Category Archives: Metagenomics & Bioinformatics

November 6, 2017

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Today we have an interesting digest with several articles about human microbiome. Additionally, today we also remark part of the recently release book “Understanding the Gut-Bone Signaling Axis”, with interesting chapters treating the connections between microbiota and bone health.

(Each file with an asterisk in the start contains open access to fulltext)

 

Human Microbiome

Bone Mechanical Function and the Gut Microbiota – C. J. Hernandez – Understanding the Gut-Bone Signaling Axis (SpringerLink)

Prebiotics and Bone – Corrie M. Whisner – Understanding the Gut-Bone Signaling Axis (SpringerLink)

Inflammatory Bowel Disease: Effects on Bone and Mechanisms – Francisco A. Sylvester – Understanding the Gut-Bone Signaling Axis (SpringerLink)

Immunology of Gut-Bone Signaling – Fraser L. Collins –  Understanding the Gut-Bone Signaling Axis (SpringerLink)

Gut Microbiota and Bone Health – Darin Quach – Understanding the Gut-Bone Signaling Axis (SpringerLink)

Increased stool immunoglobulin A level in children with autism spectrum disorders – Jiaxiu Zhou – Research in Developmental Disabilities (ScienceDirect)

Gut Microbiota and Cancer Patients: A Broad-Ranging Relationship – Giovanni Cammarota – Mayo Clinic Proceedings

* Less Invasive Screening for Colorectal Cancer by Microbiota Analysis: Is it a Reality or an Illusion? – Hisashi Onodera – EBIoMedicine

Safety and Efficacy of Fecal Microbiota Transplant for Recurrent Clostridium difficile Infection in Patients With Cancer Treated With Cytotoxic Chemotherapy: A Single-Institution Retrospective Case Series – Mehrdad Hefazi – Mayo Clinic Proceedings

Gastric microbial community profiling reveals a dysbiotic cancer-associated microbiota – Rui M Ferreira – Gut (BMJ)

Gut microbiota and hypertension: From pathogenesis to new therapeutic strategies – Yongbo Kang – Clinics and Research in Hepatology and Gastroenterology (ScienceDirect)

Associations Between Microbiota, Mitochondrial Function, and Cognition in Chronic Marijuana Users – Jun Panee – Journal of Neuroimmune Pharmacology

Genetic mannose binding lectin deficiency is associated with airway microbiota diversity and reduced exacerbation frequency in COPD – Alison J Dicker – Thorax (BMJ)

Molecular characterization of Multidrug Resistant Bacteroides isolates from Hungarian clinical samples – Károly Péter Sárvária – Journal of Global Antimicrobial Resistance (ScienceDirect)

* Commentary: Human Intestinal Microbiota and Colorectal Cancer: Moving Beyond Associative Studies – Christian Jobin – Gastroenterology

Faecal microbiota transplantation versus placebo for moderate-to-severe irritable bowel syndrome: a double-blind, randomised, placebo-controlled, parallel-group, single-centre trial – Peter Holger Johnsen – The Lancet Gastroenterology & Hepatology

Estrogens and Female Liver Health – Karen L. Chena – Steroids (ScienceDirect)

 

Beneficial microbes

(Provisionally accepted, Full text available soon) Probiotic Bacteria Alter Pattern-Recognition Receptor Expression and Cytokine Profile in a Human Macrophage Model Challenged with Candida albicans and Lipopolysaccharide – Victor H. Matsubara – Frontiers in Microbiology

* Butyrate and propionate inhibit antigen-specific CD8+ T cell activation by suppressing IL-12 production by antigen-presenting cells – Claudia Nastasi – Scientific Reports (NPG)

 

Animal Microbiome

(Provisionally accepted, Full text available soon) The Gut Entomotype of Red Palm Weevil Rhynchophorus ferrugineus Olivier (Coleoptera: Dryophthoridae) and Their Effect on Host Nutrition Metabolism – Abrar Muhammad – Frontiers in Microbiology

Porcine small and large intestinal microbiota rapidly hydrolyze the masked mycotoxin deoxynivalenol-3-glucoside and release deoxynivalenol in spiked batch cultures in vitro – Silvia W. Gratz – Applied and Environmental Microbiology (ASM)

A stable core gut microbiota across fresh- to saltwater transition for farmed Atlantic salmon – Knut Rudi – Applied and Environmental Microbiology (ASM)

Fecal microbiota transplant from highly feed efficient donors shows little effects on age-related changes in feed efficiency-associated fecal microbiota in chickens – Sina-Catherine Siegerstetter – Applied and Environmental Microbiology (ASM)

Short communication: The effect of heat treatment of bovine colostrum on the concentration of oligosaccharides in colostrum and in the intestine of neonatal male Holstein calves – Amanda J. Fischer – Journal of Dairy Science

* Progressive Colonization of Bacteria and Degradation of Rice Straw in the Rumen by Illumina Sequencing – Yanfen Cheng – Frontiers in Microbiology

* Neuroprotective effect of Ruminococcus albus on oxidatively stressed SH-SY5Y cells and animals – Jieun Park – Scientific Reports (NPG)

* Gut dysbiosis and impairment of immune system homeostasis in perinatally-exposed mice to Bisphenol A precede obese phenotype development – Yann Malaisé – Scientific Reports (NPG)

Impact of Enteric Health and Mucosal Permeability on Skeletal Health and Lameness in Poultry – L. R. Bielke – Understanding the Gut-Bone Signaling Axis (SpringerLink)

Gut Microbiota Are Disease-Modifying Factors After Traumatic Spinal Cord Injury – Kristina A. Kigerl – Neurotherapeutics (SpringerLink)

 

Food Microbes

(Provisionally accepted, Full text available soon) Extractive Fermentation of Lactic Acid in Lactic Acid Bacteria Cultivation: A Review – Majdiah Othman – Frontiers in Microbiology

* Diversity within Italian Cheesemaking Brine-Associated Bacterial Communities Evidenced by Massive Parallel 16S rRNA Gene Tag Sequencing – Marilena Marino – Frontiers in Microbiology

The main spoilage-related psychrotrophic bacteria in refrigerated raw milk – J.C. Ribeiro Júnior – Journal of Dairy Science

* Preprint: Kombucha as a model system for multispecies microbial cooperation: theoretical promise, methodological challenges and new solutions ‘in solution’ – Alexander Niall May – BioRxiv

* New microbial resource: microbial diversity, function and dynamics in Chinese liquor starter – Yuhong Huang – Scientific Reports (NPG)

 

Environmental Microbes

(Provisionally accepted, Full text available soon) Illumina-Based Analysis of Endophytic and Rhizosphere Bacterial Diversity of the Coastal Halophyte Messerschmidia sibirica – Xueying Tian – Frontiers in Microbiology

Perturbation of seafloor bacterial community structure by drilling waste discharge – Tan T. Nguyen – Marine Pollution Bulletin

November 2, 2017

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Second day of November we have quite a few job offers, nice set of microbiome news, two reviews in “gut microbiome” sector. Two (personal) highlights today would be the Thomas J. Browning’s  paper about phytoplankon nutrient co-limitation and Luke R. Thompson’s paper about The Earth Microbiome Project. Enjoy…

Events and jobs

Research Technician, University of York, UK

Postdoctoral Researcher – Molecular Microbiologist, University of Oxford, Oxford, UK

Bioinformatics Postdoc, Max Planck Institute for Infection Biology, Berlin, Germany

Microbiology Postdoctoral Scholar,  The University of California, Berkeley, California, US

Bioinformatics Analyst, Ares Genetics GmbH, Vienna, Austria

Assistant Professor of Microbiology, The University of Alabama in Huntsville, Huntsville, Alabama, US

Tenure-track Assistant Professor of Microbiology, Miami University, Miami, Ohio, US

Tenure Track Assistant Professor in Microbiology, The University of British Columbia, Vancouver,  Canada

General microbiome

Impaired competence in flagellar mutants of Bacillus subtilis is connected to the regulatory network governed by DegU – Theresa Hoelscher – bioRxiv

Gene network analysis identifies a central post-transcriptional regulator of cellular stress survival – Matthew Z. Tien – bioRxiv

Detection of cytosolic Shigella flexneri via a C-terminal triple-arginine motif of GBP1 inhibits actin-based motility – Anthony Piro – bioRxiv

Inter-species population dynamics enhance microbial horizontal gene transfer and spread of antibiotic resistance – Robert M Cooper – eLIFE

A communal catalogue reveals Earth’s multiscale microbial diversity – Luke R. Thompson – Nature

Human gut microbiome

Rapid Assessment of Microbiota Changes in Individuals with Autism Spectrum Disorder Using Bacteria-derived Membrane Vesicles in Urine – Yunjin Lee – Experimental Neurobiology

Review: Dietary and microbial metabolites in the regulation of host immunity – Jun Kunisawa – frontiers in Microbiology

Review: Gut microbiota as a potential target of metabolic syndrome: the role of probiotics and prebiotics – Mingqian He – Cell & Bioscience

Progression of Parkinson’s disease is associated with gut dysbiosis: Two-year follow-up study – Tomomi Minato – PLOS One

Animal experiments

Rapid regrowth and detection of microbial contaminants in equine fecal microbiome samples – Kalie F. Beckers – PLOS One

Cecal Microbiota in Broilers Fed with Prebiotics – Dany Mesa – Frontiers in Genetics

Commensal Lactobacillus Controls Immune Tolerance during Acute Liver Injury in Mice – Nobuhiro Nakamoto – Cell Reports

Food restriction followed by refeeding with a casein- or whey-based diet differentially affects the gut microbiota of pre-pubertal male rats – Majdi Masarwi – The Journal of Nutritional Biochemistry

Animal microbiome 
Evidence for a conserved microbiota across the different developmental stages of Plodia interpunctella – Valeria Mereghetti -Insect Science

Plant, root, and soil microbiome

Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially processed plant derived carbon – Evan P. Starr – bioRxiv

Water and extremophile microbiome 

Analysis of bacterial communities and characterization of antimicrobial strains from cave microbiota – Muhammad Yasir – Brazilian Journal of Microbiology

Highly divergent 16S rRNA sequences in ribosomal operons of Scytonema hyalinum (Cyanobacteria) – Jeffrey R. Johansen – PLOS One

Study of Microbial diversity in Ganga river water sample by the use of Metagenomics technique – Jamilah Ali Ahmed Zaed – Journal of Pharmacognosy and Phytochemistry

Niche specialization of bacteria in permanently ice-covered lakes of the McMurdo Dry Valleys, Antarctica – Miye Kwon – Environmental Microbiology

Influence of bicarbonate on the abundance of microbial communities capable of reducing U(VI) in groundwater – Dianxin Li – RSC Advances

Monitoring microbial responses to ocean deoxygenation in a model oxygen minimum zone – Steven J. Hallam – Scientific Data

Synechococcus plasticity under environmental changes – Cristiana Callieri – FEMS Microbiology Letters

Nutrient co-limitation at the boundary of an oceanic gyre – Thomas J. Browning -Nature

Evaluation of different 16S rRNA gene V regions for exploring bacterial diversity in a eutrophic freshwater lake – Junyi Zhang – Science of The Total Environment

Microbial community structures and functions of wastewater treatment systems in plateau and cold regions – Dexin Fang – Bioresource Technology

Adaptability as the key to success for the ubiquitous marine nitrite oxidizer Nitrococcus — Jessika Füssel – Science Advances

Food microbiology

Characterization of Enterococcal Community Isolated from an Artisan Istrian Raw Milk Cheese: Biotechnological and Safety Aspects – Mirna Mrkonjic Fuka – Food Technology and Biotechnology

Probiotics / prebiotics
Lactobacillus reuteri suppresses E. coli O157:H7 in bovine ruminal fluid: Toward a pre-slaughter strategy to improve food safety? – Yolande Bertin – PLOS One

Bioinformatics

MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota – Evgenii I Olekhnovich – Bioinformatics

Techniques

Quantification of diverse virus populations in the environment using the polony method – Nava Baran – Nature Microbiology

Microbes in the news 

Microbiome Link with Colorectal Cancer Drug Toxicity Points to Predictive Tests and Prevention – Genetic Engineering and Biotechnology News

Gut bacteria composition could predict toxicity of chemotherapy drugs in cancer patients – News Medical

Versatile marine bacteria could be an influence on global warming, scientists discover – Science Daily

By 2100, climate change could alter key microbial interactions in the ocean  – Phys Org

Microbes on the market 

Symbiotix Biotherapies Receives $5 Million in Institutional Financing to Advance its Development of Molecular Therapeutics that Modulate Regulatory T Cell Activity

Tina’s (non)microbiology picks 

Concept Inventory Development Reveals Common Student Misconceptions about Microbiology – Amy G. Briggs – Journal of Microbiology & Biology Education

Announcing the winner of this year’s ‘Dance Your Ph.D.’ contest – John Bohannon – Science

 

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

 

October 26, 2017

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In today’s digest we have some interesting discussion about lab/bioinformatics techniques, a few editorials on the microbiome job market, and even a little bit of philosophy learned from our tiny microbial friends.

Events and jobs

BioData World West 2018 – 13-14 March 2018 – San Francisco, CA

General microbiome

Cooperation and cheating as innovation: insights from cellular societies – Athena Aktipis – Philosophical Transactions of The Royal Society B

[Pre-Print] Metabolic Interactions Between Dynamic Bacterial Subpopulations – Adam Z Rosenthal – bioRxiv

Pregnancy and early life

Preterm Birth Affects the Risk of Developing Immune-Mediated Diseases – Sybelle Goedicke-Fritz – Frontiers in Immunology

Human oral microbiome

Metagenomic Analysis of Gingival Sulcus Microbiota and Pathogenesis of Periodontitis Associated with Type 2 Diabetes Mellitus – E. A. Babaev – Bulletin of Experimental Biology and Medicine

Human urinary tract microbiome

Re: Evaluation of the Urinary Microbiota of Women with Uncomplicated Stress Urinary Incontinence – Alan J. Wein – The Journal of Urology

Human gut microbiome

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

Plant, root, and soil microbiome

Endosphere microbiome comparison between symptomatic and asymptomatic roots of Brassica napus infected with Plasmodiophora brassicae – Ying Zhao – PLOS ONE

Ureolytic microbial community is modulated by fertilization regimes and particle-size fractions in a Black soil of Northeastern China – Li Wang – Soil Biology and Biochemistry

Water and extremophile microbiome 

Metatranscriptomic and metagenomic description of the bacterial nitrogen metabolism in waste water wet oxidation effluents – Julien Crovadore – Heliyon

Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents – Rika E. Anderson – Nature

Food microbiology

Sequence Analysis of Changes in Microbial Composition in Different Milk Products During Fermentation and Storage – Barbora Zalewska – Current Microbiology

Probiotics / prebiotics

* Pharmabiotics as an Emerging Medication for Metabolic Syndrome and Its Related Diseases – Thi Thanh Binh Nguyen – Molecules

[Review] Recurrent urinary tract infections in women: How promising is the use of probiotics? – Varsha Gupta – Indian Journal of Medical Microbiology

Bioinformatics

Using convolutional neural networks to explore the microbiome – Derek Reiman – Engineering in Medicine and Biology Society (EMBC)

Techniques

‘Gracilibacillus phocaeensis’ sp. nov., ‘Sediminibacillus massiliensis’ sp. nov. and ‘Virgibacillus ndiopensis’ sp. nov., three halophilic species isolated from salty human stools by culturomics – B. Senghor – New Microbes and New Infections

Proteomic and metaproteomic approaches to understand host-microbe interactions – Amanda E. Starr – Analytical Chemistry

Impact of Method Variables on Microbiota Sample Disruption – Jaclyn Zecca and David Burden – OPS Diagnostics LLC

Microbes on the market 

Patenting the microbiome: trends, challenges and insights – Anthony D Sabatelli – Future Science

[Editorial] The aquaculture microbiome at the centre of business creation – Karen K. Dittmann – Microbial Biotechnology

Ed’s non-microbiology picks

I put quite a few on here today – enjoy 🙂

More than 75 percent decline over 27 years in total flying insect biomass in protected areas – Caspar A. Hallman – PLOS ONE

Cavitation-Induced Synthesis of Biogenic Molecules on Primordial Earth – Natan-Haim Kalson – ACS Central Science

Games people play: How video games improve probabilistic learning – Sabrina Schenk – Behavioural Brain Research

A process-oriented model linking adolescents’ sleep hygiene and psychological functioning: the moderating role of school start times -Jack S. Peltz – Sleep Health

Decreases in self-reported sleep duration among U.S. adolescents 2009-2015 and links to new media screen time – Jean M. Twenge – Sleep Medicine

Dogs’ recognition of human selfish and generous attitudes requires little but critical experience with people – Fabricio Carballo – PLOS ONE

October 25, 2017

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A short Digest for today. The evolution of E. coli in the lab for over 60,000 generations, the necessity of including a mock community for every sequencing run, and plenty of news pieces.

Events and jobs

Free Webinar: Not Just for Neurons – Electrical Signaling in Bacterial Biofilm Communities – Select Science

Laboratory Assistant-Microbiology – Raritan New Jersey

General microbiology

*The dynamics of molecular evolution over 60,000 generations – Benjamin H. Good et al. – Nature

Press: The evolution experiment that has been watching bacteria mutate for 30 years – Rich Haridy – New Atlas

Bacterial pathogenesis: Activating Helicobacter effector delivery – Irene Vacca – Nature Reviews Microbiology

Human gut microbiome

Discovery of α-L-arabinopyranosidases from human gut microbiome expands the diversity within glycoside hydrolase family 42 – Alexander Holm Viborg et al. – Journal of Biological Chemistry

Letter: Low eukaryotic viral richness is associated with faecal microbiota transplantation success in patients with UC – Nádia Conceição-Neto et al. – Gut

Bioinformatics

*Preprint: Taxon disappearance from microbiome analysis indicates need for mock communities as a standard in every sequencing run – Yi-Chun Yeh et al. – bioRxiv

Microbes in the news

Strength in numbers: How biofilms outfox antibiotics – Yella Hewings-Martin – Medical News Today

Lung microbiome plays major role in asthma severity and response to treatment – News Medical

New way to prevent unfavorable intestinal microbiota – Hokkaido University – EurekAlert

VIDEO: Gut microbiome research sped by technology, informatics, but diet a major confounder – Eamonn M.M. Quigley – Healio

New Study Shows Link Between Gut Bacteria And Breast Cancer – CBS New York

Harvey-linked flesh-eating bacteria claims Galveston man – Todd Ackerman – Chron

Major changes in balance of gut bacteria occur soon after serious injury/trauma – Medical Xpress

‘Achilles heel’ found in antibiotic-resistant bacteria – John von Radowitz – Irish Independent

 

October 15, 2017

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General microbiome

Metagenome Analyses of Multispecies Microbial Biofilms: First Steps Toward Understanding Diverse Microbial Systems on Surfaces – Christel Schmeisser, Functional Metagenomics: Tools and Applications

Prediction analysis for microbiome sequencing data – Tao Wang, arxiv

Metagenomic Cosmid Libraries Suitable for Functional Screening in Proteobacteria – Jiujun Cheng, Functional Metagenomics: Tools and Applications

Moulds associated with contaminated ocular and injectable drugs: FDA recalls, epidemiology considerations, drug shortages, and aseptic processing – Donald G. Ahearn, Medical Mycology

Human skin microbiome

High-Altitude Living Shapes the Skin Microbiome in Humans and Pigs – Bo Zeng, Frontiers in Microbiology

Human vaginal microbiome

Role of Molecular Biology in Diagnosis and Characterization of Vulvo-Vaginitis in Clinical Practice – Donders G.G.G., Gynecologic and Obstetric Investigation

Human gut microbiome

A Review of the Oesophageal Microbiome in Health and Disease – Dervla Kelly, Methods in Microbiology

Prediction of functional profiles of gut microbiota from 16S rRNA metagenomic data provides a more robust evaluation of gut dysbiosis occurring in Japanese type 2 diabetic patients – Ryo Inoue, Journal of Clinical Biochemistry and Nutrition

Human oral microbiome

The Effect of Supragingival Biofilm Re-development on the Subgingival Microbiota in Chronic Periodontitis – Fátima Aparecida Rocha Resende Hartenbach, Archives of Oral Biology

Animal experiments

Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice – Jessica L. Mark Welch, PNAS

Comparative study of probiotic effects of Lactobacillusand Bifidobacteria strains on cholesterol levels, liver morphology and the gut microbiota in obese mice – Rostyslav V. Bubnov, The EPMA Journal

Study on improving anaerobic co-digestion of cow manure and corn straw by fruit and vegetable waste: methane production and microbial community in CSTR process – Xuemei Wang, Bioresource Technology

Animal microbiome

Perinatal Bisphenol A Exposure Induces Chronic Inflammation in Rabbit Offspring via Modulation of Gut Bacteria and Their Metabolites – Lavanya Reddivari, mSystems

Hymenobacter cavernae sp. nov., isolated from a karst cave – Hai-Zhen Zhu, International Journal of Systematic and Evolutionary Microbiology

Plant, root, and soil microbiome

Ciceribacter thiooxidans sp. nov., a novel nitrate-reducing thiosulfate-oxidizing bacterium isolated from sulfide-rich anoxic sediment – Tongchu Deng, International Journal of Systematic and Evolutionary Microbiology

Deinococcus taklimakanensis sp. nov., isolated from desert soil –  Zuobing Liu, International Journal of Systematic and Evolutionary Microbiology

Improvement of the catalytic characteristics of a salt-tolerant GH10 xylanase from Streptomyce rochei L10904 – Qin Li, International Journal of Biological Macromolecules

Trees harness the power of microbes to survive climate change – Jennifer A. Lau, PNAS

Exploring the earthworm gut as model for soil microbial ecology – Fatima Hussain, MBL

Soil proteomics for exploitation of microbial diversity in Fusarium wilt infected and healthy rhizosphere soils of tomato – R. Manikandan, Physiological and Molecular Plant Pathology

The intimate talk between plants and microorganisms at the leaf surface – Wendy Aragón, Journal of Experimental Botany

Metagenomics of Plant Microbiomes – G. Brader, Functional Metagenomics: Tools and Applications

Effects of different soil remediation methods on inhibition of lead absorption and growth and quality of Dianthus superbus L. – Xiaoyu Yang, Environmental Science and Pollution Research

Interactions of Root-Feeding Insects with Fungal and Oomycete Plant Pathogens – Telsa Willsey, Frontiers in Plant Science

Soil proteomics for exploitation of microbial diversity in Fusarium wilt infected and healthy rhizosphere soils of tomato – R. Manikandan, Physiological and Molecular Plant Pathology

Switchgrass Yield, Nutrient Uptake, And Rhizosphere Microbial Community Composition As Affected By Cultivar And Soil Fertility – Anne Sawyer, University of Minnesota Digital Conservancy

Ecoenzymatic stoichiometry and microbial nutrient limitation in rhizosphere soil in the arid area of the northern Loess Plateau, China – Yongxing Cui, Soil Biology and Biochemistry

Soil microbiota respond to green manure in organic vineyards – Claudia M. O. Longa, Journal of Applied Microbiology

Water and extremophile microbiome

Anoxynatronum buryatiense sp. nov., an anaerobic alkaliphilic bacterium from a low mineralization soda lake in Buryatia, Russia – Yana Ryzhmanova, International Journal of Systematic and Evolutionary Microbiology

100 kGy gamma-affected microbial communities within the ancient Arctic permafrost under simulated Martian conditions – Vladimir S. Cheptsov, Extremophiles

Effect of environmental parameters on biodiversity of the fungal component in lithic Antarctic communities – Laura Selbmann, Extremophiles

Biomineralisation of carbonate and sulphate by the halophilic bacterium Halomonas maura at different manganese concentrations – Almudena Rivadeneyra, Extremophiles

Biosurfactant production by haloalkaliphilic Bacillusstrains isolated from Red Sea, Egypt – Khouloud M.Barakat, The Egyptian Journal of Aquatic Research

Mass Spectrometry for the Study of Microbial Communities in Environmental Waters – Inês C. Santos, Advances in Chemical Pollution, Environmental Management and Protection

Responses of microbial community to pH stress in bioleaching of low grade copper sulfide – Yuguang Wang, Bioresource Technology

Mass Spectrometry for the Study of Microbial Communities in Environmental Waters – Inês C. Santos, Advances in Chemical Pollution, Environmental Management and Protection

Waste microbes

Microbial characteristics analysis and kinetic studies on substrate composition to methane after microbial and nutritional regulation of fruit and vegetable wastes anaerobic digestion – Chunhui Zhao, Bioresource Technology

Antibiotic resistance genes and associated microbial community conditions in aging landfill systems – Dong Wu, Environmental Science and Technology

Bioinformatics

Bioinformatics in Microbiome Analysis – Yuhan Hao, Methods in Microbiology

Techniques

Enhancing Metagenomic Approaches Through Synthetic Biology – Luana de Fátima Alves, Functional Metagenomics: Tools and Applications

Enhancing Functional Metagenomics of Complex Microbial Communities Using Stable Isotopes – Marcela Hernández, Functional Metagenomics: Tools and Applications

The P/N (Positive-to-Negative Links) Ratio in Complex Networks—A Promising In Silico Biomarker for Detecting Changes Occurring in the Human Microbiome – Zhanshan (Sam) Ma, Microbial Ecology

Challenges and Opportunities in Discovery of Secondary Metabolites Using a Functional Metagenomic Approach – Alinne L. R. Santana-Pereira, Functional Metagenomics: Tools and Applications

Emerging whole-cell modeling principles and methods – Arthur P. Goldberg, arxiv

Expression Platforms for Functional Metagenomics: Emerging Technology Options Beyond Escherichia coli – Anna Lewin, Functional Metagenomics: Tools and Applications

Microbes in the news

AST: The Linchpin of Antimicrobial Stewardship – James Lewis, ModernMedicine Network

The Black Death Rages In Madagascar –  Julianna LeMieux, American Council on Science and Health

Report: 17 New Species Of Bacteria Found Every Day In World’s Rainforest Cafés – The Onion (Satire)

October 14, 2017

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The marine sponge microbiome, bacterial communication mediated by hydrogen sulfide, a gnotobiotic pig model to study interactions between a defined gut community and antibiotics, probiotics, and rotavirus.

General microbiome

Evolutionary contribution to coexistence of competitors in microbial food webs – Teppo Hiltunen – Proceedings of the Royal Society Biological Sciences

Pregnancy and early life

Effects of Therapeutic Hypothermia on the Gut Microbiota and Metabolome of Infants suffering Hypoxic-Ischemic Encephalopathy at birth – C Watkins – The International Journal of Biochemistry and Cell Biology

Does the maternal vaginal microbiota play a role in seeding the microbiota of neonatal gut and nose? – O Sakwinska – Beneficial Microbes

Ratio of Klebsiella/Bifidobacterium in early life correlates with later development of paediatric allergy – J S Y Low – Beneficial Microbes

Human oral microbiome

Exopolysaccharides regulate calcium flow in cariogenic biofilms – Monika Astasov-Frauenhoffer – PLOS ONE

Human gut microbiome

The Gut Microbiome Feelings of the Brain: A Perspective for Non-Microbiologists – Aaron Lerner – Microorganisms

The composition and metabolism of faecal microbiota is specifically modulated by different dietary polysaccharides and mucin: an isothermal microcalorimetry study – K Adamberg – Beneficial Microbes

Review: Our gut microbiota: a long walk to homeostasis – L M T Dicks – Beneficial Microbes

Animal experiments

Flavanol-Rich Cocoa Powder Interacts with Lactobacillus rhamnossus LGG to Alter the Antibody Response to Infection with the Parasitic Nematode Ascaris suum – Saebyeol Jang – Nutrients

Effect of antibiotic, probiotic, and human rotavirus infection on colonisation dynamics of defined commensal microbiota in a gnotobiotic pig model – H C Huang – Beneficial Microbes

Animal microbiome

Pre-print: An RNA Virome associated to the Golden Orb-weaver Spider Nephila clavipes – Humberto J Debat – bioRxiv

The sponge microbiome project – Lucas Moutinho-Silva – Gigascience

Water and extremophile microbiome

Diversity and Antimicrobial Potential of Predatory Bacteria from the Peruvian Coastline – Luis Linares-Otoya – Marine Drugs

Bioinformatics

Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data – Fanny Berglund – Microbiome

More microbes

Pre-print: Two SecA/SecY Systems with Distinct Roles in the Ecological Adaptations of Bacteria – Xiaowei Jiang – bioRxiv

Pre-print: H2S mediates interbacterial communication through the air reverting intrinsic antibiotic resistance – Daniel Thomas-Lopez – bioRxiv

Pre-print: Interplay between antibiotic efficacy and drug-induced lysis underlies enhanced biofilm formation at subinhibitory drug concentrations – Wen Yu – bioRxiv

Microbes in the news

How switches work in bacteria – EurekAlert

Opinion: Microbiology Needs More Math – Mikhail Tikhonov – The Scientist

Fluctuating environments can help cooperating bacteria – Science Daily

How to study the inside of a humpback whale’s blowhole? Drones, of course – Teresa Welsh – The Sacramento Bee

Scientists Generate 3D Map of Gut Microbiome – Genetic Engineering and Biotechnology News

Microbes on the market

Research Foundation Calls for Canadian Proposals to Study Dietary Interactions with Microbiota – PR Newswire

October 10, 2017

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Effects of amino acid supplements on metabolic health, a discussion of the broader risks and benefits of microbiome research, a book chapter evaluating microbiome statistical analysis tools.

Events and jobs

Assistant Professor in Microbiology, Tenure Track – Department of Microbiology & Immunology, University of British Columbia

General microbiome

Communicating the promise, risks, and ethics of large-scale, open space microbiome and metagenome research – Daria Shamarina – Microbiome

Pregnancy and early life

Review: Early microbiota, antibiotics and health – Alicja M Nogacka – Cellular and Molecular Life Sciences

Human gut microbiome

Amino acid supplements and metabolic health: a potential interplay between intestinal microbiota and systems control – Francesco Bifari – Genes & Nutrition

Microbial dysbiosis in spouses of ulcerative colitis patients: Any clues to disease pathogenesis? – Dario Sorrentino – World Journal of Gastroenterology

Phages and viruses

Pre-print: Nasty Prophages and the Dynamics of Antibiotic-Tolerant Persister Cells – Alexander Harms – bioRxiv

Bioinformatics

Book Chapter: Processing and Analyzing Human Microbiome Data – Xuan Zhu – Statistical Human Genetics

Interpretation of microbiota-based diagnostics by explaining individual classifier decisions – A Eck – BMC Bioinformatics

Techniques

Pre-print: Umbilical cord blood diagnostics for early onset sepsis in premature infants: detection of bacterial DNA and systemic inflammatory response – Leena B Mithal – bioRxiv

Pre-print: Accuracy of microbial community diversity estimated by closed- and open-reference OTUs – Robert C Edgar – PeerJ

Microbes in the news

Bacteria with synthetic gene circuit self-assemble to build working device with gold nanoparticles – Phys Org

New test identifies antibiotic-resistant bacteria in 30 minutes – The Statesman

Microbes on the market

Summit Highlights Microbiome Preservation During Ridinilazole Treatment in Exploratory Phase 2 Clinical Trial at ID Week 2017 – Globe Newswire

October 4, 2017

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

General microbiome

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

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

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

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

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

Pregnancy and early life

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

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

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

Human gut microbiome

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

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

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

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

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

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

Animal experiments

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

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

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

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

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

Animal microbiome

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

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

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

Plant, root, and soil microbiome

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

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

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

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

Water and extremophile microbiome

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

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

Food Microbiology

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

Probiotics / prebiotics

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

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

Phages and viruses

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

Metabolomics

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

Bioinformatics

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

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

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

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

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

Techniques

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

Anitha’s non-microbiology picks

A cold, clear view of life wins chemistry Nobel

Nobel physics prize awards discovery in gravitational waves

Medicine Nobel Prize Goes to Circadian Rhythm Researchers

New portable blood analyzer could improve anemia detection worldwide

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

 

October 3, 2017

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

Human oral microbiome

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

Human gut microbiome

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

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

Animal experiments

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

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

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

Animal microbiome

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

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

Plant, root, and soil microbiome

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

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

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

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

Water and extremophile microbiome

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

Food microbiology

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

Phages and viruses

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

Bioinformatics

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

More microbes

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

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