July 11, 2017

Welcome to your Tuesday Digest. Today, some interesting pieces from Science mag about scientific career. A few pre-prints in the Plant & Soil section, including a paper by Hubbard et al. that presents an interesting concept on plant’s diel cycle and rhizosphere community. Enjoy!

Events and jobs
Director, Sterile and Microbiology Quality Assurance Job
Merck – West Point – PA, US

Multi-site human microbiome
The influence of the commensal microbiota on distal tumor-promoting inflammation.
Buchta Rosean CM, Rutkowski MR – Seminars in Immunology

Human gut microbiome
Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life
Weili Xiong et al. – Microbiome

Genome-scale model and omics analysis of metabolic capacities of Akkermansia muciniphila reveal a preferential mucin-degrading lifestyle
Ottman N et al. – Applied Environmental Microbiology

Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy
Sivaranjani Namasivayam et al. – Microbiome

Animal experiments
Host specificity of Segmented Filamentous Bacteria (SFB) flagellins affects their interaction patterns with mouse ileal mucosal proteins.
Chen H et al. – Applied Environmental Microbiology

Plant, root, and soil microbiome
Pre-print: The plant circadian clock influences rhizosphere community structure and function
Charley Hubbard et al. – bioRxiv

Microbial functional diversity responses to 2 years since biochar application in silt-loam soils on the Loess Plateau
Zhu LX et al. – Ecotoxicology and Environmental Safety

Review: Microbes from mined sites: Harnessing their potential for reclamation of derelict mine sites
Thavamani P. et al – Environmental Pollution

Review: Microbial activity and the dynamics of ecosystem processes in forest soils
Baldrian P. – Current Opinion in Microbiology

Pre-print: Maize Phyllosphere Microbial Community Niche Development Across Stages of Host Leaf Growth
Heather C. Manching et al. – bioRxiv

Water, estuarine and sediment microbiome
Distinct Aeromonas Populations in Water Column and Associated with Copepods from Estuarine Environment (Seine, France)
Gautier Chaix et al. – Frontiers in Microbiology

Vertical and horizontal assemblage patterns of bacterial communities in a eutrophic river receiving domestic wastewater in southeast China.
Gao Y et al. – Environmental Pollution

Extremophile and space microbiome
Human presence impacts fungal diversity of inflated lunar/Mars analog habitat
A. Blachowicz et al. – Microbiome

Built environment
Metagenomic analysis reveals wastewater treatment plants as hotspots of antibiotic resistance genes and mobile genetic elements
Guo J et al. – Water Research

Review: The potential implications of reclaimed wastewater reuse for irrigation on the agricultural environment: The knowns and unknowns of the fate of antibiotics and antibiotic resistant bacteria and resistance genes – A review.
Christou A et al – Water Research

New insights into the spatial variability of biofilm communities and potentially negative bacterial groups in hydraulic concrete structures.
Cai W. et al – Water Reseach

Pre-print: Cyanobacterial Growth on Municipal Wastewater Requires Low Temperatures
Travis C. Korosh et al. – bioRxiv

Microbial biotechnology
Expanding landscapes of the diversified mcr-1-bearing plasmid reservoirs
Qingjing Wang & Jian Sun et al. – Microbiome

General microbiology and evolution
Effect of a Pseudomonas fluorescens tailocin against phytopathogenic Xanthomonas observed by atomic force microscopy
M. Fernandez et al. – Journal of Biotechnology

Natural-Product Antibiotics: Cues for Modulating Bacterial Biofilm Formation
Townsley L. & Shank EA – Trends in Microbiology

Bioinformatics and statistics
VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data
Jie Ren & Nathan A. Algren et al. – Microbiome

Pre-print: A supervised statistical learning approach for accurate Legionella pneumophila source attribution during outbreaks
Andrew H. Buultjens et al. – bioRxiv

Review: Mining Metagenomic Data Sets for Ancient DNA: Recommended Protocols for Authentication
Key FM et al – Trends in Genetics

Techniques and methods
Formulation, stabilisation and encapsulation of bacteriophage for phage therapy
Malik DJ et al. – Advances in Colloid and Interface Science

A novel ultra high-throughput 16S rRNA gene amplicon sequencing library preparation method for the Illumina HiSeq platform
Eric J. de Muinck et al. – Microbiome

Microbes in the news
I gave my cat a poop transplant—here’s what happened next
Jonathan Gitlin – arstechnica

Gonorrhea is getting even harder to treat
Ashley Welch – CBS News

Science, publishing, and career
Reprogramming my career
Charmaine Tam – Science

The cyberscientist
John Bohannon – Science

The scientists’ apprentice
Tim Appenzeller – Science

Food and microbiota in the FDA regulatory framework
Jonathan M. Green et al. – Science

July 9, 2017

Double Day Digest! Today we have picks for the entire weekend in one post, so here is a great selection!

 

Events and jobs

Laboratory Technician – Cranleigh Scientific – Cambridge, England

General microbiome

Review – Food-animal production and the spread of antibiotic resistance: the role of ecology – Benjamin J Koch – Frontiers in Ecology and the Enviroment

Human skin microbiome 

Impact of coated TiO2-nanoparticles used in sunscreens on two representative strains of the human microbiota: Effect of the particle surface nature and aging – Laura Rowenczyk – Colloids and Surfaces B: Biointerfaces

Human gut microbiome

Review – Gut microbiome, metabolome, and allergic diseases – So-ichiro Hirata – Allergology International

Review – Bile Acids and Intestinal Microbiota in Autoimmune Cholestatic Liver Diseases – You Li – Autoimmunity Reviews

Bifidobacterium animalis subsp. lactis LKM512 reduces levels of intestinal trimethylamine produced by intestinal microbiota in healthy volunteers: A double-blind, placebo-controlled study – Mitsuharu Matsumoto – Journal of Functional Foods

Animal experiments

Long-term consumption of caffeine-free high sucrose cola beverages aggravates the pathogenesis of EAE in mice – Guangchao Cao  – Cell Discovery

Review – Using probiotics to improve swine gut health and nutrient utilization – Shengfa F. Liao – Animal Nutrition

Dietary and lifestyle disease indices and caecal microbiota in high fat diet, dietary fibre free diet, or DSS induced IBD models in ICR mice – Takashi Kuda – Journal of Functional Foods

Head-injury profoundly affects gut microbiota homeostasis: results of a pilot study – Anne-Judith Waligora-Dupriet – Nutrition

Animal microbiome

Review – Marine animal microbiomes: towards understanding host-microbiome interactions in a changing ocean – Amy Apprill – Frontiers in Marine Science

Influence of elevation in structuring the gut bacterial communities of Apis cerana – S Sudhagar – Journal of Entomology and Zoology Studies

Plant, root, and soil microbiome

Comparison of soil biosolarization with mesophilic and thermophilic solid digestates on soil microbial quantity and diversity – Jesús D. Fernández-Bayo – Applied Soil Ecology

Contrasting habitats but comparable microbial decomposition in the benthic and hyporheic zone – Ute Risse-Buhl – Science of The Total Environment

Beneficial traits of bacterial endophytes belonging to the core communities of the tomato root microbiome – Baoyu Tian – Agriculture, Ecosystems & Environment

Long- term grapevine cultivation and agro-environment affect rhizosphere microbiome rather than plant age – L.M. Manici – Applied Soil Ecology

Comparison of soil biosolarization with mesophilic and thermophilic solid digestates on soil microbial quantity and diversity – Jesús D. Fernández-Bayo – Applied Soil Ecology

Positive effects of plant association on rhizosphere microbial communities depend on plant species involved and soil nitrogen level – Barbara Pivato – Soil Biology and Biochemistry

Water and extremophile microbiome

Current Trend of Metagenomic Data Analytics for Cyanobacteria Blooms – JianDong Huang – Journal of Geoscience and Environment Protection

Early bacterial biofilm colonizers in the coastal waters of Mauritius – Sillma Rampadarath – Electronic Journal of Biotechnology

Metagenomic analysis reveals wastewater treatment plants as hotspots of antibiotic resistance genes and mobile genetic elements – Jianhua Guo – Water Research

Characterization of microbial signatures from advanced treated wastewater biofilms – Leddy, Menu B – AMERICAN WATER WORKS ASSOCIATION

Greater diversity of soil fungal communities and distinguishable seasonal variation in temperate deciduous forests compared with subtropical evergreen forests of eastern China – Jinhong He – FEMS Microbiology Ecology

Microbes from mined sites: Harnessing their potential for reclamation of derelict mine sites – Palanisami Thavamani – Environmental Pollution

Bacterial communities and chemical parameters in soils and coastal sediments in response to diesel spills at Carlini Station, Antarctica – Susana Vázquez – Science of The Total Environment

Food microbiology

Elucidating microbial community adaptation to anaerobic co-digestion of fats, oils, and grease and food waste – Yamrot M. Amha – Water Research

Techniques

Personalized microbiome dynamics – Cytometric fingerprints for routine diagnostics – Christin Koch – Molecular Aspects of Medicine

Development of a real-time PCR method for quantification of Prevotella histicola from the gut – Baskar Balakrishnan – Anaerobe

Microbes in the news

Why Life on Mars May Be Impossible – TIME – Jeffrey Kluger

July 6, 2017

The microbiota of spotted hyenas, a review of potential interactions between olfactory sensation and the microbiome-gut-brain axis, phylogenetic analysis of host-microbe symbioses to examine the evolution of dependence over time.

General microbiome

Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia – Sami Ben Said – Frontiers in Microbiology

The evolution of host-symbiont dependence – Roberta M Fisher – Nature Communications

Review: The microbiota revolution: Excitement and caution – Maria Rescigno – European Journal of Immunology

Review: The Microbiome and Blood Pressure: Can Microbes Regulate Our Blood Pressure? – Souhaila Al Khodor – Frontiers in Pediatrics

Human oral microbiome

Suppression of αvβ6 Integrin Expression by Polymicrobial Oral Biofilms in Gingival Epithelial Cells – Jiarui Bi – Scientific Reports

Proteomic shifts in multi-species oral biofilms caused by Anaeroglobus geminatus – Kai Bao – Scientific Reports

Human vaginal microbiome

Quantifying the human vaginal community state types (CSTs) with the species specificity index – Zhanshan Ma – PeerJ

Animal experiments

Effects of iron supplementation on growth, gut microbiota, metabolomics and cognitive development of rat pups – Erica E Alexeev – PLOS ONE

Review: Disruptive physiology: olfaction and the microbiome-gut-brain axis – John Bienenstock – Biological Reviews Cambridge Philosophical Society

Effects of melanin from Sepiella Maindroni ink (MSMI) on the intestinal Microbiome of mice – Hui Dong – BMC Microbiology

Animal microbiome

The Intestinal Eukaryotic and Bacterial Biome of Spotted Hyenas: The Impact of Social Status and Age on Diversity and Composition – Emanuel Heitlinger – Frontiers in Cellular and Infection Microbiology

Plant, root, and soil microbiome

Perspective: The deep, hot biosphere: Twenty-five years of retrospection – Daniel R Colman – PNAS

Draft Genome Sequence of Pseudomonas koreensis CI12, a Bacillus cereus “Hitchhiker” from the Soybean Rhizosphere – Gabriel L Lozano – Genome Announcements

Warmer winters increase the rhizosphere carbon flow to mycorrhizal fungi more than to other microorganisms in a temperate grassland – Johanna Birgander – Global Change Biology

Negative plant-phyllosphere feedbacks in native Asteraceae hosts – a novel extension of the plant-soil feedback framework – Briana K Whitaker – Ecology Letters

Water and extremophile microbiome

Size and composition of subseafloor microbial community in the Benguela upwelling area examined from intact membrane lipid and DNA analysis – Thomas W Evans – Organic Geochemistry

FurukawaMarine microbes as a valuable resource for brand new industrial biocatalysts – Azadeh Beygmoradi – Biocatalysts and Agricultural Biotechnology

Antagonistic Interactions and Biofilm Forming Capabilities Among Bacterial Strains Isolated from the Egg Surfaces of Lake Sturgeon (Acipenser fulvescens) – M Fujimoto – Microbial Ecology

Probiotics/prebiotics

Effects of the probiotic Bifidobacterium animalis subsp. lactis on the non-surgical treatment of periodontitis. A histomorphometric, microtomographic and immunohistochemical study in rats – Milla S T Ricoldi – PLOS ONE

Phages and viruses

Virus-host relationships of marine single-celled eukaryotes resolved from metatranscriptomics – Mohammad Moniruzzaman – Nature Communications

Occurrence of Bacillus thuringensis Bacteriophages in the Egyptian Arid Soil – Amel S M Abo-Senna – International Journal of Virology and Molecular Biology

Bioinformatics

A conceptual framework for quality assessment and management of biodiversity data – Allan Koch Veiga – PLOS ONE

Techniques

SParticle, an algorithm for the analysis of filamentous microorganisms in submerged cultures – Joost Willemse – bioRxiv

Mapping-based all-RNA-information sequencing analysis (ARIseq) pipeline simultaneously revealed taxonomic composition, gene expression, and their correlation in an acidic stream ecosystem – Arisa Tsuboi – bioRxiv

More microbes

Review: Metabolic engineering pathways for rare sugars biosynthesis, physiological functionalities, and applications – A review – Muhammad Bilal – Critical Reviews in Food Science and Nutrition

Microbes in the news

Microbes aren’t the enemy, they’re a big part of who we are – Amy Loughman – Medical Xpress

What Cheese Can Tell Us About Antibiotic Resistance – Jason Tetro – Huffington Post Canada

Cases of recurrent Clostridium difficile infection are soaring – Medical Xpress

Helium ions reveal how viruses attack bacteria – ScienceDaily

July 4, 2017

Happy 4th of July!

Events and jobs
Microbiology Team Lead – Bentleyville, PA

General microbiome
Host Microbiome Richness Predicts Resistance to Disturbance by Pathogenic Infection in a Vertebrate Host – Xavier A. Harrison – bioRxiv

Pregnancy and early life
Review: SALSA—A dance on a slippery floor with changing partners – M.P. Reichhardt – Molecular Immunology

Review: The Microbiome and Biomarkers for Necrotizing Enterocolitis: Are We Any Closer to Prediction? – Brigida Rusconi – Journal of Pediatrics

Human skin microbiome
Cutaneous Leishmaniasis Induces a Transmissible Dysbiotic Skin Microbiota that Promotes Skin Inflammation – Ciara Gimblet – Cell Host and Microbe

Human oral microbiome
Hydrogen sulfide exposure induces NLRP3 inflammasome-dependent IL-1β and IL-18 secretion in human mononuclear leukocytes in vitro – Amina Basic – Clinical and Experimental Dental Research

Human gut microbiome
Immunoregulatory effect of mast cells influenced by microbes in neurodegenerative diseases – Francesco Girolamo – Brain, Behavior, and Immunity

Review: Host Genetics and Gut Microbiome: Challenges and Perspectives – Alexander Kurilshikov – Trends in Immunology

Review: Shaping functional gut microbiota using dietary bioactives to reduce colon cancer risk – Derek V. Seidel – Seminars in Cancer Biology

Review: Extracellular vesicles in gastrointestinal cancer in conjunction with microbiota: On the border of Kingdoms – Natasha S. Barteneva – Biochimica et Biophysica Acta (BBA) – Reviews on Cancer

Microbial ecology
Small subsets of highly connected taxa predict compositional change in microbial communities – Cristina Herren – bioRxiv

Animal experiments
Effect of administration route and dose alteration on sulfadiazine-trimethoprim plasma and intestinal concentrations in pigs – Joren De Smet – International Journal of Antimicrobial Agents

Isomalto-oligosaccharides, a prebiotic, functionally augment green tea effects against high fat diet-induced metabolic alterations via preventing gut dysbacteriosis in mice – Dhirendra Pratap Singh – Pharmacological Research

6-Shogaol ameliorates injury to the intestinal mucosa and increases survival after high-dose abdominal irradiation – Jinhan Wang – Journal of Functional Foods

Total abdominal irradiation exposure impairs cognitive function involving miR-34a-5p/BDNF axis – Ming Cui – Biochimica et Biophysica Acta (BBA) – Molecular Basis of Disease

Bidirectional Brain-Gut Interactions and Chronic Pathological Changes after Traumatic Brain Injury in Mice – Elise L. Ma – Brain, Behavior, and Immunity

An increase in corn resistant starch decreases protein fermentation and modulates gut microbiota during in vitro cultivation of pig large intestinal inocula – Xiangyu He – Animal Nutrition

Animal microbiome
Natural products and morphogenic activity of γ-Proteobacteria associated with the marine hydroid polyp Hydractinia echinata – Huijuan Guo – Bioorganic and Medicinal Chemistry

Plant, root, and soil microbiome
Feedbacks between plant N demand and rhizosphere priming depend on type of mycorrhizal association – Benjamin N. Sulman – Ecology Letters

Cyanobacterial and rhizobial inoculation modulates the plant physiological attributes and nodule microbial communities of chickpea – Radha Prasanna – Archives of Microbiology

Probiotics / prebiotics
Development of Carboxymethyl Cellulose-Chitosan Hybrid Micro- and Macroparticles for Encapsulation of Probiotic Bacteria – P. Singh – Carbohydrate Polymers

Bioinformatics
Evaluating Metagenome Assembly on a Simple Defined Community with Many Strain Variants – Sherine Awad – bioRxiv

Techniques
Magic pools: parallel assessment of transposon delivery vectors in bacteria – Hualan Liu – bioRxiv

Imaging Bacterial Colonies and Phage–Bacterium Interaction at Sub-Nanometer Resolution Using Helium-Ion Microscopy – Miika Leppänen – Advanced BioSystems

Microbes in the news
Essays on health: microbes aren’t the enemy, they’re a big part of who we are – Amy Loughman and Tarsh Bates – The Conversation

Modified sugar compound can clear intestinal colonization by UPEC – Irene Vacca – Nature Reviews Microbiology
Original paper: Selective depletion of uropathogenic E. coli from the gut by a FimH antagonist – Caitlin N. Spaulding – Nature (June 14, 2017)

Human Emotions Really Are Affected by Gut Bacteria, New Study Suggests – Peter Dockrill – Science Alert
Original paper: Brain structure and response to emotional stimuli as related to gut microbial profiles in healthy women – Kirsten Tillisch – Psychosomatic Medicine (June 28, 2017)

Eliminating harmful bacteria from oil reservoirs – Newcastle University

Woman contracts flesh-eating bacteria in Fairhope – Allison Marlow – Gulf Coast News Today

Second LA Fitness also tests positive for Legionnaires’-causing bacteria – Kyle Arnold – Orlando Sentinel

Microbes on the market
EPS for DexCom, Inc. (DXCM) Expected At $-0.14; Profile of 6 Analysts Covering Seres Therapeutics (MCRB) – Clifton Ray – Herald KS

Using Microbiome Analytics to Improve Milk Safety – Joel Hans – RT Insights

Bacteria Hysteria
These terrifying photos show why you really should throw your old makeup away – Laura Capon – Cosmopolitan

Science, publishing, and career
Is the staggeringly profitable business of scientific publishing bad for science? – The Guardian
This sure made the round on Twitter a few days ago!

The vagueness problem in academic writing – The Thesis Whisperer

Laid Off From the Tenure Track – a Guest Post – The Professor is In
I read her book a while back and thought it was fantastic. Karen Kelsky’s blog focuses on academia in the humanities, but there are overlaps in science!

June 28, 2017

Human vaginal microbiome

Vaginal seeding or vaginal microbial transfer from the mother to the cesarean born neonate: a commentary regarding clinical management – Thor Haahr – BJOG

Human gut microbiome

*Review: The resilience of the intestinal microbiota influences health and disease – Felix Sommer – Nature Reviews Microbiology

Other human microbiome

Urinary catheter-associated microbiota change in accordance with treatment and infection status – Laetitia Bossa – PLOS ONE

Dynamics of the Oral Microbiota as a Tool to Estimate Time Since Death – Joe Adserias Garriga – Molecular Oral Microbiology

Animal experiments

Tuftsin-Phosphorylcholine maintains normal gut microbiota in collagen induced arthritic mice – Hila Ben-Amram – Frontiers in Microbiology

Animal microbiome

The Diet and Gut Microbial Communities of Two Closely Related Combtooth Blennies, Chasmodes saburrae and Scartella cristata – Peter J. Hundt – Copeia

Variation in the microbiome of the urogenital tract of koalas (Phascolarctos cinereus) with and without “wet bottom” – Alistair R. Legione – bioRxiv

Plant, root, and soil microbiome

Dominant Groups of Potentially Active Bacteria Shared by Barley Seeds become Less Abundant in Root Associated Microbiome – Luhua Yang – Frontiers in Plant Science

Understanding the variation of microbial community in heavy metals contaminated soil using high throughput sequencing – Honghong Guo – Ecotoxicology and Environmental Safety

Root Hair Mutations Displace the Barley Rhizosphere Microbiota – Senga Robertson-Albertyn – Frontiers in Plant Science

*Review: Below-ground connections underlying above-ground food production: a framework for optimising ecological connections in the rhizosphere – Franciska T. de Vries – Journal of Ecology

Rhizosphere microorganisms affected by soil solarization and cover cropping in Capsicum annuum and Phaseolus lunatus agroecosystems – Nancy Kokalis-Burelle – Applied Soil Ecology

Bacterial community dynamics in the rhizosphere of a long-lived, leguminous shrub across a 40-year age sequence – Xiaofan Na – Journal of Soils and Sediments

Microbial populations of stony meteorites: Substrate controls on first colonisers – Alastair W. Tait – Frontiers in Microbiology

Water and extremophile microbiome

Microbial Diversity and Community Assembly across Environmental Gradients in Acid Mine Drainage – Wenkai Teng – Minerals

Abundance and Distribution of Microbial Cells and Viruses in an Alluvial Aquifer – Donald Pan – Frontiers in Microbiology

Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat – Jackson Z Lee – bioRxiv

Bioinformatics

Mixed Effect Dirichlet-Tree Multinomial for Longitudinal Microbiome Data and Weight Prediction – Yunfan Tang – arXiv

Segal’s Law, 16S rRNA gene sequencing, and the perils of foodborne pathogen detection within the American Gut Project – James B. Pettengill – PeerJ

Techniques

Assembly and Tracking of Microbial Community Development within a Microwell Array Platform – Andrea C. Timm – JOVE

June 20, 2017

Great articles from bioRxiv today!

Events and jobs
Microbiology Clinical Laboratory Scientist OR Microbiology CLS Opening – KA Recruiting – San Francisco, CA

Acting QC Specialist: Microbiology – Johnson and Johnson – Cork, Ireland

Human vaginal microbiome
Effects of intrauterine contraception on the vaginal microbiota – Christine M. Bassis – Contraception

Human gut microbiome
**Environmental factors dominate over host genetics in shaping human gut microbiota composition – Daphna Rothschild – bioRxiv**

Review: Role of gut microbiota against calcium oxalate – Humaira Sadaf – Microbial Pathogenesis

Review: Glucocorticoids and gut bacteria: “The GALF Hypothesis” in the metagenomic era – David J. Morris – Steroids

Review: The microbiome-gut-brain axis: implications for schizophrenia and antipsychotic induced weight gain – S. Kanji – European Archives of Psychiatry and Clinical Neuroscience

Animal experiments
Glycaemic and insulinaemic responses of adult healthy warm-blooded mares following feeding with Jerusalem artichoke meal – M. Glatter – Animal Physiology and Animal Nutrition

Water and extremophile microbiome
Review: Phototrophic biofilms: diversity, ecology and applications – Asha Bharti – Journal of Applied Phycology

Built environment
Response of microbial community function to fluctuating geochemical conditions within a legacy radioactive waste trench environment – Xabier Vázquez-Campos – bioRxiv

Accelerating anodic biofilms formation and electron transfer in microbial fuel cells: Role of anionic biosurfactants and mechanism – Yunshu Zhang – Bioelectrochemistry

Food microbiology
Influence of food consumption patterns and Galician lifestyle on human gut microbiota – María Castro-Penalonga – Journal of Physiology and Biochemistry

Microbes in the news
Light-sensitive bacteria could save you during a heart attack – Jon Fingas – Engadget

Bacteria from hot springs solve mystery of metabolismBacteria from hot springs solve mystery of metabolism – Stockholm University – Science News

Common disease-causing bacteria can live airborne for 45 minutes, study shows – Queensland University of Technology – Science News

Meerkats Can Thank Bacteria for Their Signature Butt Scents – Elizabeth Preston – Discover

Microbes on the market
OptiBiotix Signs Major Supply Agreement For Its Microbiome Modulating Cholesterol-Reduction Probiotic – BioSpace

June 19, 2017

Events and jobs

QC Supervisor, Quality Control (Microbiology) – Bausch & Lomb Company Location Seal Beach, CA, US

Microbiology Lab Technician – Apex Life Sciences • Dublin Ohio, OH

General microbiome

Genome-Wide Search for Genes Required for Bifidobacterial Growth under Iron-Limitation – Lanigan N – Front Microbiol

Preprint: Phenotypic consequences of RNA polymerase dysregulation in Escherichia coli – Paramita Sarkar – bioRxiv

EsaB is a core component of the Staphylococcus aureus Type VII secretion system – M. Guillermina Casabona – bioRxiv

Multi-site human microbiome

Dysbiosis in chronic periodontitis: Key microbial players and interactions with the human host – Deng ZL – Sci Rep

Human gut microbiome

Torpor: The Rise and Fall of 3-Monoiodothyronamine from Brain to Gut-From Gut to Brain? – Glossmann HH – Front Endocrinol (Lausanne)

Bacterial Diversity of Intestinal Microbiota in Patients with Substance Use Disorders Revealed by 16S rRNA Gene Deep Sequencing – Xu Y – Sci Rep

Gut Microbiome and Bone: to Build, Destroy, or Both? – Yan J – Curr Osteoporos Rep

From clinical uncertainties to precision medicine: the emerging role of the gut barrier and microbiome in small bowel functional diseases – Marlicz W – Expert Rev Gastroenterol Hepatol

Gut microbiota composition strongly correlates to peripheral insulin sensitivity in obese men but not in women – Most J – Benef Microbes

Animal experiments

Bovine antibodies targeting primary and recurrent Clostridium difficile disease are a potent antibiotic alternative – Hutton ML – Sci Rep

Intestinal metabolites are profoundly altered in the context of HLA-B27 expression and functionally modulate disease in a rat model of spondyloarthropathy – Asquith M – Arthritis Rheumatol

Dietary advanced glycation end products modify gut microbial composition and partially increase colon permeability in rats – Qu W – Mol Nutr Food Res

The scales of the zebrafish: host–microbiota interactions from proteins to populations – Adam R Burns – Curr Opin Microbiol

Plant, root, and soil microbiome

Ecological diversity and co-occurrence patterns of bacterial community through soil profile in response to long-term switchgrass cultivation – He S – Sci Rep

Characterization of microbial communities in Chinese rice wine collected at Yichang city and Suzhou city in China – Lyu Y – J Microbiol Biotechnol

Diversity of endophytic mycobiota of tropical tree Tectona grandis Linn.f.: Spatiotemporal and tissue type effects – Singh DK – Sci Rep

Understanding and exploiting plant beneficial microbes – Finkel OM – Curr Opin Plant Biol

Water and extremophile microbiome

ELIXIR pilot action: Marine metagenomics – towards a domain specific set of sustainable services – Robertsen EM – F1000Res

Built environment

Graphene Nanolayers as a New Method for Bacterial Biofilm Prevention: Preliminary Results – Dybowska-Sarapuk Ł – J AOAC Int

Probiotics / prebiotics

Probiotic guidelines and physician practice: a cross-sectional survey and overview of the literature – Draper K – Benef Microbes

Techniques

Toward a genetic tool development pipeline for host-associated bacteria – Matthew C Waller – Curr Opin Microbiol

Microbes in the news

Bacteria eaters’ set to transform pig treatment – Lauren Dean – FG|Insight

Bacteria Hysteria

Wash your phones, too – Daily Republic – Onome Johnson

 

 

June 18, 2017

Quite a large Digest for a Sunday, with most picks being on soil microbiome and some interesting animal papers including how microbial genetic composition may tune host longevity (Bing Han – Cell)

General microbiome

Reply to Wang and Chen: An ancient origin of magnetotactic bacteria – Wei Lin – Proceedings of the National Academy of Sciences of the United States of America

Microbiome and Longevity: Gut Microbes Send Signals to Host Mitochondria – Jan Gruber – Cell

Human gut microbiome

The Human Microbiome and the Missing Heritability Problem – Santiago Sandoval-Motta – Frontiers in Genetics

Bacteriophages important for FMT efficacy – Iain Dickson – Nature Reviews Gastroenterology & Hepatology

Postmortem succession of gut microbial communities in deceased human subjects – Jennifer M. DeBruyn – Peerj

Urinary metabolic insights into host-gut microbial interactions in healthy and IBD children – Francois-Pierre Martin – World Journal of Gastroenterology

Animal experiments

Profound perturbation induced by triclosan exposure in mouse gut microbiome: a less resilient microbial community with elevated antibiotic and metal resistomes – Bei Gao – BMC Pharmacology and Toxicology

Vitamin A deficiency in mice results in a hypermetabolic state, dysbiosis and alterations in bacterial metabolism – Yuan Tian – The Journal of Immunology

Host–microbiota interactions in Caenorhabditis elegans and their significance – Michael Shapira – Current Opinion in Microbiology

Microbial Genetic Composition Tunes Host Longevity – Bing Han – Cell

Probabilistic Invasion Underlies Natural Gut Microbiome Stability – Benjamin Obadia – Current Biology

Animal microbiome

Metagenomic survey of bacteria associated with the invasive ladybird Harmonia axyridis (Coleoptera: Coccinellidae) – Krzysztof Dudek – European Journal of Entomology

Plant, root, and soil microbiome

Microbial mechanisms controlling the rhizosphere effect of ryegrass on degradation of polycyclic aromatic hydrocarbons in an aged-contaminated agricultural soil – Meixia Guo – Soil Biology and Biochemistry

Illumina-Based Analysis of Bulk and Rhizosphere Soil Bacterial Communities in Paddy Fields Under Mixed Heavy Metal Contamination – HE Huaidong  – Pedosphere

Paracoccus hibisci sp. nov., isolated from the rhizosphere of Hibiscus syriacus L. (Mugunghwa flower) – Zheng-Fei Yan – International Journal of Systematic and Evolutionary Microbiology

The role of Plant Growth Promoting Bacteria in improving nitrogen use efficiency for sustainable crop production: a focus on wheat – Nilde Antonella Di Benedetto – AIMS Microbiology Special Issue: Plant probiotic bacteria: solutions to feed the World

Molecular Communication and Nutrient Transfer of Arbuscular Mycorrhizal Fungi, Symbiotic Nitrogen-Fixing Bacteria, and Host Plant in Tripartite Symbiosis – Chunling Chang – Legume Nitrogen Fixation in Soils with Low Phosphorus Availability

Experimental study on the effects of underground CO2 leakage on soil microbial consortia – Fu Chen – International Journal of Greenhouse Gas Control

The Impact of Hydration and Temperature on Bacterial Diversity in Arid Soil Mesocosms – Adam Št’ovíček – Frontiers in Microbiology

In vitro and in silico characterization of metagenomic soil-derived cellulases capable of hydrolyzing oil palm empty fruit bunch – Laura Marcela Palma Medina – Biotechnology Reports

The impacts of organic amendments: Do they confer stability against drought on the soil microbial community? – F. Bastida – Soil Biology and Biochemistry

Techniques

Review: Harnessing Whole Genome Sequencing in Medical Mycology – Christina A Cuomo – Current Fungal Infection Reports

From complex gut communities to minimal microbiomes via cultivation – Thomas Clavel – Current Opinion in Microbiology

Microbes in the news

Microbiome ‘fingerprint’ shows donor microbes persist in fecal transplant recipients –R Kumar – Healio Gastroenterology

New Pasteurization Alternative Sanitizes Milk Without Killing Good Bacteria – Luke Dormehl – Digitaltrends

Gut Bacteria May Help Slow Down Process of Ageing – NDTV

Gut microbiota – Tiny helpers against Samonella – Innovations-report

June 16, 2017

Gut microbiome focus: Differences in the gut microbiome between children and adults can mediate the metabolism of arsenic possibly leading to differences in exposure risk, the gut microbiome’s ability to protect against salmonella infection is dependent on the IFNy producing bacteria, the microbiome of insoluble fibre is characterized, and a new in vitro technique to interrogate intestinal transport of microbiota and antigens. Plus an overview of the world data centre for microorganisms, and MicroScope for microbial genome annotation. 

  • Events and jobs

Microbiology Technologist OR Microbiology Medical Technologist – Orlando Florida  

*****************************

  • General microbiome

Conference: Current concepts in chronic inflammatory diseases: Interactions between microbes, cellular metabolism, and inflammation – Holger Garn – Allergy and Clinical Immunology

  • Human oral microbiome

Characterisation of Roseomonas mucosa isolated from the root canal of an infected tooth – Nina Diesendorf – BMC Research Notes

  • Human gut microbiome

* Interindividual variability of soil arsenic metabolism by human gut microbiota using SHIME model – Naiyi Yin – Chemosphere

* Inter-individual differences determine the outcome of wheat bran colonization by the human gut microbiome – Kim De Paepe – Environmental Microbiology

Review: Microbiota Therapy for Clostridium difficile and Antibiotic Resistant Enteric Infections – Brittany Lewis – Annual Review of Microbiology

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  • Animal experiments

* Enhancement of IFNγ Production by Distinct Commensals Ameliorates Salmonella-Induced Disease – Sophie Thiemann – Cell Host and Microbe

Efficacy of antibiotic treatment of implant-associated Staphylococcus aureus infections with moxifloxacin, flucloxacillin, rifampin, and combination therapy: an animal study – Felix Greimel – Drug Design, Development and Therapy

The scales of the zebrafish: host–microbiota interactions from proteins to populations – Adam Burns – Current Opinion in Microbiology

IL-17 Receptor A Maintains and Protects the Skin Barrier To Prevent Allergic Skin Inflammation – Achilleas Floudas – The Journal of Immunology

Irf4-dependent CD103+CD11b+ dendritic cells and the intestinal microbiome regulate monocyte and macrophage activation and intestinal peristalsis in postoperative ileus – Judith-Mira Pohl – Gut

  • Animal microbiome

Effect of three lactobacilli with strain-specific activities on the growth performance, faecal microbiota and ileum mucosa proteomics of piglets – Yating Su – Journal of Animal Science and Biotechnology

  • Plant, root, and soil microbiome

Characterization of the regulation of a plant polysaccharide utilization operon and its role in biofilm formation in Bacillus subtilis – Cameron Habib – PLOSone

Grazing of leaf-associated Cercomonads (Protists: Rhizaria: Cercozoa) structures bacterial community composition and function – Sebastian Flues – Environmental Microbiology

Green alder (Alnus viridis) encroachment shapes microbial communities in subalpine soils and impacts its bacterial or fungal symbionts differently – G Schwob – Environmental Microbiology

The role of organic acids on microbial deterioration in the Radix pseudostellariae rhizosphere under continuous monoculture regimes – Hongmiao Wu – Scientific Reports

Specificity traits consistent with legume-rhizobia coevolution displayed by Ensifer meliloti rhizosphere colonization – María Eugenia Salas – Environmental Microbiology

  • Water and extremophile microbiome

Cascading influence of inorganic nitrogen sources on DOM production, composition, lability and microbial community structure in the open ocean – SJ Goldberg – Environmental Microbiology

Functional diversity and redundancy across fish gut, sediment, and water bacterial communities – Arthur Escalas – Environmental Microbiology

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  • Phages and viruses

Preprint: Bacteria defend against phages through type IV pilus glycosylation – Hanjeong Harvey- bioRxiv

  • Techniques

Dissecting the human microbiome with single-cell genomics – Andrew Tolonen – Genome Medicine

* A human intestinal M-cell-like model for investigating particle, antigen and microorganism translocation – Ana Beloqui – Nature Protocols

  • Metagenomics

* World data centre for microorganisms: an information infrastructure to explore and utilize preserved microbial strains worldwide – Linhuan Wu – Nucleic Acids Research

* MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes – David Vallenet – Nucleic Acids Research

Bacteriocin Gene-Trait matching across the complete Lactobacillus Pan-genome – Fergus Collins – Scientific Reports

Screening and characterization of a novel thermostable lipase with detergent-additive potential from the metagenomic library of a mangrove soil – Leli Tang – Gene

  • Microbial Physiology

Preprint: Phenotypic consequences of RNA polymerase dysregulation in Escherichia coli – Paramita Sarkar – bioRxiv

Preprint: Campylobacter jejuni transcriptome changes during loss of culturability in water – Christina Bronowski – bioRxiv

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  • Microbes in the news

You Are What You Eat, And What You Eat Is Millions of MicrobesKyle Frischkorn – Smithsonian.com

John Bartlett’s Take on Critical Infectious Disease Topics: Part 3 – John Bartlett – Medscape

Placental Microbiome – Sally Robertson – Life Sciences News

Light-activated bacteria protect rats from heart attacks – Michael Price – Science

These light-eating bacteria could one day help us survive heart attacks – Alessandra Potenza – The Verge

Scientists image molecular machinery never before seen in bacteria – Brooke Hays – UPI

June 15, 2017

Today’s digest is full of plant, animal, and soil microbiome studies as well as a nice serving of human gut science, specifically about FMT.

Events and jobs

Visiting Assistant Professor of Microbiology – Methodist University, North Carolina

GENEWIZ Week – many small events, contests, giveaways, and webinars (including mine on using Metagenomics for Biomarker Discovery posted here on Sunday’s blog post. Since my webinar was yesterday, it will be archived and can be downloaded from genewiz.com, starting next week – don’t forget to check it out!)

General microbiome

* Comprehensive analysis of microorganisms accompanying human archaeological remains – Anna Philips – Gigascience

Pregnancy and early life

Relationships Among Microbial Communities, Maternal Cells, Oligosaccharides, and Macronutrients in Human Milk – Williams JE – Journal of Human Lactation

Human oral microbiome

Targeted Antimicrobial Therapy in the Microbiome Era – Victoria N. Stone – Molecular Oral Microbiology

Human gut microbiome

* Identification of donor microbe species that colonize and persist long term in the recipient after fecal transplant for recurrent Clostridium difficile – Ranjit Kumar – npj Biofilms and Microbiomes

* Fecal microbiota transplantation in metabolic syndrome: History, present and future – P. F. de Groot – Gut microbes

Intestinal microbiota, fecal microbiota transplantation, and inflammatory bowel disease – Weingarden AR – Gut Microbes

Faecal microbiota study reveals specific dysbiosis in spondyloarthritis – Maxime Breban – Annals of Rheumatic Diseases

Metaproteomic analysis of human gut microbiota: where are we heading? – Pey Yee Lee – Journal of Biomedical Science

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Variability, stability, and resilience of fecal microbiota in dairy cows fed whole crop corn silage – Minh Thuy Tang – Applied Microbiology and Biotechnology

Plantago ovata in broiler chicken nutrition: Performance, carcass criteria, intestinal morphology, immunity, and intestinal bacterial population – A. Divani – Animal Physiology and Animal Nutrition

Chronic treatment with prebiotics, probiotics and synbiotics attenuated cardiac dysfunction by improving cardiac mitochondrial dysfunction in male obese insulin-resistant rats – Tunapong W – European Journal of Nutrition

Amelioration of obesity-related characteristics by a probiotic formulation in a high-fat diet-induced obese rat model – Joo-Hyun Shin – European Journal of Nutrition

Early Gut Microbiota Intervention Suppresses DSS-Induced Inflammatory Responses by Deactivating TLR/NLR Signalling in Pigs – Yi Xiao – Scientific Reports

* Profound perturbation induced by triclosan exposure in mouse gut microbiome: a less resilient microbial community with elevated antibiotic and metal resistomes – Bei Gao – BMC Pharmacology and Toxicology

Animal microbiome (for animals in the wild)

[PrePrint] Ecophysiology of freshwater Verrucomicrobia inferred from genomes recovered through time-series metagenomics – Shaomei He – bioRxiv

Long-Term Survey Is Necessary to Reveal Various Shifts of Microbial Composition in Corals – Shan-Hua Yang – Aquatic Microbiology (Frontiers in Microbiology)

Preferential suppression of Anopheles gambiae host sequences allows detection of the mosquito eukaryotic microbiome – Eugeni Belda – Scientific Reports

Social odours covary with bacterial community in the anal secretions of wild meerkats – Sarah Leclaire – Scientific Reports

Plant, root, and soil microbiome

Imidacloprid application changes microbial dynamics and enzymes in rice soil – Bibhab Mahapatra – Ecotoxicology and Environmental Safety

Comparison of ammonia oxidation bacteria community structure in paddy soil with different utilized years – Zhao WeiYe – Southwest China Journal of Agricultural Sciences

[MS Thesis] Variation of Soil Microbial Communities within a Consociation Soil Map Unit and a Vegetative Transect through an Oak Motte – Sarah Elizabeth Shawver – Tarleton State University

Effects of different intercropping patterns on rhizosphere soil bacteria colony characteristics and flue-cured tobacco yield and quality – Wei Jun – Guangxi Academy of Agricultural Sciences

Rhizospheric bacteria diversity of Cypripedium macranthum estimated via high throughput sequencing – Zhang Jian -Southwest China Journal of Agricultural Sciences

Denitrifying bacterial communities display different temporal fluctuation patterns across Dutch agricultural soils – Lopez-Lozano NE – Antonie van Leeuwenhoek

Ecophylogeny of the endospheric root fungal microbiome of co-occurring Agrostis stolonifera – Amandine Le Van – PeerJ

Consistent effects of nitrogen fertilization on soil bacterial communities in black soils for two crop seasons in China – Jing Zhou – Scientific Reports

A next generation sequencing approach with a suitable bioinformatics workflow to study fungal diversity in bioaerosols released from two different types of composting plants – Hamza Mbareche – Science of The Total Environment

The Effects of Cropping Regimes on Fungal and Bacterial Communities of Wheat and Faba Bean in a Greenhouse Pot Experiment Differ between Plant Species and Compartment – Granzow S – Frontiers in Microbiology

Water and extremophile microbiome

Unraveling the environmental and anthropogenic drivers of bacterial community changes in the Estuary of Bilbao and its tributaries – Mikel Aguirre – PLOS ONE

Food microbiology

Metagenomics insights into food fermentations – Francesca De Filippis – Microbial Biotechnology

Probiotics / prebiotics

Effect of probiotic Lactobacillus on lipid profile: A systematic review and meta-analysis of randomized, controlled trials – Yuncheng Wu – PLOS ONE

Growing Literature but Limited Evidence: A Systematic Review regarding Prebiotic and Probiotic Interventions for those with Traumatic Brain Injury and/or Posttraumatic Stress Disorder – Lisa A. Brenner – Brain, Behavior, Immunity

Microbes on the market

$10 million gift boosts gut microbiome research at Wash U

Ed’s non-microbiology picks 

Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site – Eva-Maria Strauch – Nature Biotechnology

Aberrant telomere length and mitochondrial DNA copy number in suicide completers –  Ikuo Otsuka – Scientific Reports

Impact of nutrition on social decision making – Sabrina Strang – PNAS

Oral vitamin D rapidly attenuates inflammation from sunburn: an interventional study – Jeffrey F. Scott – JID

Adaptive self-organization of Bali’s ancient rice terraces – J. Stephen Lansing – PNAS

Ravens remember the nature of a single reciprocal interaction sequence over 2 days and even after a month – J. J. A. Muller – Animal Behaviour