Author Archives: Anitha Isaiah

May 31, 2019

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Happy Friday!! Today’s digest contains reviews on the role of microbiota in immune memory formation and bioinformatic tools for soil microbiome analysis

General microbiome

*Review: The microbiome and immune memory formation – Kathy D. McCoy – Immunology and Cell biology

Preprint – Investigating Transfusion-Related Sepsis using Culture-Independent Metagenomic Sequencing – Emily Crawford – bioRxiv

Animal experiments

Response of Fish Gut Microbiota to Toxin-Containing Cyanobacterial Extracts: A Microcosm Study on the Medaka (Oryzias latipes) – Sébastien Duperron – Environmental Science & Technology Letters

Plant, root, and soil microbiome

*Book chapter : Bioinformatics Tools for Soil Microbiome Analysis – Rama Kant Dubey – Part of the SpringerBriefs in Environmental Science book series

Book chapter: Belowground Microbial Communities: Key Players for Soil and Environmental Sustainability – Rama Kant Dubey – Part of the SpringerBriefs in Environmental Science book series

Book chapter: Single-Cell Genomics and Metagenomics for Microbial Diversity Analysis – Rama Kant Dubey – Part of the SpringerBriefs in Environmental Science book series

In vitro digestion and fermentation of three polysaccharide fractions from Laminaria japonica and their impact on lipid metabolism-associated human gut microbiota – Jie Gao – Journal of Agricultural and Food Chemistry

Preprint – Biogeographical patterns in soil bacterial communities across the Arctic region – Lucie A Malard – bioRxiv

Water and extremophile microbiome

In search of microbial indicator taxa: shifts in stream bacterial communities along an urbanization gradient – Marie Simonin – Environmental Microbiology

Phages and viruses

Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages – Jakub Barylski – Systematic Biology

Techniques

Protocol: Analysis of Microbial Siderophores by Mass Spectrometry – Tomas Pluhacek – Part of the Methods in Molecular Biology

Review: A guide to visualizing the spatial epigenome with super‐resolution microscopy – Jianquan Xu – The FEBS Journal

January 25, 2019

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General microbiome

A Comparison of Homogenization vs. Enzymatic Lysis for Microbiome Profiling in Clinical Endoscopic Biopsy Tissue Samples – A Comparison of Homogenization vs. Enzymatic Lysis for Microbiome Profiling in Clinical Endoscopic Biopsy Tissue Samples – Chao Zhang – Frontiers in Microbiology

Review: Exploring the Human Microbiome: The Potential Future Role of Next-Generation Sequencing in Disease Diagnosis and Treatment – Muneer Ahmad Malla – Frontiers in Immunology

The microbiome and its relevance in complex wounds – Francesco Drago – European Journal of Dermatology

Commentary: A Link between the Gut and Bone: Bone Health Impacted by Changes in Gut Microbiota – Larry J.Suva – The American Journal of Pathology

Pregnancy and early life

Feeding intolerance alters the gut microbiota of preterm infants – Zhenya Yuan – PLOS ONE

Multi-site human microbiome

Review: A correlation between intestinal microbiota dysbiosis and osteoarthritis – Marta AnnaSzychlinska – Heliyon

Human respiratory microbiome

A survey of fungal microbiota in airways of healthy volunteer subjects from Puglia (Apulia), Italy – Giovanna Elisiana Carpagnano – BMC Infectious Diseases

The Association Between Disease Severity and Microbiome in Chronic Rhinosinusitis – Darren Rom – The Laryngoscope

Review: Microbiota and asthma: Clinical implications – Konstantinos Katsoulis – Respiratory Medicine

Human oral microbiology

Metagenome sequencing-based strain-level and functional characterization of supragingival microbiome associated with dental caries in children – Nezar Noor Al-Hebshi – Journal of Oral Microbiology

Periodontal pathogens are a risk factor of oral cavity squamous cell carcinoma, independent of tobacco and alcohol and human papillomavirus – Ian Ganly – International Journal of Cancer

Human gut microbiome

Review: Role of diet and gut microbiota on colorectal cancer immunomodulation – Carolina Vieira De Almeida – World Journal of Gastroenterology

Review: Targeting obesity management through gut microbiota modulation by herbal products: A systematic review – Hanieh-SadatEjtahed – Complementary Therapies in Medicine

Identification of Specific Oral and Gut Pathogens in Full Thickness Colon of Colitis Patients: Implications for Colon Motility – Vasudevan Dinakaran – Frontiers in Microbiology

Animal experiments

Fecal microbiota changes associated with dehorning and castration stress primarily affects light-weight dairy calves – Raies A. Mir – PLOS ONE

Advanced Age Impairs Intestinal Antimicrobial Peptide Response and Worsens Fecal Microbiome Dysbiosis Following Burn Injury in Mice – Elizabeth G Wheatley – Shock

Effects of drought‐stressed temperate forage legumes on the degradation and the rumen microbial community in vitro – Susanne Riede – Journal of Animal Physiology and Animal Nutrition

Bacillus amyloliquefaciens ameliorates Dextran Sulfate Sodium-Induced Colitis by Improving Gut Microbial Dysbiosis in Mice Model – Guangtian Cao – Frontiers in Microbiology

Bacillus subtilis 29784 induces a shift in broiler gut microbiome toward butyrate-producing bacteria and improves intestinal histomorphology and animal performance – Vincent Jacquier – Poultry Science

Green Tea Polyphenols Modify the Gut Microbiome in db/db Mice as Co‐abundance Groups Correlating with the Blood Glucose Lowering Effect – Tingting Chen – Molecular Nutrition and Food Research

Influence of Porphyromonas gingivalis in gut microbiota of streptozotocin‐induced diabetic mice – Anri Ohtsu – Oral diseases

Plant, root, and soil microbiome

Nanopore Sequencing as a Surveillance Tool for Plant Pathogens in Plant and Insect Tissues – Aline Bronzato Badial – Plant Disease

Rhizosphere Microbiomes from Root Knot Nematode Non-infested Plants Suppress Nematode Infection – Dongmei Zhou – Microbial Ecology

Water and extremophile microbiome

Copper Affects Composition and Functioning of Microbial Communities in Marine Biofilms at Environmentally Relevant Concentrations – Natàlia Corcoll – Frontiers in Microbiology

Bark and Grape Microbiome of Vitis vinifera: Influence of Geographic Patterns and Agronomic Management on Bacterial Diversity – Nicola Vitulo – Frontiers in Microbiology

Bacterial diversity in typical abandoned multi-contaminated nonferrous metal(loid) tailings during natural attenuation – Jian-liLiu – Environmental Pollution

Long- and short-chain AHLs affect AOA and AOB microbial community composition and ammonia oxidation rate in activated sludge – Jie Gao – Journal of Environmental Sciences

Food microbiology

Dominance of wine Saccharomyces cerevisiae strains over S. kudriavzevii in industrial fermentation competitions is related to an acceleration of nutrient uptake and utilization – Javier Alonso‐del‐Real – Environmental Microbiology

Phages and viruses

Commentary : Going Viral: a Novel Role for Bacteriophage in Colorectal Cancer – Scott A. Handley – mBio

December 19, 2018

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Toady’s digest features research that gives insight on the formation of lower respiratory tract microbiota in infants and the differential role of TL1A in acute and chronic colitis.

General microbiome

Profiling mycobacterial communities in pulmonary nontuberculous mycobacterial disease – Steven A. Cowman – PLOS ONE


Pregnancy and early life

*Early-Life Formation of the Microbial and Immunological Environment of the Human Airways – CélinePattaroni – Cell Host & Microbe


Human reproductive microbiome

Review: Uterine microbiome—low biomass and high expectations – Iolanda Garcia-Grau – Biology of Reproduction


Human respiratory microbiome

Review: Microbiome and disease in the upper airway – Jivianne T. Lee – Current Opinion in Allergy and Clinical Immunology


Human gut microbiome

Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa – Cormac Brian Fitzgerald – BMC Genomics

Retrospective analysis of long-term gastrointestinal symptoms after Clostridium difficile infection in a nonelderly cohort – Tamar F. Barlam – PLOS ONE

Review: Gut microbiota: a potential manipulator for host adipose tissue and energy metabolism – Bohan Rong – The Journal of Nutritional Biochemistry


Animal experiments

*Microbiota-Induced TNF-like Ligand 1A Drives Group 3 Innate Lymphoid Cell-Mediated Barrier Protection and Intestinal T Cell Activation during Colitis – Jim G.Castellanos – Immunity

LC–MS-Based Metabolomics and Lipidomics Study of High-Density-Lipoprotein-Modulated Glucose Metabolism with an apoA-I Knockout Mouse Model – Jia Liu – Journal of Proteome Research

TLR4 deficiency reduces pulmonary resistance to Streptococcus pneumoniae in gut microbiota-disrupted mice – Hongyan Wang – PLOS ONE

Zengye decoction induces alterations to metabolically active gut microbiota in aged constipated rats – Deliang Liu – Biomedicine & Pharmacotherapy


Animal microbiome

Floral and Foliar Source Affect the Bee Nest Microbial Community – Jason A. Rothman – Microbial Ecology

Effects of urbanization on the foraging ecology and microbiota of the generalist seabird Larus argentatus – Matthew Fuirst – PLOS ONE

Disruption of the microbiota affects physiological and evolutionary aspects of insecticide resistance in the German cockroach, an important urban pest – Jose E. Pietri _ PLOS ONE

The composition and structure of the intestinal microflora of Anguilla marmorata at different growth rates: a deep sequencing study – Mao Lin – Journal of Applied Microbiology

Review: Composition and functional roles of the gut microbiota in mosquitoes – Michael R. Strand – Current Opinion in Insect Science

Review: Transcriptomic analyses uncover emerging roles of mucins, lysosome/secretory addressing and detoxification pathways in insect midguts – Walter R. Terra – Current Opinion in Insect Science

Terrestriality and bacterial transfer: a comparative study of gut microbiomes in sympatric Malagasy mammals – Amanda C. Perofsky – The ISME Journal


Plant, root, and soil microbiome

Dead or alive; or does it really matter? Level of congruency between trophic modes in total and active fungal communities in High Arctic soil – Magdalena Wutkowska – Frontiers in Microbiology


Water and extremophile microbiome

Reduced TCA cycle rates at high hydrostatic pressure hinder hydrocarbon degradation and obligate oil degraders in natural, deep-sea microbial communities – Alberto Scoma- The ISME Journal

Evidence of selective pressure in whale fall microbiome proteins and its potential application to industry – Robert Cardoso deFreitas – Marine Genomics

AgNPs change microbial community structures of wastewater – Yuting Guo – Frontiers in Microbiology

Performance and microbial community of an electric biological integration reactor (EBIR) for treatment of wastewater containing ibuprofen – Yan Feng – Bioresource Technology

 

Food microbiology

Spoilage microbial community profiling by 16S rRNA amplicon sequencing of modified atmosphere packaged live mussels at cold storage temperature – Olumide A.Odeyemi – Food Research International

Genomic resolution of bacterial populations in saccharin and cyclamate degradation – YuDeng – Science of The Total Environment


Phages and viruses

Nanopore-based detection and characterization of yam viruses – Denis Filloux – Scientific Reports


Metabolomics

Active Acupoints Differ from Inactive Acupoints in Modulating Key Plasmatic Metabolites of Hypertension: A Targeted Metabolomics Study – Mingxiao Yang – Scientific Reports


Techniques

Review: Quantifying microbial chatter: scanning electrochemical microscopy as a tool to study interactions in biofilms – Sophie E. Darch – Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences

Metabolic Fingerprinting of Bacteria Exposed to Nanomaterials, Using Online Databases, NMR, and High-Resolution Mass Spectrometry – Theodoros G. Chatzimitakos – Nanotoxicity

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Science, publishing, and career

Commentary : Communicating health risks in science publications: time for everyone to take responsibility – Alexandra L. J. Freeman – BMC Medicine

Could a double blind peer review process reduce gender bias?

Preprint: The Case For and Against Double-blind Reviews – Amelia R – bioRxiv

December 12, 2018

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Today’s digest features a citizen science project which describes the two compositional patterns (stomatotypes) in the oral microbiota of adolescents. The study also explores the role of different factors like hygeine, diet, drinking water in shaping the oral microbiota. Enjoy!

Human oral microbiome

*Citizen science charts two major “stomatotypes” in the oral microbiome of adolescents and reveals links with habits and drinking water composition – Jesse R. Willis – Microbiome

Uncovering complex microbiome activities via metatranscriptomics during 24 hours of oral biofilm assembly and maturation – Anna Edlund – Microbiome

Human gut microbiome

Review: Gut microbiota and inflammation in chronic kidney disease and their roles in the development of cardiovascular disease – Emine M. Onal – Hypertension Research

Animal experiments 

Zinc-amino-acid supplementation alters yearling ram rumen bacterial communities but zinc sulfate supplementation does not – Suzanne L Ishaq – Journal of Animal Science

Administration of antibiotics contributes to cholestasis in pediatric patients with intestinal failure via the alteration of FXR signaling – Yongtao Xiao – Experimental & Molecular Medicine

Intestinal microbiota mediates the susceptibility to polymicrobial sepsis‐induced liver injury by granisetron generation in mice – Shenhai Gong – Hepatology

Rumen microbiome in dairy calves fed copper and grape-pomace dietary supplementations: Composition and predicted functional profile – Filippo Biscarini – PLOS ONE

Plant, root, and soil microbiome

Rhizosheath microbial community assembly of sympatric desert speargrasses is independent of the plant host – Ramona Marasco – Microbiome

Water and extremophile microbiome

Review: Petroleum Hydrocarbon-Degrading Bacteria for the Remediation of Oil Pollution Under Aerobic Conditions: A Perspective Analysis – Xingjian Xu – Frontiers in Microbiology

Predominance and high diversity of genes associated to denitrification in metagenomes of subantarctic coastal sediments exposed to urban pollution – Priscila A. Calderoli – PLOS ONE

Gene probing reveals the widespread distribution, diversity and abundance of isoprene-degrading bacteria in the environment – Ornella Carrión – Microbiome

Rock substrate rather than black stain alterations drives microbial community structure in the passage of Lascaux Cave – Lise Alonso – Micrtobiome

Deep-sea anthropogenic macrodebris harbours rich and diverse communities of bacteria and archaea – Lucy C. Woodall – PLOS ONE

April 26, 2017

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General microbiome

Baseline urine metabolic phenotype in patients with severe alcoholic hepatitis and its association with outcome – Jaswinder Singh Maras – Hepatology communications

Checkpoint Checkmate: Microbiota Modulation of Cancer Immunotherapy – Eric C. Keen – Clinical chemistry

Metagenomics Analysis of Bacterial Population of Tympanosclerotic Plaques and Cholesteatomas – M. Tayyar Kalcioglu – Otolaryngology–Head and Neck Surgery

Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults – Xiaozhou Fan – Microbiome

Pregnancy and early life

Preterm infants have distinct microbiomes not explained by mode of delivery, breastfeeding duration or antibiotic exposure – Cecilie Dahl – International Journal of Epidemiology

Gut microbial functional maturation and succession during human early life – Tomás Cerdó – Environmental microbiology

Human respiratory microbiome

Modelling upper respiratory tract diseases: getting grips on host-microbe interactions in chronic rhinosinusitis using in vitro technologies – Charlotte De Rudder Microbiome

Human skin microbiome

Skin microbiota and allergic symptoms associate with exposure to environmental microbes – Jenni Lehtimäki – PNAS

Human gut microbiome

Review :Dysbiosis in Functional Bowel Disorders – Paul Enck – Annals of Nutrition and Metabolism

Review: Inflammatory Bowel Disease and Immunonutrition: Novel Therapeutic Approaches Through Modulation of Diet and the Gut Microbiome – Larissa S Celiberto- Immunology

Comment : Richness and ecosystem development across faecal snapshots of the gut microbiota – Gwen Falony – Nature microbiology
Effects of gut microbiota manipulation on ex vivo lipolysis in human abdominal subcutaneous adipocytes – Johan W. E. Jocken – Adipocyte

Chronic kidney disease, uremic milieu, and its effects on gut bacterial microbiota dysbiosis – Lee D Chaves – American Journal of Physiology-Renal Physiology

Microbiota transplantation: concept, methodology and strategy for its modernization – Faming Zhang – Protein & Cell

The effects of sequencing platforms on phylogenetic resolution in 16 S rRNA gene profiling of human feces – Tae Woong Whon – Scientific Data

Gut Microbiota: From Microorganisms to Metabolic Organ Influencing Obesity – Richard W. Stephens – Obesity

Gut Microbes and Health: A Focus on the Mechanisms Linking Microbes, Obesity, and Related Disorders – Marialetizia Rastelli – Obesity

Review article: Impact of dietary gut microbial metabolites on the epigenome – Clarissa Gerhauser – Philosophical. Transactions of the Royal Society B

Animal experiments 

Gut Microbiota-Derived Tryptophan Metabolites Modulate Inflammatory Response in Hepatocytes and Macrophages – Cell Reports – Smitha Krishnan

Modulation of Active Gut Microbiota by Lactobacillus rhamnosus GG in a Diet Induced Obesity Murine Model – Yosep Ji – Frontiers in Microbiology

Lactobacilli Are Prominent Members of the Microbiota Involved in the Ruminal Digestion of Barley and Corn – Hee E. Yang

Intestinal microbiome of broiler chickens after use of nanoparticles and metal salts – Еlena Yausheva – Environmental Science and Pollution Research

Distinct consequences of amoxicillin and ertapenem exposure in the porcine gut microbiome – Sheila Connelly – Anaerobe

Indole, a Signaling Molecule Produced by the Gut Microbiota, Negatively Impacts Emotional Behaviors in Rats – Mathilde Jaglin – Frontiers in Neuroscience

Animal microbiome 

Microbiome of Total Versus Live Bacteria in the Gut of Rex Rabbits – Xiangchao Fu – Frontiers in Microbiology

Plant, root, and soil microbiome

Inferring Roles in Defense from Metabolic Allocation of Rice Diterpenoids – Xuan Lu – The Plant Cell

Genotypic variation in Pinus radiata responses to nitrogen source are related to changes in the root microbiome – Marta Gallart – FEMS Microbiology Ecology

Competition and habitat filtering jointly explain phylogenetic structure of soil bacterial communities across elevational gradient – Qian Zhang – Environmental Microbiology

Seagrass rhizosphere microenvironment alters plant‐associated microbial community composition – Kasper Elgetti Brodersen – Environmental Microbiology

Water and extremophile microbiome

Comparing Rock-inhabiting Microbial Communities in Different Rock Types from a High Arctic Polar Desert – Yong-Hoe Choe – FEMS Microbiology Ecology

Microbial communities in bakken region produced water – Daniel Lipus – FEMS Microbiology Letters

Aerobic microbial taxa dominate deep subsurface cores from the Alberta oil sands – Christina M Ridley – FEMS Microbiology Ecology

Metal contaminations impact archaeal community composition, abundance and function in remote alpine lakes – Sergi Compte‐Port – Environmental Microbiology

 Probiotics / prebiotics

Clinical and Microbiological Effect of a Multispecies Probiotic Supplementation in Celiac Patients With Persistent IBS-type Symptoms: A Randomized, Double-Blind, Placebo-controlled, Multicenter Trial – Ruggiero Francavilla – Journal of Clinical Gastroenterology

Review: Are Probiotics Effective in Targeting Alcoholic Liver Diseases? – Meegun Hong – Probiotics and Antimicrobial Proteins

January 19, 2018

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Today’s digest features a review on gut microbial glycerol metabolism as a source of Acrolein, and an interesting article on the impact of climate cooling on ecosystem community structure and function in alpine soils. Happy reading!

 

Careers and Events

Research Fellow – National University of Singapore

Postdoctoral Fellow – Boston Children’s Hospital, Harvard Medical School

Scientific Officer/Senior Scientific Officer – The Cancer Research UK Beatson Institute

Staff Clinician – National Institutes of Health (NIH) National Heart, Blood and Lung Institute (NHLBI)

Human respiratory microbiome

Initial acquisition and succession of the cystic fibrosis lung microbiome is associated with disease progression in infants and preschool children – Marianne S. Muhlebach – Plos Pathogens

Human skin microbiome

Association of Disease Severity With Skin Microbiome and Filaggrin Gene Mutations in Adult Atopic Dermatitis – Maja-Lisa Clausen – JAMA Dermatology

Human gut microbiome

Review : Genetic and microbiome influence on lipid metabolism and dyslipidemia – Maria Matey Hernandez – Physiological Genomics

Review : Bile acids in glucose metabolism in health and disease – Hagit Shapiro – Journal of Experimental Microbiology

*Review: Gut Microbial Glycerol Metabolism as an Endogenous Acrolein Source – Jianbo Zhang – mBio

Review: How does ‘metabolic surgery’ work its magic? New evidence for gut microbiota – Peck Bailey C.E – Current Opinion in Endocrinology, Diabetes and Obesity

Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn’s disease – Gavin M. Douglas – Microbiome

Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease – Ahmed Moustafa – Clinical and translational gastroenterology

Animal experiments

Flaxseed-enriched diets change milk concentration of the antimicrobial danofloxacin in sheep – Jon Andoni Otero – BMC Veterinary Research

Colonization of the cervicovaginal space with Gardnerella vaginalis leads to local inflammation and cervical remodeling in pregnant mice – Luz-Jeannette Sierra – Plos One

Kudingcha and Fuzhuan Brick Tea Prevent Obesity and Modulate Gut Microbiota in High-Fat Diet Fed Mice – Guijie Chen – Molecular Nutrition and Food Research

Plant, root, and soil microbiome

*Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling – Linwei Wu – ISME Journal

Cultivable fungi present in Antarctic soils: taxonomy, phylogeny, diversity, and bioprospecting of antiparasitic and herbicidal metabolites – Eldon C. Q. Gomes – Extremophiles

Clearcutting alters decomposition processes and initiates complex restructuring of fungal communities in soil and tree roots – Petr Kohout – The ISME Journal

A large-scale field study of bacterial communities in cereal aphid populations across Morocco – Samir Fakhour – FEMS Microbiology Ecology

Microbial Mitigation-Exacerbation Continuum: A novel framework for microbiome effects on hosts in the face of stress – Aaron S. David – Ecology

Water and extremophile microbiome

Brief Report: Effects of grazing, phosphorus and light on the growth rates of major bacterioplankton taxa in the coastal NW Mediterranean – Olga Sánchez – Environmental Microbiology Reports

Development of a mediated whole cell-based electrochemical biosensor for joint toxicity assessment of multi-pollutants using a mixed microbial consortium – Guanyue Gao – Analytica Chimica Acta

The acute effects of erythromycin and oxytetracycline on enhanced biological phosphorus removal system: shift in bacterial community structure – Zhetai Hu – Environmental Science and Pollution Research

Probiotics / prebiotics

Valorization of Brewer’s spent grain to prebiotic oligosaccharide: production, xylanase catalyzed hydrolysis, in-vitro evaluation with probiotic strains and in a batch human fecal fermentation model – Mursalin Sajib – Journal of Biotechnology

In vitro fermentation of gum acacia – impact on the faecal microbiota – Sehad Alarifi -International Journal of Food Sciences and Nutrition

A bioluminescent test system reveals valuable antioxidant properties of lactobacillus strains from human microbiota – Maria Marsova – World Journal of Microbiology and Biotechnology

Yeasts / Fungi

Review: Sequence-based classification and identification of Fungi – David Hibbett – Mycologia

Phages and viruses

Detection of bovine Deltapapillomavirus DNA in peripheral blood of healthy sheep (Ovis aries) – S. Roperto – Transboundary and Emerging Diseases

Metagenomics

In-depth resistome analysis by targeted metagenomics – Val F. Lanza – Microbiome

Metabolomics

Qualitative metabolomics profiling of serum and bile from dogs with gallbladder mucocele formation – Jody L. Gookin – Plos One

Bioinformatics

A distance-based approach for testing the mediation effect of the human microbiome -Jie Zhang – Bioinformatics

Anitha’s non-microbiology picks

NASA test proves pulsars can function as a celestial GPS

The dark side of light: how artificial lighting is harming the natural world

Ultrathin 2-D metals get their own periodic table

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 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

December 1, 2017

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Happy December! Today’s digest features research articles on prion like domains in phages, effect of high salt challenge on gut microbiota and immune system. Enjoy!

Events and jobs

Assistant Professor, Statistics and Microbiology – The University of Manitoba

Program Manager, Microbiology – RWJ-Pathology-PISC

General microbiome

Review: Experimental design and quantitative analysis of microbial community multiomics – Himel Mallick – Genome Biology

Pregnancy and early life

Low Microbial Diversity and Abnormal Microbial Succession Is Associated with Necrotizing Enterocolitis in Preterm Infants – Priscila T. Dobbler – Frontiers in Microbiology

Human respiratory microbiome

Colonic Bacteroides are positively associated with trabecular bone structure and programmed by maternal vitamin D in male but not female offspring in an obesogenic environment – C R Villa – International Journal of Obesity

Human skin microbiome

Diversity of bacterial communities on the facial skin of different age-group Thai males – Alisa Wilantho – PeerJ

Human oral microbiome

Oral Health and the Oral Microbiome in Pancreatic Cancer: An Overview of Epidemiological Studies – Paige M Bracci – The Cancer Journal

Bacterial alterations in salivary microbiota and their association in oral cancer – Wei-Hsiang Lee – Scientific Reports

Human vaginal microbiome

Review : Is bacterial vaginosis a disease? – Gregor Reid – Applied Microbiology and Biotechnology

Human gut microbiome

The gut mycobiome of the Human Microbiome Project healthy cohort – Andrea K. Nash – Microbiome

Analyses of gut microbiota and plasma bile acids enable stratification of patients for antidiabetic treatment – Yanyun Gu – Nature Communications

*Salt-responsive gut commensal modulates TH17 axis and disease – Nicola Wilck – Nature

Interactions between diet and the intestinal microbiota alter intestinal permeability and colitis severity in mice – Sean R.Llewellyn – Gastroenterology

Psychobiotics: A new approach for treating mental illness? – Snigdha Misra – Critical Reviews in Food Science and Nutrition

Small Intestinal Bacterial Overgrowth: Should Screening Be Included in the Pre-fecal Microbiota Transplantation Evaluation? – Jessica R. Allegretti – Digestive Diseases and Sciences

Gut microbiota-mediated generation of saturated fatty acids elicits inflammation in the liver in murine high-fat diet-induced steatohepatitis – Shoji Yamada – BMC Gastroenterology

Animal experiments

Vertical vs. horizontal transmission of the microbiome in akey disease vector, Ixodes pacificus – Jessica Y. Kwan – Molecular Ecology

Gut Microbiome-induced Shift of Acetate to Butyrate Positively Manages Dysbiosis in High Fat Diet – Xu Si – Molecular Nutrition and Food Research

Increased cortical neuronal responses to NMDA and improved attentional set-shifting performance in rats following prebiotic (B-GOS®) ingestion – Benjamin Gronier – European Neuropsychopharmacology

Effects of Lactobacillus acidophilus on gut microbiota composition in broilers challenged with Clostridium perfringens – Zhui Li – Plos One

Doxycycline induces dysbiosis in female C57BL/6NCrl mice – Felicia D. Duke Boynton – BMC Research Notes

Animal microbiome

The effect of dietary energy and protein levels on body weight, size, and microflora of ostrich chicks – Tahereh Nikravesh-Masouleh – Tropical Animal Health and Production

Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion – Miriam E. Shiffman – PeerJ

The microbiomes of blowflies and houseflies as bacterial transmission reservoirs – Ana Carolina M. Junqueira – Scientific Reports

Plant, root, and soil microbiome

The Patterns and Drivers of Bacterial and Fungal β-Diversity in a Typical Dryland Ecosystem of Northwest China – Jianming Wang – Frontiers in Microbiology

Water and extremophile microbiome

Highlighting patterns of fungal diversity and composition shaped by ocean currents using the East China Sea as a model – Wei Li – Molecular Ecology

Microbial Reduction of Fe(III) and SO42− and Associated Microbial Communities in the Alluvial Aquifer Groundwater and Sediments – Ji-Hoon Lee – Microbial Ecology

The influence of complex fermentation broth on denitrification of saline sewage in constructed wetlands by heterotrophic nitrifying/aerobic denitrifying bacterial communities – Guiping Fu – Bioresource Technology

Amplicon-Metagenomic Analysis of Fungi from Antarctic Terrestrial Habitats – Marcelo Baeza – Frontiers in Microbiology

Microbial Community Structure and Arsenic Biogeochemistry in Two Arsenic-Impacted Aquifers in Bangladesh – Edwin T. Gnanaprakasam – mBio

Probiotics / prebiotics

Short communication: Does early-life administration of a Megasphaera elsdenii probiotic affect long-term establishment of the organism in the rumen and alter rumen metabolism in the dairy calf? – T.T.Yohe – Journal of Dairy Science

Review: Effect of Probiotic Supplementation on CD4 Cell Count in HIV-Infected Patients: A Systematic Review and Meta-analysis – Asma Kazemi – Journal of Dietary Supplements

Phages and viruses

*Prion-Like Domains in Phagobiota – George Tetz – Frontiers in Microbiology

Bacteriophage Distributions and Temporal Variability in the Ocean’s Interior – Elaine Luo – mBio

Anitha’s non-microbiology picks

Hubble in a bubble: Scallop eyes act just like tiny telescopes

Jackpot of fossilized pterosaur eggs unearthed in China

Sorry, Grumpy Cat: Study finds dogs are brainier than cats

November 1, 2017

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Happy November everybody! We have an interesting collection of articles today. Co-cultivation of plant beneficial fungi as an effective strategy to modulate the production of bioactive metabolites and a review on the benefits of berries and their phytochemicals on the digestive and immune systems. Enjoy!

Events and jobs

Microbiology Lab Assistant – Seattle, Washington – Labcorp

General microbiome

The Microbiome in Posttraumatic Stress Disorder and Trauma-Exposed Controls: An Exploratory Study – Hemmings, Sian M.J – Pyschosomatic Medicine

Human respiratory microbiome

Review : CF Airway Microbiome: Overturning the Old, Opening the Way for the New – George A. O’Toole – Journal of Bacteriology

Human oral microbiome

Effect of maltitol-containing chewing gum use on the composition of dental plaque microbiota in subjects with active dental caries – Erica M. Prosdocimi – Journal of Oral Microbiology

Human gut microbiome

The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis – Puneet Puri – Hepatology

Diet, Environments, and Gut Microbiota. A Preliminary Investigation in Children Living in Rural and Urban Burkina Faso and Italy – Carlotta De Filippo – Frontiers in Microbiology

Gut microbiome of mothers delivering prematurely shows reduced diversity and lower relative abundance of Bifidobacterium and Streptococcus – Cecilie Dahl – Plos One

Review : Systematic review of the effects of the intestinal microbiota on selected nutrients and non-nutrient – Colette Shortt – European Journal of Nutrition

Cereal products derived from wheat, sorghum, rice and oats alter the infant gut microbiota in vitro – Hasinika K. A. H. Gamage – Scientific Reports

Animal experiments

Antibiotic treatment disrupts bacterial communities in the colon and rectum of SIV-infected macaques – Alexander S. Zevin – FEMS Microbiology Letters

Ophiopogonin D alleviates high-fat diet–induced metabolic syndrome and changes the structure of gut microbiota in mice – Siyu Chen – The FASEB Journal

Animal microbiome

Bacterial Species Identified on the Skin of Bottlenose Dolphins Off Southern California via Next Generation Sequencing Techniques – Corey D. Russo – Microbial Ecology

Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits – Ara S. Winter – PeerJ

Analysis of the Microbial Diversity in the Fecal Material of Giraffes – Jessica M. Schmidt – Current Microbiology

Morphological and genetic factors shape the microbiome of a seabird species (Oceanodroma leucorhoa) more than environmental and social factors – Douglas S. Pearce – Microbiome

Metabolomics

Plasma Metabolites From Choline Pathway and Risk of Cardiovascular Disease in the PREDIMED (Prevention With Mediterranean Diet) Study – Marta Guasch-Ferré – Journal of the American Heart Association

Plant, root, and soil microbiome

Strong Regionality and Dominance of Anaerobic Bacterial Taxa Characterize Diazotrophic Bacterial Communities of the Arcto-Alpine Plant Species Oxyria digyna and Saxifraga oppositifolia – Manoj Kumar – Frontiers in Microbiology

An endophytic Bacillus strain promotes growth of oil palm seedling by fine root biofilm formation – MdHoirul Azri – Rhizosphere

Effect of auxin producing and phosphate solubilizing bacteria on mobility of soil phosphorus, growth rate, and P acquisition by wheat plants – Guzel R. Kudoyarova – Acta Physiologiae Plantarum

Contrasting effects of ammonium and nitrate additions on the biomass of soil microbial communities and enzyme activities in subtropical China – Chuang Zhang – Biogeosciences

Impact of land use change and soil organic carbon quality on microbial diversity in soils across Europe – Márton Szoboszlay – FEMS Microbiology Ecology

Microbial Diversity and Community Structure of Sulfate-Reducing and Sulfur-Oxidizing Bacteria in Sediment Cores from the East China Sea – Yu Zhang – Frontiers in Microbiology

Rhizosphere-associated Pseudomonas induce systemic resistance to herbivores at the cost of susceptibility to bacterial pathogens – Cara H. Haney – Molecular Ecology

*Co-Culture of Plant Beneficial Microbes as Source of Bioactive Metabolites – F. Vinale – Scientific Reports

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database – Andrew Bissett – Gigascience

Water and extremophile microbiome

Anaerobic digestion of spent mushroom substrate under thermophilic conditions: performance and microbial community analysis – Zheng Xiao – Applied Microbiology and Biotechnology

Metagenomic characterization of biofilter microbial communities in a full-scale drinking water treatment plant – Seungdae Oh – Water Research

Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau – Yong-Liang Chen – Molecular Ecology

Community composition and assembly processes of the free-living and particle-attached bacteria in Taihu Lake – Dayong Zhao – FEMS Microbiology Ecology

Food Microbiology

Anti-obesity Effect of Exopolysaccharides Isolated from Kefir Grains – Juha Lim – J. Agric. Food Chem

Modulating Effects of Dicaffeoylquinic Acids from Ilex Kudingcha on Intestinal Microecology in vitro – Minhao Xie – Journal of Agricultural Food Chemistry

*Review of the health effects of berries and their phytochemicals on the digestive and immune systems – Coen Govers – Nutrition Reviews

Probiotics / prebiotics

Single-species versus dual-species probiotic supplementation as an emerging therapeutic strategy for obesity – G.Karimi – Nutrition, Metabolism and Cardiovascular Diseases

Bioinformatics

ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores – Luis H. Orellana – Nucleic Acids Research

Phages and viruses

Review : Assessing Species Diversity Using Metavirome Data: Methods and Challenges – Damayanthi Herath – Computational and Structural Biotechnology Journal

Microbes in the news

Caves Host Gooey Biofilms Built by Methane-Eating Bacteria

3D Printed Artificial Small Intestine to Advance Research on Gut Bacteria

Enzymes from dangerous bacteria turn into important tools for protein chemistry

Microbes on the market

The University Medical Center Groningen and Novogene announce the start of the 10K Metagenome Project

Science, publishing, and career

Book Chapter : Leading Change in Undergraduate STEM Education – Adam K. Leibovich – Educational and Outreach Projects from the Cottrell Scholars Collaborative Undergraduate and Graduate Education Volume 1

Anitha’s non-microbiology picks

Congratulations Nancy Scherich! The winner of this year’s ‘Dance Your Ph.D.’ contest

ROSINA spectral measurements bring comet’s chemistry to life

Scary as they are, few vampires have a backbone