September 22, 2017

Human Microbiome

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

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

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

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

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

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

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

 

Built Site Microbiome

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

 

Food Microbiome

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

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

 

Pathogen Research

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

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

 

Beneficial Microbes

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

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

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

 

Beneficial Molecules

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

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

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

 

Microbial Evolution

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

 

Environmental Microbiology

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

 

Bioinformatics, Genomics and Methodologies

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

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

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

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

 

Other

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

 

Advertisements

September 5, 2017

Jobs

Postdoctoral fellow in genomics of uncultured microbial parasites (SciLifeLab, Sweden) via Science Careers

Call for Assistant Professors and Professors (IST Austria, including for Life Sciences) via Science Careers

 

Human Microbiome

Characterization of cervico-vaginal microbiota in women developing persistent high-risk Human Papillomavirus infection – Monica Di Paola – Scientific Reports

Collection of non-meconium stool on fecal occult blood cards is an effective method for fecal microbiota studies in infants – Wendy S.W. Wong – Microbiome (BMC)

Influence of Pregnancy History on the Vaginal Microbiome of Pregnant Women in their First Trimester – Dimitrios Nasioudis – Scientific Reports

Gut microbiome in ADHD and its relation to neural reward anticipation – Esther Aarts – PLoS ONE

A cross-sectional comparative study of gut bacterial community of Indian and Finnish children – Shreyas V. Kumbhare – Scientific Reports

Dysbiosis contributes to chronic constipation development via regulation of serotonin transporter in the intestine – Hailong Cao – Scientific Reports

Review article: the human intestinal virome in health and disease – S. R. Carding – Alimentary Pharmacology and Therapeutics

Review: Organ-specific protection mediated by cooperation between vascular and epithelial barriers – Ilaria Spadoni – Nature Reviews Immunology

Review: Microbiota of chronic diabetic wounds: ecology, impact and potential for innovative healing strategies – Sonia Gonçalves Pereira – Frontiers in Microbiology

Animal Microbiome

Comparative Analysis of the Gut Microbiota Composition between Captive and Wild Forest Musk Deer – Yimeng Li – Frontiers in Microbiology

High-fat diet increases pain behaviors in rats with or without obesity – Zongbin Song – Scientific Reports

Research Highlights: The microbiota maintains oxygen balance in the gut – Irene Vacca – Nature Reviews Microbiology

Studying the Differences of Bacterial Metabolome and Microbiome in the Colon between Landrace and Meihua Piglets – Zhuang Chen – Frontiers in Microbiology

Dietary heme induces gut dysbiosis, worsens colitis and potentiates the development of adenomas in mice – Marco Constante – Frontiers in Microbiology

Antibiotic-induced perturbations in microbial diversity during post-natal development alters amyloid pathology in an aged APPSWE/PS1ΔE9 murine model of Alzheimer’s disease – Myles R. Minter – Scientific Reports

Enrichment of beneficial bacteria in the skin microbiota of bats persisting with white-nose syndrome – Virginie Lemieux-Labonté – Microbiome (BMC)

 

Environmental and Soil Microbiome

Composted Cattle Manure Increases Microbial Activity and Soil Fertility More Than Composted Swine Manure in a Submerged Rice Paddy – Suvendu Das – Frontiers in Microbiology

Fermentative Bacteria Influence the Competition between Denitrifiers and DNRA Bacteria – Eveline M. van den Berg – Frontiers in Microbiology

Beneficial microbes

Lactobacillus casei BL23 produces microvesicles carrying proteins associated with its probiotic effect – Ana P. Domínguez Rubio – Frontiers in Microbiology

Probiotic mixture Golden Bifido prevents neonatal Escherichia coli K1 translocation via enhancing intestinal defense – Qing Zeng – Frontiers in Microbiology

Protective Effect of Akkermansia muciniphila against Immune-mediated Liver Injury in a Mouse Model – Wenrui Wu – Frontiers in Microbiology

 

Methods

Review: Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing – Luisa W. Hugerth – Frontiers in Microbiology

Total rRNA-Seq analysis gives insight into bacterial, fungal, protozoal and archaeal communities in the rumen using an optimized RNA isolation method – Chijioke O. Elekwachi – Frontiers in Microbiology

Non-Microbiology picks

The contribution of Nintendo Wii Fit series in the field of health: a systematic review and meta-analysis – Julien Tripette – PeerJ

August 23, 2017

Human Microbiome

The vaginal microbiome of pregnant women is less rich and diverse, with lower prevalence of Mollicutes, compared to non-pregnant women – Aline C. Freitas – Scientific Reports

The IBD interactome: an integrated view of aetiology, pathogenesis and therapy – Heitor S. P. de Souza – Nature Reviews Gastroenterology & Hepatology

Changes in the intestinal microbiota following the administration of azithromycin in a randomised placebo-controlled trial among infants in south India – Edward P. K. Parker – Scientific Reports

High intake of dairy during energy restriction does not affect energy balance or the intestinal microflora compared to low dairy intake in overweight individuals in a Randomized Controlled Trial – Line Quist Bendtsen – Applied Physiology, Nutrition, and Metabolism

Metabolic and functional paths of lactic acid bacteria in plant foods: get out of the labyrinth – Pasquale Filannino –  Current Opinion in Biotechnology

Differences of lung microbiome in patients with clinically stable and exacerbated bronchiectasis – Min Kwang Byun – PLoS ONE

Precision Nutrition: A Review of Personalized Nutritional Approaches for the Prevention and Management of Metabolic Syndrome – Juan de Toro-Martín – Nutrients

 

Animal Microbiome

Soy Improves Cardiometabolic Health and Cecal Microbiota in Female Low-Fit Rats – Tzu-Wen L. Cross – Scientific Reports

Modulatory influence of segmented filamentous bacteria on transcriptomic response of gnotobiotic mice exposed to TCDD – Robert Stedtfeld – Frontiers in Microbiology

Comparative analysis of the gut microbiota composition between captive and wild forest musk deer – Yimeng Li – Frontiers in Microbiology

Modulation of gut microbiome composition and function in experimental colitis treated with Sulphasalazine – Haihui Zheng – Frontiers in Microbiology

Respiratory Commensal Bacteria Corynebacterium pseudodiphtheriticum Improves Resistance of Infant Mice to Respiratory Syncytial Virus and Streptococcus pneumoniae Superinfection – Paulraj Kanmani – Frontiers in Microbiology

 

Pathogen research

Whole-genome sequencing for national surveillance of Shigella flexneri – Marie Anne Chattaway – Frontiers in Microbiology

SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data – Lennard Epping –  BioRxiv

In Vitro Antibacterial Activity of Unconjugated and Conjugated Bile Salts on Staphylococcus aureus – Thippeswamy H. Sannasiddappa –  Frontiers in Microbiology

Environmental Microbiology

Alleviation of heavy metal stress in plants and remediation of soil by rhizosphere microorganisms – Jitendra Mishra – Frontiers in Microbiology

From surface to deep-sea: Bacterial distribution to polymetallic nodule fields at 4000 m in the Clarion-Clipperton Zone of the Pacific Ocean – Markus V. Lindh – Frontiers in Microbiology

Analysis of Microbial Functions in the Rhizosphere Using a Metabolic-Network Based Framework for Metagenomics Interpretation – Shany Ofaim – Frontiers in Microbiology

 

Bioinformatics

Contradictory Results: Low rate of index hopping on the Illumina HiSeq X platform – Tom van der Valk – BioRxiv

Analyzing contentious relationships and outlier genes in phylogenomics – Joseph F. Walker – BioRxiv

Other

Metabolic Reconstruction and Modeling Microbial Electrosynthesis – Christopher W. Marshall – Scientific Reports

Receptor Uptake Arrays For Vitamin B12, Siderophores And Glycans Shape Bacterial Communities – Steven A. Frank – BioRxiv

Diversity of microbiota associated with symptomatic and non-symptomatic bacterial wilt-diseased banana plants determined using 16S rRNA metagenome sequencing – Nurul Shamsinah Mohd Suhaimi – World Journal of Microbiology and Biotechnology

News

Antarctic mystery microbe could tell us where viruses came from – Michael Marshall – New Scientist

Even the Eye Has a Microbiome – Jeff Lyon – JAMA

The Surprising Things Your Microbiome Reveals About You – Ashley Lewis – Readers Digest

Linking mental health and the gut microbiome – MedicalXpress

 

Non-microbiology picks

How to share data for collaboration – Shannon E Ellis – PeerJ preprints

 

August 22, 2017

Jobs

Postdoctoral Research Fellow in Microbiology/Molecular Ecology : Bremen, Germany (Soil microbial community interactions)

Postdoctoral Training Fellow : London, United Kingdom (M. tuberculosis and immunity)

 

Human Microbiome

Review: Human genetic variation and the gut microbiome in disease – Andrew Brantley Hall – Nature Reviews Genetics

Long-term taxonomic and functional divergence from donor bacterial strains following fecal microbiota transplantation in immunocompromised patients – Eli L. Moss – PLoS ONE

Intestinal colonisation patterns in breastfed and formula-fed infants during the first 12 weeks of life reveal sequential microbiota signatures – Harro M. Timmerman  – Scientific Reports

A prospective analysis of mucosal microbiome-metabonome interactions in colorectal cancer using a combined MAS 1HNMR and metataxonomic strategy – James Kinross – Scientific Reports

Inflammatory colonic innate lymphoid cells are increased during untreated hiv-1 infection and associated with markers of gut dysbiosis and mucosal immune activation – Stephanie Dilon- JAIDS Journal of Acquired Immune Deficiency Syndromes

The Maternal Infant Microbiome: Considerations for Labor and Birth – Alexis Dunn – MCN, American Journal of Maternal Child Nursing

Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome – Francesco Beghini – The ISME Journal

 

Animal Microbiome

The Maturing Development of Gut Microbiota in Commercial Piglets during the Weaning Transition – Limei Chen – Frontiers in Microbiology

Moderate-intensity exercise affects gut microbiome composition and influences cardiac function in myocardial infarction mice – Zuheng Liu – Frontiers in Microbiology  

Unveiling bifidobacterial biogeography across the mammalian branch of the tree of life – Christian Milani – The ISME Journal

 

Probiotics

In Vitro Evaluation of the Impact of the Probiotic E. coli Nissle 1917 on Campylobacter jejuni’s Invasion and Intracellular Survival in Human Colonic Cells – Yosra A. Helmy – Frontiers in Microbiology

 

Food Microbiology

Cell surface properties of Lactococcus lactis reveal milk protein binding specifically evolved in dairy isolates – Mariya Tarazanova – Frontiers in Microbiology

 

Pathogen Research

Metagenomic sequencing to replace semi-quantitative urine culture for detection of urinary tract infections: a proof of concept – Victoria A. Janes – BioRxiv

Burkholderia cenocepacia Infections in Cystic Fibrosis Patients: Drug Resistance and Therapeutic Approaches – Viola C. Scoffone –  Frontiers in Microbiology

 

Environmental Microbiome

Marine Microbial Gene Abundance and Community Composition in Response to Ocean Acidification and Elevated Temperature in Two Contrasting Coastal Marine Sediments – Ashleigh R. Currie – Frontiers in Microbiology

Heat Stress Dictates Microbial Lipid Composition along a Thermal Gradient in Marine Sediments – Miriam Sollich – Frontiers in Microbiology

Actinobacterial Rare Biospheres and Dark Matter Revealed in Habitats of the Chilean Atacama Desert – Hamidah Idris – Scientific Reports

A pivotal role for ocean eddies in the distribution of microbial communities across the Antarctic Circumpolar Current – – PLoS ONE

Microbial community analysis of apple rhizosphere around Bohai Gulf – Jihang Jiang – Scientific Reports

From virus isolation to metagenome generation for investigating viral diversity in deep-sea sediments – Cinzia Corinaldesi – Scientific Reports

 

Bioinformatics

PANINI: Pangenome Neighbor Identification for Bacterial PopulationsKhalil Abudahab  – BioRxiv

 

 

Non-Microbiology picks

The prehistory of biology preprints: a forgotten experiment from the 1960s – Matthew Cobb – PeerJ preprints

August 19, 2017

Today, a short Digest but with interesting features: effects of intestinal cleanout on microbiota, changes in K vitamin derivatives in human, reviews about Streptococcus group B and effect of FMT on Clostridium difficile, and more.

Human microbiome

Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment – Julia Fukuyama – PLoS Computational Biology

Research Highlight: Gut microbiota: Gas-induced GLP1 release – David Holmes – Nature Reviews Endocrinology

Maternal obesity is associated with gut microbial metabolic potential in offspring during infancy  – Tomás Cerdó – Journal of Physiology and Biochemistry

Fecal concentrations of bacterially derived vitamin K forms are associated with gut microbiota composition but not plasma or fecal cytokine concentrations in healthy adults – J Philip Karl – The American Journal of Clinical Nutrition

Temporal Stability of the Healthy Human Skin Microbiome Following Dead Sea Climatotherapy – Michael Brandwein – Acta Dermato-Venereologica

Review: Intrinsic Maturational Neonatal Immune Deficiencies and Susceptibility to Group B Streptococcus Infection – Michelle L. Korira – Clinical Microbiological Reviews

Systematic review: Faecal microbiota transplantation for Clostridium difficile infection: a multicentre study of non-responders – Paul Moayyedi – Medical Journal of Australia

 

Forensic microbiome

Daily thanatomicrobiome changes in soil as an approach of postmortem interval estimation: An ecological perspective – Joe Adserias Garriga – Forensic Science International

 

Animal microbiome

Correlations of age and growth rate with microbiota composition in Atlantic cod (Gadus morhua) larvae – Ly T. T. Trinh – Scientific Reports

Microbial community composition along the digestive tract in forage- and grain-fed bison – Gaddy T. Bergmann – BMC Veterinary Research

The effect of storage at ambient temperature on the feline fecal microbiota – Moran Tal – BMC Veterinary Research

Performance, biochemical and haematological responses, and relative organ weights of laying hens fed diets supplemented with prebiotic, probiotic and synbiotic  – Shirley Gee Hoon Tang – BMC Veterinary Research

Mosapride Stabilizes Intestinal Microbiota to Reduce Bacterial Translocation and Endotoxemia in CCl4-Induced Cirrhotic Rats – Hong Xu – Digestive Diseases and Sciences

Transition of the intestinal microbiota of cats with age – Hiroaki Masuoka – PLoS ONE

 

Pathogen research

Draft Genome Sequences of Two Enterobacter cloacae subsp. cloacae Strains Isolated from Australian Hematology Patients with Bacteremia – Lex E. X. Leonga – Genome Announcements

The impact of the Staphylococcus aureus virulome on infection in a developing country: a cohort study – Marthe Lebughe – Frontiers in Microbiology

 

 

Bioactive compounds

Regulative effects of curcumin spice administration on gut microbiota and its pharmacological implications – Liang Shen – Food & Nutrition Research

Identification of Secondary Metabolite Gene Clusters in the Pseudovibrio Genus Reveals Encouraging Biosynthetic Potential toward the Production of Novel Bioactive Compounds – Lynn M. Naughton – Frontiers in Microbiology

 

Other

Characterizing a thermostable Cas9 for bacterial genome editing and silencing – Ioannis Mougiakos – BioRxiv

Determination of geochemical bio-signatures in Mars-like basaltic environments – Karen Olsson-Francis – Frontiers in Microbiology

 

August 18, 2017

Human Microbiome: Gut

Worse inflammatory profile in omnivores than in vegetarians associates with the gut microbiota composition – Ana Carolina Franco-de-Moraes – Diabetology & Metabolic Syndrome (BMC)

News and views: Spondyloarthropathies: Ruminococcus on the horizon in arthritic disease – Lars Vereecke & Dirk Elewaut – Nature Reviews Rheumatology

Increased human intestinal barrier permeability plasma biomarkers zonulin and FABP2 correlated with plasma LPS and altered gut microbiome in anxiety or depression – Bruce R Stevens – Gut (BMJ)

 

Human Microbiome: Respiratory tract

Strain level Streptococcus colonization patterns during the first year of life – Meredith Wright – Frontiers in Microbiology

State of the art: The airway microbiota in early cystic fibrosis lung disease – Katherine B. Frayman – Pediatric Pulmonology (Wiley)

 

Human Microbiome: Mouth

The saliva microbiome profiles are minimally affected by collection method or DNA extraction protocols – Yenkai Lim – Scientific Reports

 

Built microbiome

Bacterial diversity among four healthcare-associated institutes in Taiwan – Chang-Hua Chen – Scientific Reports

 

Animal Microbiome

Host Ecology Rather Than Host Phylogeny Drives Amphibian Skin Microbial Community Structure in the Biodiversity Hotspot of Madagascar – Molly C. Bletz – Frontiers in Microbiology

Microbiota in the coelomic fluid of two common coastal starfish species and characterization of an abundant Helicobacter-related taxon – Satoshi Nakagawa – Scientific Reports

Stability in metabolic phenotypes and inferred metagenome profiles before the onset of colitis-induced inflammation – M. Glymenaki – Scientific Reports

Microbiome-mediated neutrophil recruitment via CXCR2 and protection from amebic colitis – Koji Watanabe – PLoS Pathogens

Gut microbiota of a long-distance migrant demonstrates resistance against environmental microbe incursions – Alice Risely – Molecular Ecology (Wiley)

Unraveling the Fecal Microbiota and Metagenomic Functional Capacity Associated with Feed Efficiency in Pigs – Hui Yang –  Frontiers in Microbiology

Research Highlight: Tell me who you are and I’ll tell you what you eat – Irene Vacca – Nature Reviews Microbiology

Mucus organisation is shaped by colonic content; a new view – J. B. J. Kamphuis – Scientific Reports

Effect of barley supplementation on the fecal microbiota, caecal biochemistry, and key biomarkers of obesity and inflammation in obese db/db mice – Jose F. Garcia-Mazcorro – European Journal of Nutrition

Associations Between Nutrition, Gut Microbiome, and Health in A Novel Nonhuman Primate Model – Jonathan B. Clayton – BioRxiv

Milk microbiome and bacterial load following dry cow therapy without antibiotics in dairy cows with healthy mammary gland – Erika C. R. Bonsaglia –  Scientific Reports

Space-type radiation induces multimodal responses in the mouse gut microbiome and metabolome – David Casero – Microbiome (BMC)

 

Probiotics, Prebiotics and Synbiotics

Secretome of intestinal bacilli: a natural guard against pathologies – Olga N. Ilinskaya – Frontiers in Microbiology

The Probiotic Combination of Bifidobacterium longum subsp. infantis CECT 7210 and Bifidobacterium animalis subsp. lactis BPL6 Reduces Pathogen Loads and Improves Gut Health of Weaned Piglets Orally Challenged with Salmonella Typhimurium – Emili Barba-Vidal –  Frontiers in Microbiology

Bifidobacterium pseudocatenulatum LI09 and Bifidobacterium catenulatum LI10 attenuate D-galactosamine-induced liver injury by modifying the gut microbiota – Daiqiong Fang – Scientific Reports

Administration of two probiotic strains during early childhood does not affect the endogenous gut microbiota composition despite probiotic proliferation – Martin Frederik Laursen – BMC Microbiology

A randomized synbiotic trial to prevent sepsis among infants in rural India – Pinaki Panigrahi – Nature

 

Pathogen Research

High-Resolution Microbiome Profiling for Detection and Tracking of Salmonella enterica – Christopher J. Grim – Frontiers in Microbiology

In situ architecture, function, and evolution of a contractile injection system – Désirée Böck – Science

 

Bioactive compounds

Onion Peel Ethylacetate Fraction and Its Derived Constituent Quercetin 4`-O-Β-D Glucopyranoside Attenuates Quorum Sensing Regulated Virulence and Biofilm Formation – Hanan AlYousef – Frontiers in Microbiology

Promysalin is a salicylate-containing antimicrobial with a cell-membrane-disrupting mechanism of action on Gram-positive bacteria – Rahul D. Kaduskar – Scientific Reports

 

Bacteriophages

Selection of Functional Quorum Sensing Systems by Lysogenic Bacteriophages in Pseudomonas aeruginosa  – Miguel-Angel Saucedo-Mora – Frontiers in Microbiology

Characterization and formulation into solid dosage forms of a novel bacteriophage lytic against Klebsiella oxytoca – Teagan L. Brown – PLoS ONE

 

Soil and Environmental Microbiology

Distinct Seasonal Patterns of Bacterioplankton Abundance and Dominance of Phyla α-Proteobacteria and Cyanobacteria in Qinhuangdao Coastal Waters Off the Bohai Sea – Yaodong He – Frontiers in Microbiology

The Rhizosphere Bacterial Microbiota of Vitis vinifera cv. Pinot Noir in an Integrated Pest Management Vineyard – Giorgia Novello – Frontiers in Microbiology

Perspective: How microbes survive in the open ocean – Jonathan P. Zehr – Science

Ecophysiology of freshwater Verrucomicrobia inferred from metagenome-assembled genomes – Shaomei He – BioRxiv

Impact of litter quantity on the soil bacteria community during the decomposition of Quercus wutaishanica litter – Quanchao Zeng – PeerJ preprints

Microbial phylogeny determines transcriptional response of resistome to dynamic composting processes – Cheng Wang – Microbiome (BMC)

 

Bioinformatics and Genomics

Abundance-based reconstitution of microbial pan-genomes from whole-metagenome shotgun sequencing data – Florian Plaza Oñate – BioRxiv

Evaluation of the impact of Illumina error correction tools on de novo genome assembly – Mahdi Heydari –  BMC Bioinformatics

 

Non-microbiology picks

A pathology atlas of the human cancer transcriptome – Mathias Uhlen – Science

Increasing Symptoms in Irritable Bowel Symptoms With Ingestion of Galacto-Oligosaccharides Are Mitigated by α-Galactosidase Treatment – C J Tuck – The American Journal of Gastroenterology

Lessons from between the white lines for isolated data scientists – Benjamin S Baumer ​- PeerJ preprints

 

July 28, 2017

Microbiome Research

High spatial and temporal variations of microbial community along the southern catfish gastrointestinal tract: insights into dynamic food digestion – Zhimin Zhang – Frontiers in Microbiology

Host ecology rather than host phylogeny drives amphibian skin microbial community structure in the biodiversity hotspot of Madagascar – Molly C. Bletz – Frontiers in Microbiology

A pilot study demonstrating the altered gut microbiota functionality in stable adults with Cystic Fibrosis – F. Fouhy  – Scientific Reports

Research Highlight: Baby bugs can’t stop the thugs… – Yvonne Bordon – Nature Reviews Immunology

Chondroitin sulfate disaccharides modified the structure and function of the murine gut microbiome under healthy and stressed conditions – Fang Liu – Scientific Reports

Nasopharyngeal microbiome in premature infants and stability during rhinovirus infection – Geovanny F Perez – Journal of Investigative Medicine

Microbiomarkers in inflammatory bowel diseases: caveats come with caviar – Felix Sommer – Gut (BMJ)

Kynurenines: Tryptophan’s metabolites in exercise, inflammation, and mental health – Igor Cervenka – Science

 

Probiotics, Prebiotics and bioactive compounds

Protection mechanism of Clostridium butyricum against Salmonella enteritidis infection in broilers – Xiaonan Zhao – Frontiers in Microbiology

Isolation of human intestinal bacteria capable of producing the bioactive metabolite isourolithin A from ellagic acid – Maria V. Selma – Frontiers in Microbiology

Anti-obesity and anti-inflammatory effects of synthetic acetic acid vinegar and Nipa vinegar on high-fat-diet-induced obese mice – Boon Kee Beh – Scientific Reports

Antimicrobial activities of widely consumed herbal teas, alone or in combination with antibiotics: an in vitro study – Mayram Hacioglu – PeerJ

 

Food microbiology

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

 

Bioinformatics

PhaMers identifies novel bacteriophage sequences from thermophilic hot springs – Jonathan Deaton -BioRxiv

PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens – Philipp N. Spahn – BioRxiv

 

Pathogens

PyroTyping, a novel pyrosequencing-based assay for Mycobacterium tuberculosis genotyping –  B. Molina-Moya – Scientific Reports

Vibrio cholerae genomic diversity within and between patients – Inès Levade – BioRxiv

Experimental evolution and genome data analysis of Candida albicans reveals cryptic bacteria in single yeast colonies – Danielle C. F. Bruno – BioRxiv

Comments and Opinion: The theory of disappearing microbiota and the epidemics of chronic diseases – Martin J. Blaser – Nature Reviews Immunology

Bactericidal and anti-biofilm effects of polyhexamethylene biguanide in models of intracellular and biofilm of Staphylococcus aureus isolated from bovine mastitis -Nor Fadhilah Kamaruzzaman – Frontiers in Microbiology

Clinicians should assess the benefits and risks of using bezlotoxumab for reducing the risk of recurrent Clostridium difficile infection – Habiba Hassouna – Evidence based Medicine

Whole RNA-sequencing and transcriptome assembly of Candida albicans and Candida africana under chlamydospore-inducing conditions – Domenico Giosa – Genome Biology and Evolution

 

Soil/Environmental Microbiome

The rhizosphere bacterial microbiota of Vitis vinifera cv. Pinot Noir in an integrated pest management vineyard – Giorgia Novello – Frontiers in Microbiology

Microbial Community Structure and the Persistence of Cyanobacterial Populations in Salt Crusts of the Hyperarid Atacama Desert from Genome-Resolved Metagenomics – Kari M. Finstad – Frontiers in Microbiology

Long term fertilization structures Bacterial and Archaeal communities along soil depth gradient in a paddy soil – Yunfu Gu – Frontiers in Microbiology

Drought and host selection influence bacterial community dynamics in the grass root microbiome – Dan Naylor – The ISME Journal

 

Other (Non-microbiology picks)

Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus – Yuki Yoshida – Plos Biology