February 22, 2018

 

Events and jobs

Microbiology Adjunct Instructor – Diablo Valley College

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Pregnancy and early life

Review: Maternal Microbiota, Prepregnancy Weight, and Mode of Delivery
Intergenerational Transmission of Risk for Childhood Overweight and Obesity – Giulia Paolella – JAMA Pediatrics

 

Human ear, nose and throat microbiome

*A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera – Rachael Lappan – BMC Microbiology

The Tracheal Microbiota in Patients with a Tracheostomy Before, During, and After an Acute Respiratory Infection – Pérez-Losada, Marcos – The Pediatric Infectious Disease Journal

Human oral microbiome

Shift of microbial composition of peri-implantitis-associated oral biofilm as revealed by 16S rRNA gene cloning – Ali Al-Ahmad – Journal of Medical Microbiology

Human vaginal microbiome

Short- and long-term influence of the levonorgestrel-releasing intrauterine system (Mirena®) on vaginal microbiota and Candida – Gilbert Gerard Ghislain Donders – Journal of Medical Microbiology

Human gut microbiome

Transitional and temporal changes in the mucosal and submucosal intestinal microbiota in advanced Crohn’s disease of the terminal ileum – Rodrick J. Chiodini – Journal of Medical Microbiology

Gut microbiota trajectory in early life may predict development of celiac disease – Marta Olivares – BMC Microbiome

A comparison of the microbial community structure between inflamed and non-inflamed sites in patients with ulcerative colitis – Atsushi Hirano – Journal of Gastroenterology and Hepatology

The Impact of NOD2 Variants on Fecal Microbiota in Crohn’s Disease and Controls Without Gastrointestinal Disease – Nicholas A Kennedy – Inflammatory Bowel Diseases

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Animal experiments

Regulation of vitamin D metabolism following disruption of the microbiota using broad spectrum antibiotics – Stephanie A. Bora – The Journal of Nutritional Biochemistry

Soluble dietary fiber improves energy homeostasis in obese mice by remodeling the gut microbiota – Haiyuan Wang – Biochemical and Biophysical Research Communications

Lactobacillus and Bifidobacterium Ameliorate Memory and Learning Deficits and oxidative stress in Aβ (1-42) Injected Rats – Somayeh Athari Nik Azm – Applied Physiology, Nutrition, and Metabolism

*Chronic helminth infection perturbs the gut-brain axis, promotes neuropathology and alters behaviour – Paul R Giacomin – The Journal of Infectious Diseases

*Endometriosis induces gut microbiota alterations in mice – Ming Yuan – Human Reproduction

*Strain differences in the susceptibility to the gut–brain axis and neurobehavioural alterations induced by maternal immune activation in mice – Morais, Livia H – Behavioural Pharmacology

Specific synbiotics in early life protect against diet-induced obesity in adult mice
Mona Mischke – Diabetes, Obesity, and Metabolism

Transcriptomic and Proteomic Profiling Revealed High Proportions of Odorant Binding and Antimicrobial Defense Proteins in Olfactory Tissues of the House Mouse – Barbora Kuntová – Frontiers in Genetics

Lactobacillus accelerates ISCs regeneration to protect the integrity of intestinal mucosa through activation of STAT3 signaling pathway induced by LPLs secretion of IL-22 – Qihang Hou – Cell Death and Differentiation

Animal microbiome

Review: Gut barrier function: Effects of (antibiotic) growth promoters on key barrier components and associations with growth performance – Leon J Broom – Poultry Science

Fecal microbiota transplantation in puppies with canine parvovirus infection – Giorgio Q. Pereira – Journal of Veterinary Internal Medicine

Water and extremophile microbiome

Phylogeny and bioactivity of epiphytic Gram-positive bacteria isolated from three co-occurring antarctic macroalgae – Pamela Alvarado – Antonie van Leeuwenhoek

 

Resistome

The antibiotic resistome and microbiota landscape of refugees from Syria, Iraq and Afghanistan in Germany – Robert Häsler – BMC Microbiome

Transferable vancomycin resistance in clade B commensal-type Enterococcus faecium – François Lebreton – Journal of Antimicrobial Chemotherapy

 

Bioinformatics

Deciphering the trophic interaction between Akkermansia muciniphila and the butyrogenic gut commensal Anaerostipes caccae using a metatranscriptomic approach – Loo Wee Chia – Antonie van Leeuwenhoek

Biotechnology

*A 3D intestinal tissue model supports Clostridioides difficile germination, colonization, toxin production and epithelial damage – Lamyaa Shaban – Anaerobe

Design of synthetic bacterial communities for predictable plant phenotypes – Sur Herrera Paredes – PLOS Biology

Harnessing a Methane-Fueled, Sediment-Free Mixed Microbial Community for Utilization of Distributed Sources of Natural Gas – Jeffrey J. Marlow – Biotechnology and Bioengineering

Dissertation: Microbial Communities Involved in Carbon Monoxide and Syngas Conversion to Biofuels and Chemicals – Sofia Victoria Esquivel Elizondo – Arizona State University

 

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Microbes in the news

This Vibrant Bacteria Could Be Used to “Grow” Paint – Meilan Solly – Smithsonian

Bacteria-eaters to prevent food poisoning? Phages eliminate Yersinia from food – Science Daily

A ‘Grueling and Grotesque’ Biohacking Experiment – Kate McLean – The Atlantic

 

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February 13, 2018

The gut microbiome of honey bee workers, a review of “Foodomics” approaches to studying digestion and bioactivity, and a new genome sequence for a bacterium isolated from a cell phone screen.

Human gut microbiome

Review: Causal effects of the microbiota on immune-mediated diseases – June L Round – Science Immunology

Possible correlation between gut microbiota and immunity among healthy middle-aged and elderly people in southwest China – Xi Shen – Gut Pathogens

Animal experiments

Pre-print: Clostridium difficile alters the structure and metabolism of distinct cecal microbiomes during initial infection to promote sustained colonization – Matthew L Jenior – bioRxiv

Pre-print: Microbiota metabolic product deoxycholic acid controls chicken necrotic enteritis – Hong Wang – bioRxiv

Effects of Bentonite Bgp35b-p on the Gut Microbiota of Mice Fed a High-Fat Diet – Eun-Sook Lee – Science of Food and Agriculture

Animal microbiome

The role of the gut microbiome in health and disease of adult honey bee workers – Kasie Raymann – Current Opinion in Insect Science

Bacterial density rather than diversity correlates with hatching success across different avian species – Juan Manuel Peralta-Sánchez – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Influence of metal contamination in soil on metabolic profiles of Miscanthus x giganteus belowground parts and associated bacterial communities – Hoang Nam Pham – Applied Soil Ecology

Pre-print: In situ relationships between microbiota and potential pathobiota in Arabidopsis thaliana – Claudia Bartoli – bioRxiv

Effects of Using Arbuscular Mycorrhizal Fungi to Alleviate Drought Stress on the Physiological Traits and Essential Oil Yield of Fennel – Sedigheh Gheisari Zardak – Rhizosphere

Water and extremophile microbiome

Pre-print: Environmental determinants of pyoverdine production, exploitation and competition in natural Pseudomonas communities – Elena Butaitė – bioRxiv

Bacteria from Coral Ecosystem of Kiltan Island, Lakshadweep: Resource for Hydrolytic Enzymes – L Ramlath – International Journal of Cell Science and Biotechnology

Built environment

Microbacterium telephonicum sp. nov., isolated from the screen of a cellular phone – Praveen Rahi – International Journal of Systematic and Evolutionary Microbiology

Food microbiology

Review: The role of Foodomics to understand the digestion/bioactivity relationship of food – Grégory Pimentel – Current Opinion in Food Science

Phages and viruses

Virus-mediated transfer of nitrogen from heterotrophic bacteria to phytoplankton – Emma J Shelford – Biogeosciences

Small RNA-omics for virome reconstruction and antiviral defense characterization in mixed infections of cultivated Solanum plants – Silvia Turco – Molecular Plant-Microbe Interactions

Metabolomics

UPLC-QTOF-MS metabolomics analysis revealed the contributions of metabolites to the pathogenesis of Rhizoctonia solani strain AG-1-IA – Wenjin Hu – PLOS ONE

Microbes in the news

New imaging technique reveals how dragonfly wings tear bacteria apart – Alayna Hansen – New Atlas

Exploring the microbiome of an ocean bacteria – Kyle Frischkorn – Phys.Org

Microbes on the market

Rebiotix Develops Microbiome Health Index™ to Identify Indicators for Microbiome Restoration – PR Newswire

Bristol-Myers taps Sirenas for ‘global microbiome’ drug discovery – Amirah Al Idrus – FierceBiotech

Givaudan, Unilever target the microbiome – Marc S Reisch – Chemical & Engineering News

November 15, 2017

Virome analysis of bats and archaea, bioinformatics tools for metatranscriptomics analysis, using mass spectrometry for studying microbiome metabolomics.

General microbiome

Review: An integrative omics perspective for the analysis of chemical signals in ecological interactions – A E Brunetti – Chemical Society Reviews

Pregnancy and early life

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

Human respiratory microbiome

The role of the microbiome in childhood asthma – Giovanna Pisi – Immunotherapy

Human vaginal microbiome

Pre-print: A new sequencing-based women’s health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis – Elisabeth M Bik – bioRxiv

Human gut microbiome

Gut microbiota and body composition in anorexia nervosa inpatients in comparison to athletes, overweight, obese, and normal weight controls – Sabrina Mörkl – International Journal of Eating Disorders

Review: Gut Microbiota-Dependent Modulation of Energy Metabolism – C N Heiss – Journal of Innate Immunity

Animal experiments

Antimicrobial emulsifier – glycerol monolaurate induces metabolic syndrome, gut microbiota dysbiosis and systemic low-grade inflammation in low-fat diet fed mice – Zengliang Jiang – Molecular Nutrition and Food Research

A temperature sensitive Mycobacterium paragordonae induces enhanced protective immune responses against mycobacterial infections in the mouse model – Byoung-Jun Kim – Scientific Reports

Animal microbiome

Review: The B vitamin nutrition of insects: the contributions of diet, microbiome and horizontally acquired genes – Angela E Douglas – Current Opinion in Insect Science

Plant, root, and soil microbiome

Brassica napus has a key role in the recovery of the health of soils contaminated with metals and diesel by rhizoremediation – Rafael G Lacalle – Science of the Total Environment

Water and extremophile microbiome

Purification of eutrophic water containing chlorpyrifos by aquatic plants and its effects on planktonic bacteria – Xing-Jian Xu – Chemosphere

Cultivation of an immobilized (hyper)thermophilic marine microbial community in a bioreactor – M Landreau – FEMS Microbiology Letters

Pre-print: Dynamics of finely resolved, abundant symbiotic marine plankton and other interacting microbes via automated high-frequency sampling – David M Needham – bioRxiv

Food microbiology

Pre-print: Fusicatenibacter Is Associated with Kefir Drinking – Richard Sprague – bioRxiv

Probiotics/prebiotics

A novel double-layer mucoadhesive tablet containing probiotic strain for vaginal administration: Design, development and technological evaluation – María Teresa Sánchez – European Journal of Pharmaceutical Sciences

Efficacy and Safety of a Multistrain Probiotic Formulation Depends from Manufacturing – Vito Trinchieri – Frontiers in Immunology

Phages and viruses

Virome analysis of two sympatric bat species (Desmodus rotundus and Molossus molossus) in French Guiana – Arielle Salmier – PLOS ONE

Review: The enigmatic archaeal virosphere – David Prangishvili – Nature Reviews Microbiology

Bioinformatics

Old meets new: most probable number validation of metagenomic and metatranscriptomic datasets in soil – Tim H Mauchline – Letters in Applied Microbiology

Pre-print: AQMM: Enabling Absolute Quantification of Metagenome and Metatranscriptome – Xiao-Tao Jiang – bioRxiv

Metabolomics

Review: Mass spectrometry-based metabolomics: Targeting the crosstalk between gut microbiota and brain in neurodegenerative disorders – Hemi Luan – Mass Spectrometry Reviews

Pre-print: Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function – Chase Clark – bioRxiv

Techniques

Evaluating in vitro culture medium of gut microbiome with orthogonal experimental design and metaproteomics approach – Leyuan Li – Journal of Proteome Research

More microbes

Pre-print: Chemotaxis allows bacteria to overcome host-generated reactive oxygen species that constrain gland colonization – Kieran D Collins – bioRxiv

Microbes in the news

Specimens of Earth’s Oldest Known Life Forms Have Been Discovered in Tasmania – Michelle Starr – Science Alert

Shape-shifting agent targets harmful bacteria in the stomach – Phys.Org

Opinion: Not Just Antibiotics: Is Cancer Chemotherapy Driving Antimicrobial Resistance? – Lito E Papanicolas – Trends in Microbiology

Microbes on the market

A Silicon Valley Startup Wants Women To Test Their Vaginal Microbiota At Home – Ellie Kincaid – Forbes

Seres teams with cancer heavyweights for microbiome-checkpoint inhibitor combination trial – Nick Paul Taylor – FierceBiotech

October 28, 2017

A huge Saturday digest (150+ alerts), with many articles in the gut and animal microbiome.

Events and jobs
Postdoctoral researcher in Human Microbiome-Immune System Interactions – University of Luxembourg

Microbiome in Sexual, Maternal and Child Health Symposium – November 29, 2017

Pregnancy and early life
Gut microbiome in gestational diabetes: A Cross-sectional study of mothers and offspring 5 years post-partum – Sayyid Hasan – Acta Obstetricia et Gynecologica Scandivanica

The Influence of Proton Pump Inhibitors on the Fecal Microbiome of Infants with Gastroesophageal Reflux-A Prospective Longitudinal Interventional Study
Christoph Castellani – Frontiers in Cellular and Infection Microbiology

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

2 articles on iron supplements in the American Journal of Nutrition:
Review: Effects of iron fortification and supplementation on the gut microbiome and diarrhea in infants and children: a review – Daniela Paganini – American Journal of Clinical Nutrition

Review: Excess iron intake as a factor in growth, infections, and development of infants and young children – Bo Lönnerdal – American Journal of Clinical Nutrition

Human skin microbiome
RNase 7 participates in cutaneous innate control of Corynebacterium amycolatum – Stephanie Walter – Scientific Reports

FKBP12-Dependent Inhibition of Calcineurin Mediates Immunosuppressive Antifungal Drug Action in Malassezia – Giuseppe Ianiri – mBio

Human oral microbiome
Changes in periodontal and microbial parameters after the space maintainers application – M Aydinbelge – Nigerian Journal of Clinical Practice

Microbiome associated with dentures malodour – Shai Yitzhaki – Journal of Breath Research

Human gut microbiome
Gut microbiomes of mobile predators vary with landscape context and species identity – Julia Tiede – Ecology and Evolution

Distinct Microbial Communities Trigger Colitis Development upon Intestinal Barrier Damage via Innate or Adaptive Immune Cells – Urmi Roy – Cell Reports

Bile salt hydrolase-mediated inhibitory effect of Bacteroides ovatus on growth of Clostridium difficile – Soobin Yoon – Journal of Microbiology

Small-molecule inhibitors directly target CARD9 and mimic its protective variant in inflammatory bowel disease – Elizaveta S. Leshchiner – PNAS

Guiding longitudinal sampling in IBD cohorts – Yoshiki Vázquez-Baeza – Gut
Paper referenced: A microbial signature for Crohn’s disease – Victoria Pascal – Gut

Distinctive Gut Microbiota Is Associated with Diarrheagenic Escherichia coli Infections in Chilean Children – Pablo Gallardo – Frontiers in Cellular and Infection Microbiology

Gut Microbiota Perturbations in Reactive Arthritis and Post-Infectious Spondyloarthritis – Julia Manasson – Arthritis and Rheumatology

Severe intestinal dysbiosis is prevalent in primary Sjögren’s syndrome and is associated with systemic disease activity – Thomas Mandl – Arthritis Research and Therapy

Review: Salmonella enterica Serovar Typhimurium Strategies for Host Adaptation – Christopher J. Anderson – Frontiers in Microbiology

Review: Visceral Congestion in Heart Failure: Right Ventricular Dysfunction, Splanchnic Hemodynamics, and the Intestinal Microenvironment – Vincenzo B. Polsinelli – Current Heart Failure Reports

Review: Gut Microbiota Contribute to Age-Related Changes in Skeletal Muscle Size, Composition, and Function: Biological Basis for a Gut-Muscle Axis – Gregory J. Grosicki – Calcified Tissue International

Animal experiments
Multi-omics Comparative Analysis Reveals Multiple Layers of Host Signaling Pathway Regulation by the Gut Microbiota – Nathan P. Manes – MSystems

The yeast form of the fungus Candida albicans promotes persistence in the gut of gnotobiotic mice – Lena Böhm – PLoS Pathogens

Clinical Effect of IRT-5 Probiotics on Immune Modulation of Autoimmunity or Alloimmunity in the Eye – Jaeyoung Kim – Nutrients

Periodontal pathogenic bacteria, Aggregatibacter actinomycetemcomitans affect non-alcoholic fatty liver disease by altering gut microbiota and glucose metabolism – Rina Komazaki – Scientific Reports

β-Glucans in food modify colonic microflora by inducing antimicrobial protein, calprotectin, in a Dectin-1-induced-IL-17F-dependent manner – T Kamiya – Mucosal Immunology

Microbiome-driven allergic lung inflammation is ameliorated by short-chain fatty acids – A Cait – Mucosal Immunology

Effects of direct-fed microorganisms and enzyme blend co-administration on intestinal bacteria in broilers fed diets with or without antibiotics – T E Askelson – Poultry Science

16S rDNA analysis of the effect of fecal microbiota transplantation on pulmonary and intestinal flora – Tianhao Liu – 3 Biotech

Adaptation to Chronic Nutritional Stress Leads to Reduced Dependence on Microbiota in Drosophila melanogaster – Berra Erkosar – mBio

Characterization of fecal fat composition and gut derived fecal microbiota in high-fat diet fed rats following intervention with chito-oligosaccharide and resistant starch complexes – Wenting Shang – Food and Function

Genetic ablation of Cyp8b1 preserves host metabolic function by repressing steatohepatitis and altering gut microbiota composition – Jay V Patankar – American Journal of Physiology – Endocrinology and Metabolism

Effects of a probiotic (SLAB51™) on clinical and histologic variables and microbiota of cats with chronic constipation/megacolon: a pilot study – G. Rossi – Beneficial Microbes

Bacteriocin biosynthesis contributes to the anti-inflammatory capacities of probiotic Lactobacillus plantarum – X. Yin – Beneficial Microbes

Animal microbiome
Large-scale cultivation of the bumblebee gut microbiota reveals an underestimated bacterial species diversity capable of pathogen inhibition – Jessy Praet – Environmental Microbiology

Bacterial community of a spider, Marpiss magister (Salticidae) – Lihua Zhang – 3 Biotech

Fecal bacterial communities of wild-captured and stranded green turtles (Chelonia mydas) on the Great Barrier Reef – S Shamim – FEMS Microbiology Ecology

RECRUITMENT AND ESTABLISHMENT OF THE GUT MICROBIOME IN ARCTIC SHOREBIRDS – Kirsten Frond – FEMS Microbiology Ecology

The gorgonian coral Eunicella labiata hosts a distinct prokaryotic consortium amenable to cultivation – Tina Keller-Costa – FEMS Microbiology Ecology

Inheritance and Establishment of Gut Microbiota in Chickens – Jinmei Ding – Frontiers in Microbiology

Diversity and Transmission of Gut Bacteria in Atta and Acromyrmex Leaf-Cutting Ants during Development – Mariya Zhukova – Frontiers in Microbiology

Seawater transfer alters the intestinal microbiota profiles of Atlantic salmon (Salmo salar L.) – Carola E. Dehler – Scientific Reports

Plant, root, and soil microbiome
Characterizing endophytic competence and plant growth promotion of bacterial endophytes inhabiting the seed endosphere of Rice – Denver I. Walitang – BMC Microbiology

Pseudomonas syringae pv. syringae B728a Regulates Multiple Stages of Plant Colonization via the Bacteriophytochrome BphP1 – Regina McGrane – mBio

The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project – David J. Weston – New Phytologist

Bacterial Synergism in Lignocellulose Biomass Degradation – Complementary Roles of Degraders As Influenced by Complexity of the Carbon Source – Larisa Cortes-Tolalpa – Frontiers in Microbiology

Modulation of the efficiency of trace metal phytoremediation by Sedum plumbizincicola by microbial community structure and function – Jinyu Hou – Plant and Soil

Water and extremophile microbiome
Microbial community differentiation between active and inactive sulfide chimneys of the Kolumbo submarine volcano, Hellenic Volcanic Arc – Christos A. Christakis – Extremophiles

Variability in carbon uptake and (re)cycling in Antarctic cryptoendolithic microbial ecosystems demonstrated through radiocarbon analysis of organic biomarkers – A. L. Brady – GE Biology

High reactivity of deep biota under anthropogenic CO2 injection into basalt – Rosalia Trias – Nature Communications

Editorial: Marine microbiome as source of natural products – Fernando de la Calle – Microbial Biotechnology

Elucidating the impact of microbial community biodiversity on pharmaceutical biotransformation during wastewater treatment – Lauren B. Stadler – Microbial Biotechnology

Magnetite production and transformation in the methanogenic consortia from coastal riverine sediments – Shiling Zheng – Journal of Microbiology

Opportunistic Pathogens and Microbial Communities and Their Associations with Sediment Physical Parameters in Drinking Water Storage Tank Sediments – Ke Qin – Pathogens

Review: Methods of ammonia removal in anaerobic digestion: a review – Niclas Krakat – Water Science and Technology

Response of marine bacteria to oil contamination and to high pressure and low temperature deep sea conditions – Hanna Fasca – Microbiology Open

Built environment
The York Gospels: a 1000-year biological palimpsest – Matthew D. Teasdale – Royal Society Open Science (sequencing of parchment)

Conductive properties of methanogenic biofilms – Cheng Li – Bioelectrochemistry

Pulse electromagnetic fields enhance extracellular electron transfer in magnetic bioelectrochemical systems – Huihui Zhou – Biotechnology for Biofuels

Microbes in space
Microbial biodiversity assessment of the European Space Agency’s ExoMars 2016 mission – Kaisa Koskinen – Microbiome

Food microbiology
Safety assessment of transgenic canola RF3 with bar and barstar gene on Sprague-Dawley (SD) rats by 90-day feeding test – Tianqi Lang – Regulatory Toxicology and Pharmacology

Review: The role of wine and food polyphenols in oral health – Adelaida Esteban-Fernández – Trends in Food Science & Technology

Review: The agri-food chain and antimicrobial resistance: A review – John A. Hudson – Trends in Food Science & Technology

Review: Food derived anti-adhesive components against bacterial adhesion: Current progresses and future perspectives – Xiaohong Sun – Trends in Food Science & Technology

Probiotics / prebiotics / antibiotics
Effect of a yoghurt drink containing Lactobacillus strains on bacterial vaginosis in women – a double-blind, randomised, controlled clinical pilot trial – C. Laue – Beneficial Microbes

Bifidobacterium longum BB536 alleviated upper respiratory illnesses and modulated gut microbiota profiles in Malaysian pre-school children – A.S.-Y. Lau – Beneficial Microbes

Prebiotics for the prevention of allergies: A systematic review and meta-analysis of randomized controlled trials – C. Cuello-Garcia – Clinical and Experimental Allergy

Review: Metronidazole: an update on metabolism, structure-cytotoxicity and resistance mechanisms – Simon A Dingsdag – Journal of Antimicrobial Chemotherapy

Selective Proteomic Analysis of Antibiotic-Tolerant Cellular Subpopulations in Pseudomonas aeruginosa Biofilms – Brett M. Babin – mBio

Phages and viruses
Diel cycling and long-term persistence of viruses in the ocean’s euphotic zone – Frank O. Aylward – PNAS

Bioinformatics
MegaGTA: a sensitive and accurate metagenomic gene-targeted assembler using iterative de Bruijn graphs – Dinghua Li – BMC Bioinformatics

EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies – Alex L. Mitchell – Nucleic Acids Research

Techniques
A novel baiting microcosm approach used to identify the bacterial community associated with Penicillium bilaii hyphae in soil – Behnoushsadat Ghodsalavi – PLoS One

New Genomes
Bacillus kwashiorkori sp. nov., a new bacterial species isolated from a malnourished child using culturomics – El hadji Seck – Microbiology Open

Genome Sequence of Geobacillus stearothermophilus DSM 458, an Antimicrobial-Producing Thermophilic Bacterium, Isolated from a Sugar Beet Factory – Kevin Egan – Genome Announcements

Microbes in the news
Doctors warn new parents: Step away from the vaginal fluid swabs – Beth Mole – ARS Technica

New study details bacteria’s ‘sense of touch’ – Brooks Hays – UPI
Paper: Obstruction of pilus retraction stimulates bacterial surface sensing – Courtney K. Ellison – Science

T-Cell Enzyme Uses Deadly Multipronged Attack on Bacteria – GEN News
Paper: Granzyme B Disrupts Central Metabolism and Protein Synthesis in Bacteria to Promote an Immune Cell Death Program – Farokh Dotiwala – Cell

Gut bacteria could determine whether you develop PTSD – Sian Bradley – Wired (Paper from July 19)

Gut bacteria bolster disease research in labs – UNC Health Care

The Next Big Performance Enhancing Drug: Bacteria From Elite Athletes’ Guts? – Peter Audrey Smith – Men’s Journal

Microbes on the market
French Biotech’s Crohn’s Candidate Glides Through Phase I – Alex Dale – Lab Biotech

Enterome’s EB8018, a First-in-class Drug Candidate Targeting Crohn’s Disease, Successfully Completes Phase I Study in Healthy Volunteers – Enterome – Cision (same as above link, more detail)

October 24, 2018

Today’s digest is full of REALLY cool science and features including a 3D image of the human lung microbiome and metabolome, how gut microbiome of wild mice promotes fitness, and an interesting perspective piece on how environmental filtering applies to microbiomes.

General microbiome

Environmental Filtering Is a Relic. A Response to Cadotte and Tucker.

Aguilar-Trigueros CA- Trends in Ecology and Evolution

Gut microbiome

The Leaky Gut and Altered Microbiome in Chronic Kidney Disease.

Lau WL- Journal of Renal Nutrition

Linking the Gut Microbial Ecosystem with the Environment: Does Gut Health Depend on Where We Live?

Tasnim N- Frontiers in Microbiology

Skin microbiome

High-Altitude Living Shapes the Skin Microbiome in Humans and Pigs.

Zeng B- Frontiers in Microbiology

Lung microbiome

Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung

Garg N- Cell Host and Microbe

Animal microbiome

Wild Mouse Gut Microbiota Promotes Host Fitness and Improves Disease Resistance

Rosshart SP- Cell

Plant and soil microbiome

Soil bacterial community mediates the effect of plant material on methanogenic decomposition of soil organic matter

Yuan Q- Soil Biology and Biochemistry

Bacterial communities in soil become sensitive to drought under intensive grazing

Jurburg SD- Science of the Total Environment

Prokaryotic Community Distribution along an Ecological Gradient of Salinity in Surface and Subsurface Saline Soils.

Xie K- Scientific reports

Marine and inland water microbiome

Transcriptional activities of the microbial consortium living with the marine nitrogen-fixing cyanobacterium Trichodesmium reveal potential roles in community-level nitrogen cycling

Lee MD-Applied and Environmental Microbiology

Dynamic microbial populations along the Cuyahoga River.

Cannon MV-  PloS one

Preprint

High degree of virulence gene diversity in Streptococcus pyogenes isolated in Central Italy

Bencardino D- BioRxiv

Microbiome News

I Wish I’d Known This Before I Gave Birth

-mindbodygreen.com

October 8, 2017

General microbiome

Repurposed kinase inhibitors and β-lactams as a novel therapy for antibiotic resistant bacteria – Nathan Wlodarchak, bioRxiv

Isolation and whole genome analysis of endospore-forming bacteria from heroin – Jörn Kalinowski, Forensic Science International: Genetics

Events and jobs

DOCTORAL STUDENT / POSTDOCTORAL RESEARCHER, EARLY INTERACTIONS OF INTESTINAL MICROBIOTA AND THE IMMUNE SYSTEM – University of Helsinki

Director of the Microbiome Research Laboratory – Microbiome Research Laboratory (MRL) at UT Southwestern

Microbiology Faculty Position – University of Chicago

Human gut microbiome

Microbiome, inflammation and colorectal cancer – Ju Chen, Seminars in Immunology

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

Targeting gut microbiota: Lactobacillus alleviated type 2 diabetes via inhibiting LPS secretion and activating GPR43 pathway – Kai-Kai Li, Journal of Functional Foods

Volatile Organic Compounds in Feces Associate With Response to Dietary Intervention in Patients With Irritable Bowel Syndrome – Megan Rossi, Clinical Gastroenterology and Hepatology

Proteomics Dataset: The Colon Mucosa from Inflammatory Bowel Disease Patients, Gastrointestinal Asymptomic Rheumatoid Arthritis Patients, and Controls – Tue Bjerg Bennike, Data in Brief

The mycobiome: Role in health and disease, and as a potential probiotic target in gastrointestinal disease – Christopher L. Hager, Digestive and Liver Disease

Overview of paediatric IBD – David C. Wilson, Seminars in Pediatric Surgery

Improvement of Insulin Sensitivity after Lean Donor Feces in Metabolic Syndrome Is Driven by Baseline Intestinal Microbiota Composition – Ruud S. Kootte, Cell Metabolism

Fasting the Microbiota to Improve Metabolism? – Joel T. Haas, Cell Metabolism

Fecal Transplant in Inflammatory Bowel Disease – Alexander S. Browne, Gastroenterology Clinics of North America

The Brain-Gut Axis and Stress in Inflammatory Bowel Disease  – Charles N. Bernstein, Gastroenterology Clinics of North America

Human oral microbiome

The oral microbiota in colorectal cancer is distinctive and predictive – Burkhardt Flemer, Gut microbiota

Animal experiments

Interhost dispersal alters microbiome assembly and can overwhelm host innate immunity in an experimental zebrafish model – Adam R. Burns, PNAS

Ganoderma lucidum polysaccharides improve insulin sensitivity by regulating inflammatory cytokines and gut microbiota composition in mice – S. Xua, Journal of Functional Foods

Effect of enzymatically hydrolyzed scallop visceral protein powder used as a replacement of fish meal on the growth performance, immune responses, intestinal microbiota and intestinal morphology of broiler chickens – R.E. Xing, Livestock Science

Intestinal microbiota impact sepsis associated encephalopathy via the vagus nerve – Suyan Li, Neuroscience Letters

Animal microbiome

Environmental proteomics reveals taxonomic and functional changes in an enriched aquatic ecosystem – Amanda C. Northrop, Ecosphere

Plant, root, and soil microbiome

Characterization of the first rice paddy cluster I isolate, Methyloterricola oryzae gen. nov., sp. nov. and amended description of Methylomagnum ishizawai –  Katharina Frindte, International Journal of Systematic and Evolutionary Microbiology

Water and extremophile microbiome

Ultrastructural observations on prokaryotic associates of benthic foraminifera: Food, mutualistic symbionts, or parasites? – Joan M. Bernhard, Marine Micropaleontology

Food microbiology

Potentially active spoilage bacteria community during the storage of vacuum packaged beefsteaks treated with aqueous ozone and electrolyzed water – Cristian Botta, International Journal of Food Microbiology

Next generation of microbiological risk assessment: Potential of omics data for exposure assessment – Heidy M.W. den Besten, International Journal of Food Microbiology

Characterization of lactic acid bacteria recovered from atole agrio, a traditional Mexican fermented beverage – Kati Väkeväinen, LWT – Food Science and Technology

Probiotics / prebiotics

Prebiotics and Inflammatory Bowel Disease – Heather E. Rasmussen, Gastroenterology Clinics of North America

Probiotics in Inflammatory Bowel Disease – Bincy P. Abraham, Gastroenterology Clinics of North America

Enhancing the viability of Lactobacillus rhamnosus GG after spray drying and during storage – Géraldine Broeckx, International Journal of Pharmaceutics

Microbes in the news

Second grade handwashing experiment leads to big decrease in bacteria, illness – INFECTIOUS DISEASES SOCIETY OF AMERICA, EurekAlert!

UTHealth awarded $3.1 million NIH grant to study how gut bacteria relates to diabetes – UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT HOUSTON, EurekAlert!

Scientists are trying to figure out how to keep bacteria from running rampant on space missions –  Claire Maldarelli, Popular Science

“Good” Gut Bacteria Linked to Melanoma Immunotherapy Response – GEN

August 1, 2017

Today’s digest is relatively short, but there is an amazing commentary on rhizosheath and advantages of using phylogenetic distances to examine the microbial communities

Human gut microbiome

Maternal modifiers of the infant gut microbiota: metabolic consequences

Mulligan CM. Journal of Endocrinology

Association between gut microbiota and bone health: potential mechanisms and prospective

Chen YC. The Journal of Clinical Endocrinology & Metabolism

Plant, soil, and air microbiome

Amynthas agrestis invasion increases microbial biomass in Mid-Atlantic deciduous forests

Chang CH. Soil Biology and Biochemistry

Effect of nanoparticles on crops and soil microbial communities

Rajput VD. Journal of Soils and Sediments

Bottom-up effects on herbivore-induced plant defences: a case study based on compositional patterns of rhizosphere microbial communities.

Benítez E. Scientific reports

Unwrapping the rhizosheath

Pang J. Plant and Soil

Marine and inland waters

Marine archaea and archaeal viruses under global change

Danovaro R-F1000 Research

Bacterial community structure in the intertidal biofilm along the Yangtze Estuary, China

Guo X .Marine Pollution Bulletin

Fronts at the surface ocean can shape distinct regions of microbial activity and community assemblages down to the bathypelagic zone: The Azores Front as a case study

Baltar F. Frontiers in Marine Science

Microbiome Approaches/Techniques

A deep metaproteomics approach for the study of human microbiomes

Zhang X Analytical Chemistry, 2017

Advantages of phylogenetic distance based constrained ordination analyses for the examination of microbial communities.

Shankar V. Scientific reports

Oral/Nasal Microbiome 

The periodontal war: microbes and immunity

Ebersole JL. PERIODONTOLOGY 2000

Design and validation of a DNA-microarray for phylogenetic analysis of bacterial communities in different oral samples and dental implants

Parolin C. Scientific Reports

Influence of the pneumococcal conjugate vaccines on the temporal variation of pneumococcal carriage and the nasal microbiota in healthy infants: a longitudinal analysis of a case–control study

Mika M. Microbiome

Food Microbiology 

Comparison study of the volatile profiles and microbial communities of Wuyi Qu and Gutian Qu, two major types of traditional fermentation starters of Hong Qu glutinous rice wine

Liu Z.Food Microbiology

Plant-mediated restriction of Salmonella enterica on tomato and spinach leaves colonized with Pseudomonas plant growth-promoting rhizobacteria

Hsu CK.International Journal of Food Microbiology, 2017