenia Arkhipova – The ISME Journal

Bioinformatics

A confidence interval analysis of sampling effort, sequencing depth, and taxonomic resolution of fungal community ecology in the era of high-throughput sequencing – Ryoko Oono – PLOS One

Techniques

Performance of DNA metabarcoding, standard barcoding, and morphological approach in the identification of host–parasitoid interactions – Martin Šigut – PLOS One

** Successful collection of stool samples for microbiome analyses from a large community-based population of elderly men – Melanie Abrahamson – Contemporary Clinical Trials Communications

Microbes on the market 

BiomX Acquires RondinX to Boost Microbiome Discovery and Development Capabilities

Vanterra Capital Backs BIOHM Health, A Total Microbiome Company

Second Genome Advances Lead, Oral Small Molecule SGM-1019, Toward Clinical Investigation in NASH After Demonstrating Safety and Tolerability in Phase 1 Study

Ed’s non-microbiology picks 

Cannabidiol (CBD) as an Adjunctive Therapy in Schizophrenia: A Multicenter Randomized Controlled Trial – Philip McGuire – The American Journal of Psychiatry

Effects of Legal Access to Cannabis on Scheduled II–V Drug Prescriptions – Sarah S. Stith – JAMDA

Ticks parasitised feathered dinosaurs as revealed by Cretaceous amber assemblages – Enrique Peñalver – Nature Communications

Induced and controlled dietary ketosis as a regulator of obesity and metabolic syndrome pathologies – Madeline K. Gibas – Diabetes & Metabolic Syndrome: Clinical Research & Reviews

The effect of vitamin D supplement on the score and quality of sleep in 20-50 year-old people with sleep disorders compared with control group – Mohammad Shahi Majid – Nutritional Neuroscience

Engineers create plants that glow – MIT

December 19, 2017

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Changes to the oral microbiota are associated with risk factors for oral cancer, the benefits of endophytic bacteria on plants, analysis of biofilms from a worldwide sampling of shower hoses.

Pregnancy and early life

Diversity of vaginal microbiota increases by the time of labor onset – Ekaterina Avershina – Scientific Reports

Human oral microbiome

Alterations in oral bacterial communities are associated with risk factors for oral and oropharyngeal cancer – Daniela Börnigen – Scientific Reports

Oral Microbiota: Microbial Biomarkers of Metabolic Syndrome Independent of Host Genetic Factors – Jiyeon Si – Frontiers in Cellular and Infection Microbiology

Animal experiments

Pre-print: Antenatal microbial colonisation of mammalian gut – Elisa Borghi – bioRxiv

Metagenome Analysis of Bodily Microbiota in a Mouse Model of Alzheimer Disease Using Bacteria-derived Membrane Vesicles in Blood – Jin-Young Park – Experimental Neurobiology

Animal microbiome

Differential Ecological Specificity of Protist and Bacterial Microbiomes across a Set of Termite Species – Lena Waidele – Frontiers in Microbiology

Plant, root, and soil microbiome

Pre-print: The ecological genetics of Pseudomonas syringae residing on the kiwifruit leaf surface – Christina Straub – bioRxiv

Inner Plant Values: Diversity, Colonization and Benefits from Endophytic Bacteria – Hongwei Liu – Frontiers in Microbiology

Frankia diversity in host-plant root nodules is independent of abundance or relative diversity of Frankia in corresponding rhizosphere soils – Seifeddine Ben Tekaya – Applied and Environmental Microbiology

Correlated production and consumption of chloromethane in the Arabidopsis thaliana phyllosphere – Muhammad Farhan Ul Haque – Scientific Reports

Rhizodeposition under drought is controlled by root growth rate and rhizosphere water content – Maire Holz – Plant and Soil

Water and extremophile microbiome

Localized high abundance of Marine group II archaea in the subtropical Pearl River Estuary: implications for their niche adaptation – Wei Xie – Environmental Microbiology

Thermophilic bacterial communities inhabiting the microbial mats of “indifferent” and chalybeate (iron-rich) thermal springs: Diversity and biotechnological analysis – Ramganesh Selvarajan – MicrobiologyOpen

Distribution and phylogeny of anaerobic anammonium-oxidizing (anammox) bacteria in water column of the central Pacific Ocean – Koji Hamasaki – Deap Sea Research Part II: Topical Studies in Oceanography

Built environment

Biofilms in shower hoses – Caitlin R Proctor – Water Research

Phages and viruses

Pre-print: Human Herpes Virus 6 (HHV-6) – Pathogen or Passenger? A pilot study of clinical laboratory data and next generation sequencing – Colin Sharp – bioRxiv

Pre-print: ACI-1 class A beta-lactamase is widespread across human gut microbiomes due to transposons harboured by tailed prophages – Chris M Rands – bioRxiv

Bioinformatics

Pre-print: How, when, and where relic DNA biases estimates of microbial diversity – J T Lennon – bioRxiv

Metabolomics

Plasma microbiome-modulated indole- and phenyl-derived metabolites associate with advanced atherosclerosis and postoperative outcomes – Cori A Cason – Journal of Vascular Surgery

Best-matched internal standard normalization in liquid chromatography-mass spectrometry metabolomics applied to environmental samples – Angela K Boysen – Analytical Chemistry

Techniques

Microfluidics: A new tool for microbial single cell analyses in human microbiome studies – Yuguang Liu – Biomicrofluidics

Pre-print: CLIQ-BID: A method to quantify bacteria-induced damage to eukaryotic cells by automated live-imaging of bright nuclei – Yann Wallez – bioRxiv

Mapping the ecological networks of microbial communities – Yandong Xiao – Nature Communications

More microbes

Pre-print: Molecular insights into Vibrio cholerae’s intra-amoebal host-pathogen interactions – Charles Van der Henst – bioRxiv

Nature to the natural rescue: Silencing microbial chats – Diby Paul – Chemico-Biological Interactions

Microbes in the news

Tracking effects of a food preservative on the gut microbiome – EurekAlert

Microbiome intervention with niacin aids insulin sensitivity – Medical Xpress

Wound scanner shows bacteria glowing if your body is infected – New Scientist

Engineering new cellular scaffolding for bacteria – Celia Henry Arnaud – Chemical & Engineering News

Viruses can transfer genes across the superkingdoms of life – ScienceDaily

Microbes on the market

British Health Technology Company Expanding Into Ten European Countries – PR Newswire

December 15, 2017

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The leaders of ten research universities/institutes pledge to report student and postdoc outcomes in biomedical research as the Coalition for Next Generation Life Science initiative, commensal fungi and their cell-wall mannans can functionally replace benefits of intestinal bacteria, a new cheese starter system with improved bacteriophage resistance and antimicrobial activity.

Events and jobs

Postdoctoral Fellow, Functional Microbiome – Claesen Group, Department of Cellular and Molecular Medicine, Cleveland Clinic (also looking for interested graduate students)

Human nearly-sterile sites

Microorganisms in the human placenta are associated with altered CpG methylation of immune and inflammation-related genes – Martha Scott Tomlinson – PLOS ONE

Human gut microbiome

Faecal microbiota transplantation for Clostridium difficile infection using a lyophilized inoculum from non-related donors: A case series involving 19 patients – Vigvári Szabolcs – Acta Microbiologica et Immunologica Hungarica

Animal experiments

Commensal Fungi Recapitulate the Protective Benefits of Intestinal Bacteria – Tony T Jiang – Cell Host & Microbe

CCL28-Deficient Mice Have Reduced IgA Antibody–Secreting Cells and an Altered Microbiota in the Colon – Kazuhiko Matsuo – The Journal of Immunology

Animal microbiome

Behavior of bacteriome symbionts during transovarial transmission and development of the Asian citrus psyllid – Hiroki Dan – PLOS ONE

Plant, root, and soil microbiome

Root-derived carbon and nitrogen from beech and ash trees differentially fuel soil animal food webs of deciduous forests – Sarah L Zieger – PLOS ONE

Historical and recent land use affects ecosystem functions in subtropical grasslands in Brazil – Jan L G Leidinger – Ecosphere

Mechanisms of arsenic sequestration by Prosopis juliflora during phytostabilization of metalliferous mine tailings – Corin M Hammond

Transfer Mechanism, Uptake Kinetic Process and Bioavailability of P, Cu, Cd, Pb and Zn in Macrophyte Rhizosphere Using DGT – Shengrui Wang – Environmental Science & Technology

Food microbiology

A Multibacteriocin Cheese Starter System, Comprising Nisin and Lacticin 3147 in Lactococcus lactis, in Combination with Plantaricin from Lactobacillus plantarum – S Mills – Applied and Environmental Microbiology

Bioinformatics

Colonic Butyrate-Producing Communities in Humans: an Overview Using Omics Data – Marius Vital – mSystems

Discovery of carbamate degrading enzymes by functional metagenomics – Lisa Ufarté – PLOS ONE

Science, career, and publishing

A new data effort to inform career choices in biomedicine – Rebecca Blank – Science

News Feature: The science that’s never been cited – Richard Van Noorden – Nature

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

 

December 7, 2017

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Meta-analysis of a collection of gut microbiome studies, characterization of two dandelion viruses, evaluation of an inclusive Research Education Community for engaging undergraduates in scientific research.

General microbiome

Bacterial social interactions and the emergence of community-intrinsic properties – Jonas Stenløkke Madsen – Current Opinion in Microbiology

Pregnancy and early life

Pre-print: Hospitalized premature infants are colonized by related bacterial strains with distinct proteomic profiles – Christopher T Brown – bioRxiv

Human gut microbiome

Gut microbiota in early life and its influence on health and disease: A position paper by the Malaysian Working Group on Gastrointestinal Health – Yeong Yeh Lee – Journal of Paediatrics and Child Health

Animal experiments

Moving beyond microbiome-wide associations to causal microbe identification – Neeraj K Surana – Nature

Plant, root, and soil microbiome

Arbuscular mycorrhizal fungus causes increased condensed tannins concentrations in shoots but decreased in roots of Lotus japonicus L – Zakaria M Solaiman – Rhizosphere

Shifts in soil microbial community, soil enzymes and crop yield under peanut/maize intercropping with reduced nitrogen levels – Jun Chen – Applied Soil Ecology

Multifarious plant growth promotion by an entomopathogenic fungus Lecanicillium psalliotae – C M Senthil Kumar – Microbiological Research

Water and extremophile microbiome

Pre-print: Optogenetics reprogramming of planktonic cells for biofilm formation – Aiguo Xia – bioRxiv

Phages and viruses

Pre-print: Molecular Identification and Characterization of Two Rubber Dandelion Amalgaviruses – Humberto J Debat – bioRxiv

Internalization of a polysialic acid-binding Escherichia coli bacteriophage into eukaryotic neuroblastoma cells – Timo A Lehti – Nature Communications

Bioinformatics

Pre-print: Personalized modeling of the human gut microbiome reveals distinct bile acid deconjugation and biotransformation potential in healthy and IBD individuals – Almut Heinken – bioRxiv

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses – Claire Duvallet – Nature Communications

Techniques

In vitro enteroid-derived three-dimensional tissue model of human small intestinal epithelium with innate immune responses – Ying Chen – PLOS ONE

More microbes

Galectin-3 impacts Cryptococcus neoformans infection through direct antifungal effects – Fausto Almeida – Nature Communications

Microbes in the news

Lemur study highlights role of diet in shaping gut microbiome – Erin Mckenney – Phys.Org

What Bacteria Can Tell Us About Human Evolution – Tara C Smith – Quanta Magazine

Duke launches new microbiome center, reflecting popularity of microbiome studies – Sean Cho – Duke Chronicle

Study shows first extensive and stable microbiome remodeling via B. infantis in infants – Weber Shandwick – EurekAlert

Air-eating bacteria found in Antarctica – Cosmos

The Microbes Making Themselves at Home on the Space Station – Marina Koren – The Atlantic

Microbes on the market

Breakthrough Evidence on Vomaris Bioelectric Technology’s Impact on Wound Biofilm Infection – PR Newswire

Precision Driven Health and Orion Health release Microbiome report – Voxy

Worldwide microbiome drugs market is likely to grow substantially by 2022 – Digital Journal

Science, career, and publishing

How to Keep Students in Science – Howard Hughes Medical Institute

An inclusive Research Education Community (iREC): Impact of the SEA-PHAGES program on research outcomes and student learning – David I Hanauer – PNAS

Pre-print: Assessing the Landscape of U.S. Postdoctoral Salaries – Rodoniki Athanasiadou – bioRxiv

Editorial: Great mentoring is key for the next generation of scientists – Nature

Amy’s non-microbiology picks

Organocalcium-mediated nucleophilic alkylation of benzene – Andrew S S Wilson – Science

December 6, 2017

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General microbiome

Review: The Role of High-Mobility Group Box-1 and Its Crosstalk with Microbiome in Rheumatoid Arthritis – Federico Biscetti – Mediators of Inflammation

Review: The human microbiota, infectious disease, and global health: challenges and opportunities – Abraham J. Waldman – ACS Infectious Diseases

Human respiratory microbiome

The lung microbiome in patients with pneumocystosis – J. Kehrmann – BMC Pulmonary Medicine

Review: Interplay between the lung microbiome and lung cancer – Qixing Mao – Cancer Letters

 
Human skin microbiome

Effect of alcohol-based hand rub on hand microbiome and hand skin health in hospitalized adult stem cell transplant patients: a pilot study – Pranab K. Mukherjee – Journal of the American Academy of Dermatology

Human vaginal microbiome

Cervicovaginal cytokines, sialidase activity and bacterial load in reproductive-aged women with intermediate vaginal flora – Mariana Morena de VieiraSantos-Greatti – Journal of Reproductive Immunology

Human gut microbiome

The gastrointestinal behavior of saponins and its significance for their bioavailability and bioactivities – Joaquín Navarro del Hierro – Journal of Functional Foods

Anthropometric and metabolic improvements in human type 2 diabetes after introduction of an Okinawan-based Nordic diet are not associated with changes in microbial diversity or SCFA concentrations – Fang Huang – International Journal of Food Sciences and Nutrition

Systematic review: ileoanal pouch microbiota in health and disease – J. P. Segal – Alimentary Pharmacology and Therapeutics

Systematic review: human gut dysbiosis induced by non-antibiotic prescription medications – Q. Le Bastard – Alimentary Pharmacology and Therapeutics

Review: The “Gut Feeling”: Breaking Down the Role of Gut Microbiome in Multiple Sclerosis – Samantha N. Freedman – Neurotherapeutics

Alternation of Gut Microbiota in Patients with Pulmonary Tuberculosis – Mei Luo – Frontiers in Microbiology

Postoperative changes of the microbiome: are surgical complications related to the gut flora? A systematic review – Ann-Kathrin Lederer – BMC Surgery

Animal experiments

Flos Lonicera Combined with Metformin Ameliorates Hepatosteatosis and Glucose Intolerance in Association with Gut Microbiota Modulation – Na R. Shin – Frontiers in Microbiology

Microbial Mechanistic Insight into the Role of Inulin in Improving Maternal Health in a Pregnant Sow Model – Pan Zhou – Frontiers in Microbiology

Review: Nano-Se Assimilation and Action in Poultry and Other Monogastric Animals: Is Gut Microbiota an Answer? – Peter F. Surai – Nanoscale Research Letters

Interactive effects of protein and carbohydrates on production of microbial metabolites in the large intestine of growing pigs – Marcin Taciak – Archives of Animal Nutrition

Flavonoid metabolite 3-(3-hydroxyphenyl)propionic acid formed by human microflora decreases arterial blood pressure in rats – Iveta Najmanová – Molecular Nutrition & Food Research

Animal microbiome

Review: The Microbiota Regulates Immunity and Immunologic Diseases in Dogs and Cats – Ian R. Tizard – Veterinary Clinics of North America: Small Animal Practice

Exploring fish microbial communities to mitigate emerging diseases in aquaculture – Irene de Bruijn – FEMS Microbiology Ecology

Bacterial community composition in the gut content of Lampetra japonica revealed by 16S rRNA gene pyrosequencing – Yu Zuo – Plos One

Review: Measuring the gut microbiome in birds: comparison of faecal and cloacal sampling – Elin Videvall – Molecular Ecology Resources

Social behaviour and gut microbiota in red-bellied lemurs (Eulemur rubriventer): In search of the role of immunity in the evolution of sociality – Aura Raulo – Journal of Animal Ecology

Gene expression in the chicken caecum is dependent on microbiota composition – Jiri Volf – Veterinary Research

The response of canine faecal microbiota to increased dietary protein is influenced by body condition – Jia Xu – BMC Veterinary Research

Plant, root, and soil microbiome

Soil microbial communities of three grassland ecosystems in the Bayinbuluke, China – Keqiang Shao – Canadian Journal of Microbiology

Simultaneous adaptation and maladaptation of tree populations to local rhizosphere microbial communities at different taxonomic scales – Richard A. Lankau – New Phytologist

Water and extremophile microbiome

Phylogenetic structure and metabolic properties of microbial communities in arsenic-rich waters of geothermal origin – Simona Crognale – Frontiers in Microbiology

Differences in planktonic microbial communities associated with three types of macrophyte stands in a shallow lake – Anikó Mentes – FEMS Microbiology Ecology

Probiotics / prebiotics

Designing synbiotics for improved human health – Sean M. Kearney – Microbial Biotechnology

Metabolomics

Blood serum metabolome of atopic dermatitis: Altered energy cycle and the markers of systemic inflammation – Aigar Ottas – Plos One

Comprehensive characterization of the in vitro and in vivo metabolites of limonin in human samples using LC-Q-TOF/MS – ShijiaLiu – Journal of Chromatography B

Anitha’s non-microbiology picks

Experiment demonstrates quantum mechanical effects from biological systems

IUCN Red List: Wild crops listed as threatened