Category Archives: Microbes and the market

April 25, 2018

Posted on by

Method for cell-free transcription-translation to characterize nonmodel bacteria, a review of bile acid metabolism by the gut microbiota, altitude affects on the lizard intestinal microbiota.

Events and jobs

Research Applications Programmer – UC San Diego Center for Microbiome Innovation

Pregnancy and early life

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

Multi-site human microbiome

Bifidobacteria isolated from vaginal and gut microbiomes are indistinguishable by comparative genomics – Aline C Freitas – PLOS ONE

Human skin microbiome

The Skin Commensal Yeast Malassezia globosa Thwarts Bacterial Biofilms to Benefit the Host – Giuseppe Ianiri – Journal of Investigative Dermatology

Human gut microbiome

A repeat offender: recurrent extraintestinal Clostridium difficile infection following fecal microbiota transplantation – Bradley J Gardiner – Anaerobe

Next-Generation Immune Repertoire Sequencing as a Clue to Elucidate the Landscape of Immune Modulation by Host–Gut Microbiome Interactions – Tatsuo Ichinohe – Frontiers in Immunology

Review: Metabolism of hydrogen gases and bile acids in the gut microbiome – Phillip B Hylemon – FEBS Letters

Animal experiments

Beneficial effects of a selected probiotic mixture administered to high fat-fed mice before and after the development of obesity – Marianna Roselli – Journal of Functional Foods

Emodin ameliorates ulcerative colitis by the flagellin-TLR5 dependent pathway in mice – Shuang Luo – International Immunopharmacology

Pre-print: Probiotics enhance susceptibility of mice to cryptosporidiosis – Bruno C M Oliveira – bioRxiv

Review: Using murine colitis models to analyze probiotics–host interactions – Rebeca Martín – FEMS Microbiology Reviews

Dietary Clostridium Butyricum induces a phased shift in fecal microbiota structure and increases the acetic acid-producing bacteria in a weaned piglet model – Jie Zhang – Journal of Agricultural and Food Chemistry

Animal microbiome

Changes in intestinal microbiota across an altitudinal gradient in the lizard Phrynocephalus vlangalii – Wenya Zhang – Ecology and Evolution

New York City House Mice (Mus musculus) as Potential Reservoirs for Pathogenic Bacteria and Antimicrobial Resistance Determinants – Simon H Williams – mBio

Glucocorticoids modulate gastrointestinal microbiome in a wild bird – José C Noguera – Royal Society Open Science

Plant, root, and soil microbiome

Insights to plant‐microbe interactions provide opportunities to improve resistance breeding against root diseases in grain legumes – Lukas Wille – Plant, Cell & Environment

Rice Phyllosphere Bacillus Species and Their Secreted Metabolites Suppress Aspergillus flavus Growth and Aflatoxin Production In Vitro and in Maize Seeds – Subbaiah Chalivendra – Toxins

Root diameter predicts the extramatrical hyphal exploration distance of the ectomycorrhizal fungal community – Weile Chen – Ecosphere

Isolation and characterization of phosphofungi, and screening of their plant growth-promoting activities – Xiaohui Wang – AMB Express

Plants regulate the effects of experimental warming on the soil microbial community in an alpine scrub ecosystem – Zhiliang Ma – PLOS ONE

Pre-print: Effects of fertilizations on soil bacteria and fungi communities in a degraded arid steppe revealed by high through-put sequencing – Luhua Yao – PeerJ

Water and extremophile microbiome

Life on the edge: active microbial communities in the Kryos MgCl2-brine basin at very low water activity – Lea Steinle – The ISME Journal

Light availability impacts structure and function of phototrophic stream biofilms across domains and trophic levels – Mia M Bengtsson – Molecular Ecology

Bacterial Community in Water and Air of Two Sub-Alpine Lakes in Taiwan – Kshitij Tandon – Microbes and Environments

Microbes in space

Book chapter: The Search for Signatures of Life and Habitability on Planets and Moons of Our Solar System – Oliver Funke – Biological, Physical and Technical Basis of Cell Engineering

Bioinformatics

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information – Stefan Janssen – mSystems

Pre-print: Fusobacterium genomics using MinION and Illumina sequencing enables genome completion and correction – S Michelle Todd – bioRxiv

Pre-print: FusoPortal: An interactive repository of hybrid MinION-sequenced Fusobacterium genomes improves gene identification and characterization – Blake E Sanders – bioRxiv

Comparison of normalization methods for the analysis of metagenomic gene abundance data – Mariana Buongermino Pereira – BMC Genomics

Pre-print: Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences – Robert C Edgar – PeerJ

Pre-print: Natural history bycatch: a pipeline for identifying metagenomic sequences in RADseq data – Iris Holmes – PeerJ

Metabolomics

Exploring the Genetic Landscape of Metabolic Phenotypes with MetaboSignal – Andrea Rodriguez-Martinez – Current Protocols in Bioinformatics

Tissue Multiplatform-Based Metabolomics/Metabonomics for Enhanced Metabolome Coverage – Panagiotis A Vorkas – Metabolic Profiling

Review: Current and future perspectives of functional metabolomics in disease studies–A review – Min Yan – Analytica Chimica Acta

Techniques

Rapid acquisition and model-based analysis of cell-free transcription–translation reactions from nonmodel bacteria – Simon J Moore – PNAS

Pre-print: Impact of DNA sequencing and analysis methods on 16S rRNA gene bacterial community analysis in dairy products – Zhengyao Xue – bioRxiv

Methodological considerations for the identification of choline and carnitine-degrading bacteria in the gut – Eleanor Jameson – Methods

More microbes

Omics and multi-omics approaches to study the biosynthesis of secondary metabolites in microorganisms – Emilia Palazzotto – Current Opinion in Microbiology

Helicobacter pylori the Latent Human Pathogen or an Ancestral Commensal Organism – Jackie Li – Frontiers in Microbiology

Microbes in the news

Wiping out the gut microbiome could help with heart failure – ScienceDaily

How bacteria are changing your mood – James Gallagher – BBC News

Drinkers have more bad mouth bacteria, study finds – Susan Scutti – CNN

$11.2 million federal grant to support microorganism and disease research – EurekAlert

A Surprising Way Dogs Are Similar to Humans – Julissa Treviño – Smithsonian

Could Your Diet Be The Cause Of Your Arthritis Pain? – Robert Glatter – Forbes

Growing evidence that probiotics are good for your liver – ScienceDaily

Just being outside can improve your psychological health, and maybe your physical health too – Zoë Schlanger – Quartz

Role of Mosquito Microbiota in Reducing Malaria Transmission – JoAnna Pendergrass – American Veterinarian

A search for some of Earth’s most extreme creatures in the West Coast’s deepest underwater canyon – Amina Khan – Los Angeles Times

How plastic-eating bacteria actually work—a chemist explains – Emily Flashman – Phys.org

Far-red fluorescent silk can kill harmful bacteria as biomedical and environmental remedy – Kayla Wiles – Phys.org

Antibiotic-resistant bacteria cross oceans hidden in cargo ships – Inga Vesper – New Scientist

Fight against Zika, dengue get boost from reliable spread of bacteria – EurekAlert

Microbes on the market

Rebiotix Presents Posters at ECCMID 2018 Highlighting Microbiome Health Index™ Value Potential and RBX2660 Phase 2 Clinical Program Data – PR Newswire

Kaleido Biosciences Announces Appointment of Joshua Brumm as Chief Financial Officer – Citizen Tribune

Science, career, and publishing

Pre-print: Aligning interests: Integrating Citizen Science Efforts into Schools Through Service Requirements – Ginger Tsueng – bioRxiv

Randomly auditing research labs could be an affordable way to improve research quality: A simulation study – Adrian G Barnett – PLOS ONE

April 19, 2018

Posted on by

Today we have a few day’s worth of microbiome science to chew on… some interesting skin microbiome studies, bioinformatics publications, and our typical servings of gut /plant-root-soil/animal/water-extremophiles/general microbiome studies.  Dig in!

Events and jobs

Manager, QC Microbiology – Celgene – Phoenix, AZ

Pathology and Microbiology & IPID Graduate Student Research Seminar – UNMC

General microbiome

Cost-benefit analysis of introducing next-generation sequencing (metagenomic) pathogen testing in the setting of pyrexia of unknown origin – Jia Hui Chai – PLOS ONE

* [pre-print] Phylogenetically novel uncultured microbial cells dominate Earth microbiomes – Karen G. Lloyd – bioRxiv

Hologenomics: Systems-Level Host Biology – Kevin R. Theis – mSystems

Antibiotics as Instigators of Microbial Dysbiosis: Implications for Asthma and Allergy – Tomasz P. Wypych – Trends in Immunology

[perspective] Function and functional redundancy in microbial systems – Stilianos Louca – Nature Ecology & Evolution

Human oral microbiome

Comparison of the oral microbiome in mouthwash and whole saliva samples – Xiaozhou Fan – PLOS ONE

Oral Dysbiotic Communities and Their Implications in Systemic Diseases – Preethi Sudhakara – Dentistry Journal

Human skin microbiome

[pre-print] Umbilical Microbiome and Laparoscopic Surgery: A Descriptive Clinical Study – Aiolfi Alberto – Journal of Laparoendoscopic & Advanced Surgical Techniques

The skin microbiome of wound scars and unaffected skin in patients with moderate to severe burns in the subacute phase – Su‐Hsun Liu – Wound Repair and Regeneration

Human gut microbiome

Microbiome-Mediated Bile Acid Modification: Role in Intestinal Drug Absorption and Metabolism – Elaine F. Enright – Pharmacological Research

Non-microbicidal small molecule inhibition of polysaccharide metabolism in human gut microbes: a potential therapeutic avenue – Anthony D. Santilli – ACS Chemical Biology

The Use of Antimicrobials as Adjuvant Therapy for the Treatment of Obesity and Insulin Resistance: Effects and Associated Mechanisms – Sandra Aparecida dos Reis – Diabetes / Metabolism Research and Reviews

* Human Gut Microbiota Predicts Susceptibility to Vibrio cholerae Infection – Firas S Midani – The Journal of Infectious Disease

Interactions of Dihydromyricetin, a Flavonoid from Vine Tea (Ampelopsis grossedentata) with Gut Microbiota – Li Fan – Journal of Food Science

Characteristics of the gut microbiota in adult patients with type 1 and 2 diabetes based on the analysis of a fragment of 16S rRNA gene using next-generation sequencing – Dominika Salamon – Polish Archives of Internal Medicine

The Intestinal Microbiota in Colorectal Cancer -Herbert Tilg – Cancer Cell

The Endotoxemia Marker Lipopolysaccharide‐Binding Protein is Reduced in Overweight‐Obese Subjects Consuming Pomegranate Extract by Modulating the Gut Microbiota: A Randomized Clinical Trial – Antonio González‐Sarrías – Molecular Nutrition

Hepatocellular Carcinoma is Associated with Gut Microbiota Profile and Inflammation in Non-Alcoholic Fatty Liver Disease – Francesca Romana Ponziani – Hepatology

Antibiotic‐Associated Disruption of Microbiota Composition and Function in Cirrhosis is Restored by Fecal Transplant – Jasmohan S Bajaj – Hepatology

Does the gastrointestinal microbiome contribute to the “obesity paradox” in melanoma survival? – E A Langan – British Journal of Dermatology

Animal experiments

Obese Mice Losing Weight Due to trans-10,cis-12 Conjugated Linoleic Acid Supplementation or Food Restriction Harbor Distinct Gut Microbiota – Laura J den Hartigh – JN The Journal of Nutrition

Tuna oil alleviate D-galactose induced aging in mice accompanied by modulating gut microbiota and brain protein expression – Dijun Zhang – Journal of Agricultural and Food Chemistry

Dietary Mannan Oligosaccharides Modulate Gut Microbiota, Increase Fecal Bile Acid Excretion, and Decrease Plasma Cholesterol and Atherosclerosis Development – Lisa R. Hoving – Molecular Nutrition

[Review] The Role of the Gut Microbiota in the Metabolism of Polyphenols as Characterized by Gnotobiotic Mice – Pasinetti, Giulio Mari – Journal of Alzheimer’s Disease

Animal microbiome 

Shared larval rearing environment, sex, female size and genetic diversity shape Ae. albopictus bacterial microbiota – Guillaume Minard – PLOS ONE

Metatranscriptome analysis of the microbial fermentation of dietary milk proteins in the murine gut – Floor Hugenholtz – PLOS ONE

Water system is a controlling variable modulating bacterial diversity of gastrointestinal tract and performance in rainbow trout – Omolola C. Betiku – PLOS ONE

* Bacterial communities associated with honeybee food stores are correlated with land use – Philip Donkersley – Ecology and Evolution

Evaluating the microbiome of two sampling locations in the nasal cavity of cattle with bovine respiratory disease complex (BRDC) – Tara G McDaneld – Journal of Animal Science

Controlling ticks and tick-borne diseases…looking forward – José de la Fuente – Ticks and Tick-borne Diseases

The inside tract: The appendicular, cecal, and colonic microbiome of captive aye‐ayes – Lydia K. Greene – American Journal of Physical Anthropology

Water system is a controlling variable modulating bacterial diversity of gastrointestinal tract and performance in rainbow trout – Omolola C. Betiku – PLOS ONE

Comparative Analysis of the Microbiota Between Sheep Rumen and Rabbit Cecum Provides New Insight Into Their Differential Methane Production – Lan Mi – Frontiers in Microbiology

Tracing of the fecal microbiota of commercial pigs at five growth stages from birth to shipment – Geon Goo Han – Nature Scientific Reports

Development of the tonsillar microbiome in pigs from newborn through weaning – Luis Carlos Pena Cortes – BMC Microbiology

Plant, root, and soil microbiome

Antimicrobial peptide expression in a wild tobacco plant reveals the limits of host-microbe-manipulations in the field – Arne Weinhold – eLife

Identification of Major Rhizobacterial Taxa Affected by a Glyphosate-Tolerant Soybean Line via Shotgun Metagenomic Approach – Gui-Hua Lu – Genes

Culture‐independent analysis of hydrocarbonoclastic bacterial communities in environmental samples during oil‐bioremediation – Narjes Dashti – MicrobiologyOpen

Embracing Community Ecology in Plant Microbiome Research – Francisco Dini-Andreote – Trends in Plant Science

Cultivated bacterial diversity associated with the carnivorous plant Utricularia breviscapa (Lentibulariaceae) from floodplains in Brazil – Felipe Rezende Lima – Brazilian Journal of Microbiology

Soil microbial communities and glyphosate decay in soils with different herbicide application history – Keren Hernández Guijarro – Science of the Total Environment

Shining a light on the dark world of plant root-microbe interactions – Philip Poole – PNAS

Water and extremophile microbiome 

Microbial diversity and biomarker analysis of modern freshwater microbialites from Laguna Bacalar, Mexico – D. B. Johnson – gebiology

Effect of salinity on diazotrophic activity and microbial composition of phototrophic communities from Bitter-1 soda lake (Kulunda Steppe, Russia) – Zorigto Namsarae – Extremophiles

The ecology and diversity of microbial eukaryotes in geothermal springs – Angela M. Oliverio – The ISME Journal

Built environment

Deposition of Bacteria and Bacterial Spores by Bathroom Hot Air Hand Dryers – Luz del Carmen Huesca-Espitia – American Society for Microbiology

Food microbiology

Bacterial Communities in Serpa Cheese by Culture Dependent Techniques, 16S rRNA Gene Sequencing and High-throughput Sequencing Analysis – Maria Teresa P. Gonçalves – Journal of Food Science

Revealing the microbiota of marketed edible insects through PCR-DGGE, metagenomic sequencing and real-time PCR – Andrea Osimani – International Journal of Food Microbiology

Bioinformatics

Computer-guided design of optimal microbial consortia for immune system modulation – Richard R Stein – eLife

[uncorrected proof] Using pseudoalignment and base quality to accurately quantify microbial community composition – Mark Reppell – PLOS Computational Biology

Fast Metagenomic Binning via Hashing and Bayesian Clustering – Popic Victoria – Journal of Computational Biology

* Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity – Luis M. Rodriguez-R – mSystems

Algorithms and strategies in short‐read shotgun metagenomic reconstruction of plant communities – Robert S. Harbert – Applications in Plant Science

Microbes in the news

Scientists Accidentally Make Plastic-Eating Bacteria Even More Efficient

New York City Mice: Here Are The Bacteria And Viruses That They Carry

Fecal microbiota transplant improves brain function in hepatic encephalopathy

Microbes on the market

Seres Therapeutics (MCRB) Presents New Preclinical Data Supporting the Development of Microbiome Therapeutics for Immuno-Oncology at AACR

Science, publishing, and career

Personal microbiome analysis improves student engagement and interest in Immunology, Molecular Biology, and Genomics undergraduate courses – K. Scott Weber – PLOS ONE

Ed’s non-microbiology picks

News articles below have actual study links inside.

Since 2016, Half of All Coral in the Great Barrier Reef Has Died

Marijuana’s effects on young brains diminish 72 hours after use, research says

Cannabinoids are easier on the brain than booze, study finds

Stem cell treatment drastically reduces drinking in alcoholic rats

The Ecology Of Disadvantage: Obesity Is Not Randomly Distributed Across The U.S., According To New Study

How your next meal could help fight depression, stress

Study: People with less political knowledge think they know a lot about politics

March 28, 2018

Posted on by

The impact of the microbiota on bone marrow transplantation in mice, differences in phage infection efficiency in nearly identical hosts, bacterial diversity of Brazilian artisanal cheese.

Events and jobs

Research Associate in the Department of Twin Research and Genetic Epidemiology, School of Life Cours – King’s College London

Research Associate in Department of Twin Research_School of Life Course Sciences – King’s College London

General microbiome

Variations in the relative abundance of Wolbachia in the gut of Nasutitermes arborum across life stages and castes – Michel Diouf – FEMS Microbiology Letters

Pregnancy and early life

HIV-exposure, early life feeding practices and delivery mode impacts on faecal bacterial profiles in a South African birth cohort – Shantelle Claassen-Weitz – Scientific Reports

Human respiratory microbiome

Exacerbation induces a microbiota shift in sputa of COPD patients – Eric Jubinville – PLOS ONE

Human oral microbiome

Review: Insights into the human oral microbiome – Digvijay Verma – Archives of Microbiology

Pre-print: Characterization of the salivary microbiome in people with obesity – Yujia Wu – PeerJ

Review: The oral microbiota – a mechanistic role for systemic diseases – G Jia – British Dental Journal

Human gut microbiome

Differences in epidemiological features between ulcerative colitis and Crohn’s disease: the early life-programmed versus late dysbiosis hypothesis – Laurent Beaugerie – Medical Hypotheses

Analysis of changes in intestinal flora and intravascular inflammation and coronary heart disease in obese patients – Xv Li – Experimental and Therapeutic Medicine

Animal experiments

Nutritional Support from the Intestinal Microbiota Improves Hematopoietic Reconstitution after Bone Marrow Transplantation in Mice – Anna Staffas – Cell Host & Microbe

High salt intake increases plasma trimethylamine N-oxide (TMAO) concentration and produces gut dysbiosis in rats – Klaudia Bielinska – Nutrition

High salt diet exacerbates colitis in mice by decreasing Lactobacillus levels and butyrate production – Pedro M Miranda – Microbiome

The Pancreatic Cancer Microbiome Promotes Oncogenesis by Induction of Innate and Adaptive Immune Suppression – Smruti Pushalkar – Cancer Discovery

Predominant gut Lactobacillus murinus strain mediates anti-inflammaging effects in calorie-restricted mice – Fengwei Pan – Microbiome

Deletion of choline acetyltransferase in enteric neurons results in postnatal intestinal dysmotility and dysbiosis – Carl D Johnson – The FASEB Journal

At-hatch administration of probiotic to chickens can introduce beneficial changes in gut microbiota – Stephen Baldwin – PLOS ONE

Impact of parenteral antimicrobial administration on the structure and diversity of the fecal microbiota of growing pigs – Mohamed Zeineldin – Microbial Pathogenesis

Pre-print: Metabolic retroconversion of trimethylamine N-oxide and the gut microbiota – Lesley Hoyles – bioRxiv

Pre-print: Isolation of a natural DNA virus of Drosophila melanogaster, and characterisation of host resistance and immune responses – William H Palmer – bioRxiv

Proanthocyanidin‐Rich Grape Seed Extract Modulates Intestinal Microbiota in Ovariectomized Mice – Guangwen Jin – Journal of Food Science

Evaluation of the nutrition and function of cow and goat milk based on intestinal microbiota by metagenomic analysis – Zhaoxia Wang – Food & Function

Animal microbiome

Pre-print: Characterisation of gut microbiota of farmed Chinook salmon using metabarcoding – Milica Ciric – bioRxiv

Variation in the microbiome of the urogenital tract of Chlamydia-free female koalas (Phascolarctos cinereus) with and without ‘wet bottom’ – Alistair R Legione – PLOS ONE

Pre-print: Characterization of shifts of koala (Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment – Katherine E Dahlhausen – PeerJ

Comparison of gizzard and intestinal microbiota of wild neotropical birds – M Alexandra García-Amado – PLOS ONE

Fecal microbiota in the female prairie vole (Microtus ochrogaster) – J Thomas Curtis – PLOS ONE

Disentangling factors that shape the gut microbiota in German Shepherd dogs – Åsa Vilson – PLOS ONE

Yeast culture dietary supplementation modulates gut microbiota, growth and biochemical parameters of grass carp – Han Liu – Microbial Biotechnology

Fecal Microbiota Transplantation in Gestating Sows and Neonatal Offspring Alters Lifetime Intestinal Microbiota and Growth in Offspring – Ursula M McCormack – mSystems

Plant, root, and soil microbiome

Tetracycline resistance genes are more prevalent in wet soils than in dry soils – Yijun Kang – Ecotoxicology and Environmental Safety

Functional diversity of ectomycorrhizal fungal communities is reduced by trace element contamination – Álvaro López-García – Soil Biology and Biochemistry

Long- and short-term effects of mercury pollution on the soil microbiome – Aline Frossard – Soil Biology and Biochemistry

Structure of surface polysaccharides from Aeromonas sp. AMG272, a plant-growth promoting rhizobacterium isolated from rice rhizosphere – Rocío Contreras Sánchez-Matamoros – Carbohydrate Research

Review: Sniffing bacterial volatile compounds for healthier plants – Rouhallah Sharifi – Current Opinion in Plant Biology

Arbuscular mycorrhizal fungi influence decomposition and the associated soil microbial community under different soil phosphorus availability – Jing Xu – Soil Biology and Biochemistry

Water and extremophile microbiome

Habitat filtering of bacterioplankton communities above polymetallic nodule fields and sediments in the Clarion-Clipperton zone of the Pacific Ocean – Markus V Lindh – Environmental Microbiology Reports

Microbial communities in seawater from an Arctic and a temperate Norwegian fjord and their potentials for biodegradation of chemically dispersed oil at low seawater temperatures – Deni Ribicic – Marine Pollution Bulletin

Built environment

Pre-print: Half-lives of PAHs and temporal microbiota changes in commonly used urban landscaping materials – Marja I Roslund – PeerJ

Food microbiology

Interspecies variation in biofilm-forming capacity of psychrotrophic bacterial isolates from Chinese raw milk – Lei Yuan – Food Control

Bacterial diversity of artisanal cheese from the Amazonian region of Brazil during the dry and rainy seasons – Mayra Carla de Freitas Martins – Food Research International

Probiotics/prebiotics

Salecan stabilizes the microstructure and improves the rheological performance of yogurt – Renjie Fu – Food Hydrocolloids

Probiotic Lactobacillus casei Zhang (LCZ) alleviates respiratory, gastrointestinal & RBC abnormality via immuno-modulatory, anti-inflammatory & anti-oxidative actions – Yan-Yan Hor – Journal of Functional Foods

Routine Supplementation of Lactobacillus rhamnosus GG and Risk of Necrotizing Enterocolitis in Very Low Birth Weight Infants – Andrea F Kane – The Journal of Pediatrics

Phages and viruses

Continued Need for Comprehensive Genetic and Phenotypic Characterization of Viruses: Benefits of Complementing Sequence Analyses with Functional Determinations – Aaron C Brault – The American Journal of Tropical Medicine and Hygiene

Detection of Hantaviruses and Arenaviruzses in three-toed jerboas from the Inner Mongolia Autonomous Region, China – Zhiqiang Wu – Emerging Microbes & Infections

Enteric Virome Sensing—Its Role in Intestinal Homeostasis and Immunity – Rebecca N Metzger – Viruses

Commentary: Bacteriophage transfer during faecal microbiota transplantation in Clostridium difficile infection is associated with treatment outcome – Blessing O Anonye – Frontiers in Cellular and Infection Microbiology

Multiple mechanisms drive phage infection efficiency in nearly identical hosts – Cristina Howard-Verona – The ISME Journal

Early MinION™ nanopore single-molecule sequencing technology enables the characterization of hepatitis B virus genetic complexity in clinical samples – Virginie Sauvage – PLOS ONE

A metagenomic viral discovery approach identifies potential zoonotic and novel mammalian viruses in Neoromicia bats within South Africa – Marike Geldenhuys – PLOS ONE

Pre-print: Ecological and evolutionary consequences of viral plasticity – Melinda Choua – bioRxiv

Bioinformatics

Pre-print: Taxonomy annotation errors in 16S rRNA and fungal ITS sequence databases – Robert C Edgar – bioRxiv

Metabolomics

Analysis of paper foxing by newly available omics techniques – Justyna Szulc – International Biodeterioration & Biodegradation

Review: Targeting human urinary metabolome by LC–MS/MS: a review – Jose Rodríguez-Morató – Bioanalysis

GC-MS Based Metabolomics and NMR Spectroscopy Investigation of Food Intake Biomarkers for Milk and Cheese in Serum of Healthy Humans – Alessia Trimigno – Metabolites

Techniques

KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples – Jeremiah J Minich – mSystems

eDNA from roots: a robust tool for determining Phytophthora communities in natural ecosystems – Ihsanul Khaliq – FEMS Microbiology Ecology

A silica sands-based method for faithful analysis of microbial communities and DNA isolation from a wide range of species – Xia Liu – Preparative Biochemistry and Biotechnology

More microbes

Review: New therapeutics from Nature: The odd case of the bacterial cytotoxic necrotizing factor 1 – Zaira Maroccia – Biomedicine & Pharmacotherapy

Pre-print: An attenuated CRISPR-Cas system in Enterococcus faecalis permits DNA acquisition – Karthik Hullahalli – bioRxiv

Microbes in the news

Here’s Why Antibiotics May Give Viruses a Leg Up – Christopher Wanjek – Live Science

‘Nanobot’ viruses tag and round up bacteria in food and water – Carolyn Wilke – ScienceNews

Your rubber ducky is probably crawling with bacteria, scientists say – STAT

Newly discovered bacteria can break down biomass – Phys.Org

Microbes on the market

Biocodex funds microbiome research on link between diet, colon cancer, IBD – Healio

Rebiotix’s Lee Jones to Receive TRUST 2018 Courageous Women in Health Care Award – PR Newswire

March 21, 2018

Posted on by

A long digest today – lots of science on the gut, environment, and some interesting editorials on techniques, bioinformatics, and methodologies applied to microbiome studies.

General microbiome

[pre print] Oscillating bacterial expression states generate herd immunity to viral infection – Christopher J. R. Turkington – bioRxiv

Retraction: Microbiome restoration diet improves digestion, cognition and physical and emotional wellbeing – The PLOS ONE Editors – PLOS ONE

DNA metabarcoding uncovers fungal diversity of mixed airborne samples in Italy – Elisa Banchi – PLOS ONE

Mobile Technologies for the Discovery, Analysis, and Engineering of the Global Microbiome – Zachary S. Ballard – ACS Nano

Unraveling Interactions between the Microbiome and the Host Immune System To Decipher Mechanisms of Disease – Catherine A. Lozupone – mSystems

Making Millennial Medicine More Meta – Peter J. Turnbaugh – mSystems

Pregnancy and early life

Neonatal intestinal dysbiosis in necrotizing enterocolitis – Naomi-Liza Denning – Molecular Medicine

Prenatal and postnatal antibiotic exposure influences the gut microbiota of preterm infants in neonatal intensive care units – Zhi-Hui Zou – Annals of Clinical Microbiology and Antimicrobials

* The Effect of Early Limited Formula on Breastfeeding, Readmission, and Intestinal Microbiota: A Randomized Clinical Trial – Valerie J. Flaherman – The Journal of Pediatrics

Multi-site human microbiome

The Complex Interplay between Chronic Inflammation, the Microbiome, and Cancer: Understanding Disease Progression and What We Can Do to Prevent It – Heather Armstrong – Cancers

Human oral microbiome

Salivary microbial profiles in relation to age, periodontal, and systemic diseases – Ronaldo Lira-Junior – PLOS ONE

Human respiratory microbiome

Translating Lung Microbiome Profiles into the Next-Generation Diagnostic Gold Standard for Pneumonia: a Clinical Investigator’s Perspective – Georgios D. Kitsios – mSystems

Host-Microbe Interactions in Airway Disease: toward Disease Mechanisms and Novel Therapeutic Strategies – Emily K. Cope – mSystems

Human gut microbiome

The role of inflammation in temporal shifts in the inflammatory bowel disease mucosal microbiome – Christopher John Kiely – Gut Microbes

Species Level Description of the Human Ileal Bacterial Microbiota – Heidi Cecilie Villmones – Nature

* Systematic Bias Introduced by Genomic DNA Template Dilution in 16S rRNA Gene-Targeted Microbiota Profiling in Human Stool Homogenates – Francesco Multinu – mSphere

* Extensive impact of non-antibiotic drugs on human gut bacteria – Lisa Maier – Nature

In this issue: Effect of gut microbiome on mucosal immunity and enteric diseases – Kumar, Himanshu – International Reviews of Immunology

Characterization of intestinal microbiota in alcoholic patients with and without alcoholic hepatitis or chronic alcoholic pancreatitis – Dragos Ciocan – Nature

Clostridium difficile Exposures, Colonization, and the Microbiome: Implications for Prevention – Sara L. Revolinski – Infection Control and Hospital Epidemiology

* Of Microbes and Minds: A Narrative Review on the Second Brain Aging – Riccardo Calvani – Frontiers in Medicine

Microbiome: Viral hormones activate human insulin signalling – Ashley York – Nature

Modulation of Gut Microbiota: A Novel Paradigm of Enhancing the Efficacy of Programmed Death-1 and Programmed Death Ligand-1 Blockade Therapy – Yiming Wang – Frontiers in Immunology

* Assessing the Influence of Vegan, Vegetarian and Omnivore Oriented Westernized Dietary Styles on Human Gut Microbiota: A Cross Sectional Study – Carmen Losasso – Frontiers in Microbiology

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies – Melanie Tramontano – Nature

Animal experiments

Characterization of shifts of koala (Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment – Katherine E. Dahlhausen – PeerJ

Low dose brain estrogen prevents menopausal syndrome while maintaining the diversity of the gut microbiomes in estrogen-deficient rats – Sunmin Park – American Journal of Physiology-Endocrinology and Metabolism

Oral supplementation of Bifidobacterium longum strain BR-108 alters cecal microbiota by stimulating gut immune system in mice irrespectively of viability – Yuko Makioka – Bioscience, Biotechnology, and Biochemistry

Animal microbiome

Mapping the virome in wild-caught Aedes aegypti from Cairns and Bangkok – Martha Zakrzewski – Nature

Changes in Larval Mosquito Microbiota Reveal Non-target Effects of Insecticide Treatments in Hurricane-Created Habitats – Joseph P. Receveur – Microbial Ecology

Dissecting cause and effect in host-microbiome interactions using the combined worm-bug model system – Marina Ezcurra – Biogerontology

Plant, root, and soil microbiome

[pre print] Diversity analysis and function prediction of rhizo- and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range – Dandan Cheng – PeerJ pre prints

Changes in the Metagenome of Prokaryotic Community as an Indicator of Fertility of Arable Soddy-Podzolic Soils upon Fertilizer Application – A. N. Naliukhin – Eurasian Soil Science

Assessing soil bacterial community and dynamics by integrated high-throughput absolute abundance quantification – Jun Lou – PeerJ

Plant growth-promoting rhizobacteria associated with avocado display antagonistic activity against Phytophthora cinnamomi through volatile emissions – Alfonso Méndez-Bravo – PLOS ONE

Composition and diversity of rhizosphere fungal community in Coptis chinensis Franch. continuous cropping fields – Xuhong Song – PLOS ONE

Genomic insights into the broad antifungal activity, plant-probiotic properties, and their regulation, in Pseudomonas donghuensis strain SVBP6 – Betina Cecilia Agaras – PLOS ONE

Water and extremophile microbiome

Microbial communities underpinning mesophilic anaerobic digesters treating food wastewater or sewage sludge: a full-scale study – Joonyeob Lee – Bioresource Technology

Bacteria from Antarctic environments: diversity and detection of antimicrobial, antiproliferative, and antiparasitic activities – Tiago R. Silva – Polar Biology

Responses of Salt Marsh Plant Rhizosphere Diazotroph Assemblages to Drought – Debra A. Davis – Microorganisms

Diversity and assembly patterns of activated sludge microbial communities: A review – Yu Xia – Biotechnology Advances

Temperature-induced changes in a microbial community under autotrophic denitrification with sulfide – Michal Sposob – Process Biochemistry

Metagenomic Exploration of Microbial Signatures on Periyar River Sediments from the Periyar Tiger Reserve in the Western Ghats – Aparna Chakkamadathil Rajeev – Genome Announcements

Occurrence and seasonal dynamics of RNA viral genotypes in three contrasting temperate lakes – Ian Hewson – PLOS One

Shifts in dissolved organic matter and microbial community composition are associated with enhanced removal of fecal pollutants in urban stormwater wetlands – Xiao Huang – Water Research

Effect of semi-permeable cover system on the bacterial diversity during sewage sludge composting – Tatiana Robledo-Mahón – Journal of Environmental Management

* Life at extreme elevations on Atacama volcanoes: the closest thing to Mars on Earth? – S. K. Schmidt – Antonie van Leeuwenhoek

Rapid alterations to marine microbiota communities following an oil spill – Brad J. Gemmell – Ecotoxicology

Microbial communities and their potential for degradation of dissolved organic carbon in cryoconite hole environments of Himalaya and Antarctica – Aritri Sanyal – Microbiological Research

Built environment

Microbiome Profiles of Commercial Broilers Through Evisceration and Immersion Chilling During Poultry Slaughter and the Identification of Potential Indicator Microorganisms – John A. Handley – Frontiers in Microbiology

Food microbiology

Characterization of Bacteria in Nigerian Yogurt as Promising Alternative to Antibiotics in Gastrointestinal Infections – Anthony Opeyemi Ayeni – Journal of Dietary Supplements

Probiotics / prebiotics

Polyphenols’ Gut Microbiota Metabolites: Bioactives or Biomarkers? -Francisco A. Tomas-Barberan – Journal of Agriculture and Food Chemistry

* A Multi-strain Probiotic Reduces the Fatty Liver Index, Cytokines and Aminotransferase levels in NAFLD Patients: Evidence from a Randomized Clinical Trial – Nazarii Kobyliak – Journal of Gastrointestinal and Liver Diseases

Bioinformatics

Species classifier choice is a key consideration when analysing low-complexity food microbiome data – Aaron M. Walsh – Microbiome

Data and Statistical Methods To Analyze the Human Microbiome – Levi Waldron – mSystems

* Discovery of enzymes for toluene synthesis from anoxic microbial communities – Beller HR – Nature

Techniques

Community Assembly Processes of the Microbial Rare Biosphere – Xiu Jia – Trends in Microbiology

* Metabolomics: A High-Throughput Platform for Metabolite Profile Exploration – Jing Cheng – Computational Systems Biology

[Patent] Spectrometric Analysis of Microbes – Zoltan Takats

* Development and evaluation of a culture-free microbiota profiling platform (MYcrobiota) for clinical diagnostics – Stefan A. Boers – European Journal of Clinical Microbiology & Infectious Diseases

Comparative analysis of four commercial on-farm culture methods to identify bacteria associated with clinical mastitis in dairy cattle – Jair C. Ferreira – PLOS One

Beyond Structure: Defining the Function of the Gut Using Omic Approaches for Rational Design of Personalized Therapeutics – Casey M. Theriot – mSystems

Synergy among Microbiota and Their Hosts: Leveraging the Hawaiian Archipelago and Local Collaborative Networks To Address Pressing Questions in Microbiome Research – Nicole A. Hynson – mSystems

Microbiomes In Natura: Importance of Invertebrates in Understanding the Natural Variety of Animal-Microbe Interactions – Jillian M. Petersen – mSystems

Microbial Eukaryotes: a Missing Link in Gut Microbiome Studies – Isabelle Laforest-Lapointe – mSystems

Microbes on the market 

DuPont Expands Microbiome Research Program, Adds Second Partnership with Fermentation Specialist

Science, publishing, and career

Biocodex Microbiota Foundation Awards Grants to Two Innovative Researchers in the Microbiome Field

Early-Career Systems Microbiology Scientists – Jack A. Gilbert – mSystems

Ed’s non-microbiology picks (can use your own name of course!) (cool non-microbiology science)

Self-employed people happier and more engaged at work, study finds

Health Care Spending in the United States and Other High-Income Countries

Ancient DNA Is Rewriting Human (and Neanderthal) History

Sturdy Insulator Made of Wood

How exercise in old age prevents the immune system from declining

March 20, 2018

Posted on by

Still short and sweet. Highlights include combining bacterial and archaeal membranes, a reference catalog for the rumen microbiome and your gut microbiome keeping you awake at night, but really?

Jobs

Research Associate, Microbiology – Kintai Therapeutics – Cambridge, MA

Partners with relevant publications are needed – Faculty of Agriculture, Ain Shams University – Egypt

Biomedical Scientist or Trainee Biomedical Scientist (Microbiology) – York Teaching Hospital, UK

General microbiology

Identification of Biofilm Inhibitors by Screening Combinatorial Libraries of Metal Oxide Thin Films – Michal M. Dykas et al. – Applied Materials and Interfaces

** Converting Escherichia coli into an archaebacterium with a hybrid heterochiral membrane – Antonella Caforio et al. – PNAS, USA

Press: Scientists engineer new life form with mixed Bacteria and Archaea membrane – Tibi Puiu – ZME Science

Preprint: Antibiotic-induced cell chaining triggers pneumococcal competence by reshaping quorum sensing to autocrine signaling – Arnau Domenech et al. – bioRxiv

Animal microbiome

** Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection – Rekha Seshadri et al. – Nature Biotechnology

Press: A reference catalog for the rumen microbiome – Joint Genome Institute, DOE

Water and extremophile microbiome

Preprint: Growth arrest in the active rare biosphere – Bela Hausmann et al. – bioRxiv

Phages and viruses

Preprint: Avian keratin disorder of Alaska black-capped chickadees is associated with Poecivirus infection – Maxine Zylberberg et al. -bioRxiv

Technology

Essay: Which experimental systems should we use for human microbiome science? – Angela E. Douglas – PLoS Biology

Preprint: Efficient genome editing of Magnetospirillum magneticum AMB-1 by CRISPR-Cas9 system for analyzing magnetotactic behavior – Haitao Chen et al. – bioRxiv

Microbes in the news

Could the Microbiome Treat Side Effects of Stem Cell Transplants? – Alexander Burik – Labiotech

Rapid Starch Increases, Decreases in Horse Diets Upset Gut Microbiome – Kristen M. Janicki – the Horse

** Could it be your gut keeping you awake at night? – Kate Leaver – the Guardian

Molecular cuisine for gut bacteria – ScienceDaily

Bacteria churn out a million potential protein drugs – KATRINA KRÄMER – ChemistryWorld

Bacteria that can kill wild sheep and goats has never turned up in Alaska — until now – Zaz Hollander – Anchorage Daily News

News Bites: New molecule able to kill drug-resistant bacteria, FDA approves at-home breast cancer risk test – Chu Meiyi – MIMS Today

Non-antibiotic drugs promote antibiotic resistance – The Economist

Microbes on the market

Microbiome Therapeutics Market Overview with Qualitative analysis, Competitive landscape & Forecast 2023 – Healthcare Journal

March 18, 2018

Posted on by

An interesting book and multiple animal microbiome papers for today’s digest!

General microbiome
Book: Clinical Immunology (Fifth Edition): Principles and Practice – Robert R. Rich, Thomas A. Fleisher, William T. Shearer, Harry W. Schroeder, Anthony J. Frew, Cornelia M. Weyand
Multiple chapters may be of interest, including:

Human skin microbiome
Review: Cutaneous Barriers and Skin Immunity: Differentiating A Connected Network – Stefanie Eyerich – Trends in Immunology

Human gut microbiome
TonB-dependent transport by the gut microbiota: novel aspects of an old problem – David N Bolam – Current Opinion on Structural Biology

Review: Frailty and the gut – Antonio Di Sabatino – Digestive and Liver Disease

Animal experiments
Chronic exposure to low concentrations of lead induces metabolic disorder and dysbiosis of the gut microbiota in mice – Jizhou Xia – Science of the Total Environment

Polystyrene microplastics induce gut microbiota dysbiosis and hepatic lipid metabolism disorder in mice – Liang Lu – Science of the Total Environment

Expression of recombinant human lysozyme in bacterial artificial chromosome transgenic mice promotes the growth of Bifidobacterium and inhibits the growth of Salmonella in the intestine – Lu Dan – Journal of Biotechnology

Comparative analysis of gut microbial community in healthy and tibial dyschondroplasia affected chickens by high throughput sequencing – Xiaole Tong – Microbial Pathogenesis

Polysaccharide of Hericium erinaceus Attenuates Colitis in C57BL/6 Mice via Regulation of Oxidative Stress, Inflammation-related Signaling Pathways and Modulating the Composition of the Gut Microbiota – Yilin Ren – The Journal of Nutritional Biochemistry

Variations in methane yield and microbial community profiles in the rumen of dairy cows as they pass through stages of first lactation – Tamsin Lyons – Journal of Dairy Science

Animal microbiome
Allelic variation in a single genomic region alters the microbiome of the snail Biomphalaria glabrata – Euan R O Allan – Journal of Heredity

Microbiomes associated with bovine periodontitis and oral health – Ana C. Borsanelli – Veterinary Microbiology

Review: Current perspectives of the chicken gastrointestinal tract and its microbiome – D. Borda-Molina – Computational and Structural Biotechnology Journal

Built environment
Review: Bioremediation of a pentacyclic PAH, Dibenz(a,h)Anthracene- A long road to trip with bacteria, fungi, autotrophic eukaryotes and surprises – Vidya Vasudevan – Chemosphere

Food microbiology
Microbial community dynamics of a blue-veined raw milk cheese from the United Kingdom – Dewi Yunita – Journal of Dairy Science

Probiotics / prebiotics / antibiotics
A mathematical model of multiple delayed feedback control system of the gut microbiota—Antibiotics injection controlled by measured metagenomic data – Yueping Dong – Nonlinear Analysis: Real World Applications

Review: Synthetic biology in probiotic lactic acid bacteria: At the frontier of living therapeutics – Zachary JS Mays – Current Opinion in Biotechnology

Review: The role of the gut microbiota in the pathology and prevention of liver disease – Alejandra Altamirano-Barrera – The Journal of Nutritional Biochemistry

Phages and viruses
Preprint: Avian influenza viruses in wild birds: virus evolution in a multi-host ecosystem – Divya Venkatesh – bioRxiv

New Genomes
Sanguibacter massiliensis sp. nov., Actinomyces minihominissp. nov., Clostridium minihomine sp. nov., Neobittarella massiliensis gen. nov., and Miniphocibacter massiliensis gen. nov., new bacterial species isolated by culturomics from human stool samples. – Melhem Bilen – New Microbes and New Infections

Microbes in the news
Weighty challenge: Untangling obesity’s hidden picture – Jamie Morton – NZ Herald

Microbes on the market
Seres Therapeutics (NASDAQ:MCRB) Upgraded at Zacks Investment Research – Amber Thompson – Register Journal

March 14, 2018

Posted on by

Today’s Digest adds to the growing literature of microbiome research. Highlights include the synergistic relationship between fungi and an invasive plant, enteral nutrition may help maintain the gastrointestinal function of critically ill patients, and the NCI calls for advancing epidemiologic research on the human microbiome.

Jobs

Student Trainee Microbiology Student Trainee Usda Pathways Internship Program Job in SAINT LOUIS, MO – Opening from 3/12-3/16, 2018

General microbiology

Antibiotic-induced population fluctuations and stochastic clearance of bacteria – Jessica Coates et al. – eLife

Press: Biophysicists discover how small populations of bacteria survive treatment – Science Daily

Preprint: Division of labor during biofilm matrix production – Anna Dragos et al. – bioRxiv

Isolation and characterization of two novel groups of kanamycin-resistance ColE1-like plasmids in Salmonella enterica serotypes from food animals – Chin-Yi Chen et al. – PLoS One

Human nasal microbiome

Genomic differences between nasal Staphylococcus aureus from hog slaughterhouse workers and their communities – Yaqi You et al. – PLoS One

Human oral microbiome

In vitro: pH changes of mixed biofilms of Streptococcus mutans and Candida albicans after exposure to sucrose solutions in vitro – Thamires Priscila Cavazana et al. – Archives of Oral Biology

Human lung microbiome

Fluctuations in airway bacterial communities associated with clinical states and disease stages in cystic fibrosis – Lisa A. Carmody et al. – PLoS One

Human gut microbiome

** Review: Effects of enteral nutrition on gastrointestinal function in patients who are critically ill – Michael Schörghuber and Sonja Fruhwald – The Lancet Gastroenterology & Hepatology

An overview on the interplay between nutraceuticals and gut microbiota – Adrian Catinean et al. – PeerJ

Animal experiments

Aronia berry (Aronia mitschurinii ‘Viking’) inhibits colitis in mice and inhibits T cell tumour necrosis factor-α secretion – Derek A. Martin et al. – Journal of Functional Foods

Mouse: Diet, Genetics, and the Gut Microbiome Drive Dynamic Changes in Plasma Metabolites – Shiho Fujisaka et al. – Cell Reports

Animal microbiome

Pathology and bacteria related to digital dermatitis in dairy cattle in all year round grazing system in Brazil – Tiago F. Moreira et al. – PLoS One

Food microbiology

The potential use of leaf extracts of two Newtonia (Fabaceae) species to treat diarrhoea – K.E. Motlhatlego et al. – South African Journal of Botany

Editorial: The interactions between food components and human nutrition – Charles Brennan – International Journal of Food Science & Technology

Plant, root and soil microbiome

** The unspecificity of the relationships between the invasive Pennisetum setaceum and mycorrhizal fungi may provide advantages during its establishment at semiarid Mediterranean sites – G. Rodríguez-Caballero et al. – Science of the Total Environment

Review: Environmental and public health related risk of veterinary zinc in pig production – Using Denmark as an example – John Jensen et al. – Environment International

Hydrophobins contribute to root colonization and stress responses in the rhizosphere-competent insect pathogenic fungus Beauveria bassiana – Soumya Moonjely et al. – Microbiology

Perspective: Tracing the role of human civilization in the globalization of plant pathogens – Alberto Santini et al. – ISME

Water and extremophile microbiome

Review: Surface water flooding, groundwater contamination, and enteric disease in developed countries: A scoping review of connections and consequences – L. Andrade et al. – Environmental Pollution

Domestic wastewater treatment and power generation in continuous flow air-cathode stacked microbial fuel cell: Effect of series and parallel configuration – Edson Baltazar Estrada-Arriaga et al. – Journal of Environmental Management

Effect of particle size and heterogeneity on sediment biofilm metabolism and nutrient uptake scaled using two approaches – Samuel P. Parker et al. – Ecosphere

Phages and viruses

Differential impact of lytic viruses on prokaryotic morphopopulations in a tropical estuarine system (Cochin estuary, India) – Vijayan Jasna et al. – PLoS One

Bioinformatics

A Bayesian Semiparametric Regression Model for Joint Analysis of Microbiome Data – Juhee Lee and Marilou Sison-Mangus – Frontiers in Microbiology

A systems pharmacology model for inflammatory bowel disease – Violeta Balbas-Martinez et al. – PLoS One

Microbes in the news

** Of Microbes and Men: Advancing Epidemiologic Research on the Human Microbiome – Victoria Fisher – National Cancer Institute

Opinion: Inflammatory bowel disease: complexity and variability need integration – Claudio Fiocchi – Frontiers in Medicine

Stress: How social conflict alters gut bacteria – Maria Cohut – Medical News Today

High-Fiber Generates Gut Bacteria Good for Type 2 Diabetes – Becky McCall – Medscape

New pathway may lead to improved probiotic products – Tim Lundeen – Feedstuffs

Probiotic potential: Specific gut microbes could cut severity of parasitic infections in developing countries – Nathan Gray – NUTRAingredients

Wandering Gut Bacteria Could Be Behind Conditions Like Lupus – Abby Norman – Futurism

Model Can Predict Which Bacteria will Engraft after FMT – Rachel Lutz – MD Magazine

Can Coral Microbes Protect Reefs From Climate Change? – Amelia Urry – NewsDeeply

Study: Several important vaginal metabolites elevated in smokers – Bob Kronemyer – Modern Medicine

Doctors collect viruses from pond and employ them to combat a man’s antibiotic resistance infection in man’s heart – Mark Kaufman – Mashable

Making good bacteria more resilient – Gali Weinreb – Globes

Study links decline of ‘good’ bacteria in infants to higher long-term increases in pH of poo – Tim Cutcliffe – NUTRAingredients

Microbes on the market

German biotech company wants to turn old PCs into gold – Jeremy Gray – Handelsblatt Global – European Business & Finance News

 

March 6, 2018

Posted on by

In today’s digest we have many interesting articles, particularly in “General Microbiome” section. Check a review on integrative view of cell cycle control in E. coli by L. Dewachter, an article on the return of cultures in microbiology by V. Marx, an article on microbial altruism and cheating in social amoebas by S. Noh. Don’t miss great articles from other sections, like “Water microbiome” where I would recommend an article deciphering the evolution and metabolism of an anammox bacterium by M. Strous and an article about globally overlooked nanoplanktonic diatoms by K. Leblanc. Happy reading!

Events

The Human Microbiome, EMBL Heidelberg, Germany, 16 – 19 Sep 2018

Jobs

Qc Analyst- Microbiology, Liverpool, UK

General microbiome

Commensal Koch’s postulates: establishing causation in human microbiota research – Anne Neville – Current Opinion in Microbiology

Escherichia coli Lrp regulates one-third of the genome via direct, cooperative, and indirect routes – Grace M. Kroner – bioRxiv

Review: An integrative view of cell cycle control in Escherichia coli – Liselot Dewachter – FEMS Microbiology Reviews

[Section Head] is Ravdin Lecture in the Basic and Surgical Sciences Microbiome Medicine: This Changes Everything  – John C. Alverdy – Journal of the American College of Surgeons

Regulation of Allergic Immune Responses by Microbial Metabolites – Hyun Jung Park – Immune Network

Microbiology: the return of culture – Vivien Marx – Nature Methods

Review: Bacterial microcompartments – Cheryl A. Kerfeld – Nature Reviews Microbiology

Proposal of the suffix –ota to denote phyla. Addendum to ‘Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes’ – William B. Whitman – International Journal of Systematic and Evolutionary Microbiology

Genetic signatures of microbial altruism and cheating in social amoebas in the wild – Suegene Noh – PNAS

The use of SWATH to analyse the dynamic changes of bacterial proteome of carbapanemase-producing Escherichia coli under antibiotic pressure – Hanna E. Sidjabat – Scientific Reports

Pregnancy and early life

Early fecal microbiota composition in children who later develop celiac disease and associated autoimmunity – Anniina Rintala – Scandinavian Journal of Gastroenterology

Human oral microbiome

Eliminating bias and accelerating the clinical translation of oral microbiome research in oral oncology – Rohit Kunnath Menon  – Oral Oncology

Acid-resistant genes of oral plaque microbiome from the functional metagenomics – Meng Zhang – Journal of Oral Microbiology

Oral microbiota in autoimmune polyendocrine syndrome type 1 – Øyvind Bruserud – Journal of Oral Microbiology

Human vaginal microbiome

Impact of contraceptive initiation on vaginal microbiota  – Sharon L. Achilles – American Journal of Obstetrics and Gynecology

Human gut microbiome

Gut Microbiome Composition Predicts Infection Risk during Chemotherapy in Children with Acute Lymphoblastic Leukemia – Hana Hakim – Clinical Infectious Diseases

Review: Flavonoid metabolism: the interaction of metabolites and gut microbiota – Kaeko Murota – Bioscience, Biotechnology, and Biochemistry

Data Descriptor: Gut bacterial communities of diarrheic patients with indications of Clostridioides difficile infection – Dominik Schneider – Scientific Data

Animal experiments 

Dietary Tryptophan Restriction Dose-Dependently Modulates Energy Balance, Gut Hormones, and Microbiota in Obesity-Prone Rats – Rizaldy C. Zapata – Obesity

Prevalence of microorganisms associated with feline gingivostomatitis – Hitoshi Nakanishi – Journal of Feline Medicine and Surgery

Effects of Rubus coreanus byproducts on intestinal microbiota and the immune modulation – Da Yoon Yu – Asian-Australasian Journal of Animal Sciences (AJAS)

Host and Environmental Factors Affecting the Intestinal Microbiota in Chickens – Jannigje G. Kers – Frontiers in Microbiology

Effect of urea-supplemented diets on the ruminal bacterial and archaeal community composition of finishing bulls – Zhenming Zhou – Applied Microbiology and Biotechnology

Animal microbiome 

Metagenomic Study Suggests That the Gut Microbiota of the Giant Panda (Ailuropoda melanoleuca) May Not Be Specialized for Fiber Fermentation – Wei Guo – Frontiers in Microbiology

Plant, root, and soil microbiome

Ecological selection for small microbial genomes along a temperate-to-thermal soil gradient – Jackson W Sorensen – bioRxiv

Phyllosphere microbiology: at the interface between microbial individuals and the plant host – Mitja N. P. Remus-Emsermann – New Phtyologist

Plant Rhizosphere Selection of Plasmodiophorid Lineages from Bulk Soil: The Importance of “Hidden” Diversity – David Bass – Frontiers in Microbiology

Microbial community structure with trends in methylation gene diversity and abundance in mercury-contaminated rice paddy soils in Guizhou, China – Tatiana A. Vishnivetskaya – Environmental Science: Processes & Impacts

Drought consistently alters the composition of soil fungal and bacterial communities in grasslands from two continents – Raúl Ochoa-Hueso – Global Change Biology

Temporal succession of soil antibiotic resistance genes following application of swine, cattle and poultry manures spiked with or without antibiotics – Yu-Jing Zhang – Environmental Pollution

Water and extremophile microbiome 

Light-dependent processes on the cathode enhance the electrical outputs of sediment microbial fuel cells – Ivo Bardarov – Bioelectrochemistry

Diversity of culturable filamentous Ascomycetes in the eastern South Pacific Ocean off Chile – Jeanett Vera – World Journal of Microbiology and Biotechnology

Stepwise impact of urban wastewater treatment on the bacterial community structure, antibiotic contents, and prevalence of antimicrobial resistance – Mingyu Wang – Environmental Pollution

Nanoplanktonic diatoms are globally overlooked but play a role in spring blooms and carbon export – Karine Leblanc – Nature Communications

A novel genus of the class Actinobacteria, Longivirga aurantiaca gen. nov., sp. nov., isolated from lake sediment – Jian-Hang Qu – International Journal of Systematic and Evolutionary Microbiology

Desulfothermobacter acidiphilus gen. nov., sp. nov., a thermoacidophilic sulfate-reducing bacterium isolated from a terrestrial hot spring –  E. N. Frolov – International Journal of Systematic and Evolutionary Microbiology

Deciphering the evolution and metabolism of an anammox bacterium from a community genome – Marc Strous –  Nature

Food microbiology

Dynamics of biofilm formation by Listeria monocytogenes on stainless steel under mono-species and mixed-culture simulated fish processing conditions and chemical disinfection challenges – Eleni Papaioannou – International Journal of Food Microbiology

Probiotics / prebiotics

Novel consortium of Klebsiella variicola and Lactobacillus species enhances the functional potential of fermented dairy products by increasing the availability of branched-chain amino acids and the amount of distinctive volatiles – H. Rosales-Bravo – Journal of Applied Microbiology

Bioinformatics

Updating the 97% identity threshold for 16S‌ ribosomal RNA OTUs – Robert C Edgar – Bioinformatics

Biotechnology

Selection and characterization of an anaerobic microbial consortium with high adaptation to crude glycerol for 1,3-propanediol production – Jin-Jie Zhou – Applied Microbiology and Biotechnology

Microbes in the news

Studying how tiny microbes thrive in harsh environments could lead to better treatments for human diseases

Microbes on the market 

FDA fast-tracks Finch’s microbiome capsule for C. difficile

Science, publishing, and career 

Uniting science and stories: Perspectives on the value of storytelling for communicating science

New round of science journalism projects awarded

 

March 3, 2017

Posted on by

Antiphage defense systems in microbial genomes, oral pathogen inhibition by wine polyphenols and an oral probiotic, and analysis of E. coli gene expression in simulated spaceflight.

Events and jobs

Call for Expressions of Interest: Microbiology Twitter Teachers for New MOOC – Spanish Society for Microbiology

Endowed Chair in Molecular Genetics Waksman Institute of Microbiology – Rutgers University

General microbiome

Creating a 3D microbial and chemical snapshot of a human habitat – Clifford A Kapono – Scientific Reports

Human oral microbiome

Inhibition of Oral Pathogens Adhesion to Human Gingival Fibroblasts by Wine Polyphenols Alone and in Combination with an Oral Probiotic – Adelaida Esteban-Fernández – Journal of Agricultural and Food Chemistry

Human vaginal microbiome

Metatranscriptome analysis of the vaginal microbiota reveals potential mechanisms for protection against metronidazole in bacterial vaginosis – Zhi-Luo Deng – bioRxiv

Human gut microbiome

Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia – Bruce A Rosa – Microbiome

Animal experiments

Pre-print: Orthogonal dietary niche enables reversible engraftment of a gut bacterial commensal – Sean M Kearney – bioRxiv

Pre-print: Clearing the FoG: Antifungal tolerance is a subpopulation effect that is distinct from resistance and is associated with persistent candidemia – Alexander Rosenberg – bioRxiv

Blueberry Supplementation Influences the Gut Microbiota, Inflammation, and Insulin Resistance in High-Fat-Diet–Fed Rats – Sunhye Lee – Journal of Nutrition

Animal microbiome

Woody forages effect the intestinal bacteria diversity of golden pompano Trachinotus ovatus – Biao Chen – AMB Express

Water and extremophile microbiome

Pre-print: Microzooplankton distribution in the Amundsen Sea Polynya (Antarctica) during an extensive Phaeocystis antarctica bloom – Rasmus Swalethorp – bioRxiv

Microbes in space

Pre-print: Analysis of Escherichia coli Flagellin Gene Expression in Simulated Spaceflight Growth Conditions – Kyle M Hetrick – bioRxiv

Phages and viruses

Systematic discovery of antiphage defense systems in the microbial pangenome – Shany Doron – Science

Bioinformatics

Pre-print: VirTect: a computational method for detecting virus species from RNA-Seq and its application in head and neck squamous cell carcinoma – Atlas Khan – bioRxiv

Techniques

Pre-print: Performance of convolutional neural networks for identification of bacteria in 3D microscopy datasets – Edouard A Hay – bioRxiv

Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem – Stilianos Louca – Microbiome

Improving saliva shotgun metagenomics by chemical host DNA depletion – Clarisse A Marotz – Microbiome

Microbes in the news

Your skin is crawling with bacteria, and some of them might help fight cancer – Claire Maldarelli – Popular Science

Most Viruses And Bacteria Fall From The Sky – Astrobiology Web

Microbes on the market

Six Leading Pharma Firms to Participate at Pharmaceutical Microbiology Event in San Diego – Technology Networks

Science, career, and publishing

Pre-print: Persistent Underrepresentation of Women’s Science in High Profile Journals – Yiqin Alicia Shen – bioRxiv

Pre-print: Female grant applicants are equally successful when peer reviewers assess the science, but not when they assess the scientist – Holly O Witteman – bioRxiv

February 16, 2018

Posted on by

Happy Lunar New Year of the Dog!

Today’s Digest contains many news pieces, and also features a major paper on strain tracking post fecal microbiota transplantation, a review on antibacterial proteins shaping the intestinal microbiota, and a call for action to build communities for bioinformatics programming.

Jobs

Postdoctoral Scholars of Microbiology, School of Life Sciences – University of Nevada Las Vegas

General microbiology

Book chapter: Agro-industrial Lignocellulosic Waste: An Alternative to Unravel the Future Bioenergy – Nidhi V. Maheshwari – Biofuels: Greenhouse Gas Mitigation and Global Warming

Review: Evolutionary Mechanisms Shaping the Maintenance of Antibiotic Resistance – Paulo Durão et al. – Trends in Microbiology

A single amino acid change in the response regulator PhoP acquired during Yersinia pestis evolution affects PhoP target gene transcription and polymyxin B susceptibility – Fukuto HS et al. – Journal of Bacteriology

Validated measurements of microbial loads on environmental surfaces in intensive care units before and after disinfecting cleaning – H. Frickmann et al. – Journal of Applied Microbiology

Human gut microbiome

Review: Proceedings of the 2017 ASPEN Research Workshop—Gastric Bypass: Role of the Gut – Ajay Kumar Jain et al. – Journal of Parenteral & Enteral Nutrition

A Phase 1 Study in Healthy Subjects to Assess the Safety, Tolerability, Pharmacokinetics, and Pharmacodynamics of Multiple Oral Doses of DS-2969b, a Novel GyrB Inhibitor – Vandell AG et al. – Antimicrobial Agents and Chemotherapy

* Antibacterial Weapons: Targeted Destruction in the Microbiota – Benoit Chassaing and Eric Cascales – Trends in Microbiology

Perspective: How to train your microbiome to eat broccoli – Sam H. Au – Science Translational Medicine

* Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation – Christopher S. Smillie – Cell Host & Microbe

Press: Model of fecal transplantation predicts which bacteria will flourish – Medical Xpress

Preprint: Spatial variation of the native colon microbiota in healthy adults – Kaitlin J Flynn et al. – bioRxiv

Preprint: The intestinal microbiota predisposes to traveller’s diarrhoea and to the carriage of multidrug-resistant Enterobacteriaceae after travelling to tropical regions – Stefano Leo et al. – bioRxiv

Animal experiments

Extracellular cholesterol oxidase production by Streptomyces aegyptia, in vitro anticancer activities against rhabdomyosarcoma, breast cancer cell-lines and in vivo apoptosis – Noura El-Ahmady El-Naggar et al. – Scientific Reports

Molecular analyses of two bacterial sampling methods in ligature-induced periodontitis in rats – Carla Raquel Fontana et al. – Clinical and Experimental Dental Research

Animal microbiome

Preprint: Drosophila melanogaster establishes a species-specific mutualistic interaction with stable gut-colonizing bacteria – Ines Silva Pais et al. – bioRxiv

Plant, root and soil microbiome

Removal of metals and their pools in plant in response to plant diversity in microcosms of floating constructed wetlands – Wenjuan Han et al. – Ecological Engineering

The Sesamum indicum rhizosphere associated bacterium: A source of Antifungal compound – Renu Chaudhary et al. – Current Topics in Medicinal Chemistry

Intensifying rotations increases soil carbon, fungi, and aggregation in semi-arid agroecosystems – Steven T. Rosenzweig et al. – Agriculture, Ecosystems & Environment

Impact of oxytetracycline and bacterial bioaugmentation on the efficiency and microbial community structure of a pesticide-degrading biomixture – Víctor Castro-Gutiérrez et al. – Environmental Science and Pollution Research

Indigenous endophytic seed bacteria promote seedling development and defend against fungal disease in browntop millet (Urochloa ramosa L.) – S.K. Verma and J.F. White – Journal of Applied Microbiology

Water and extremophile microbiome

Halophilic starch degrading bacteria isolated from Sambhar Lake, India, as potential anode catalyst in Microbial fuel cell: A promising process for saline water treatment – Ankisha Vijay et al. – Bioresource Technology

Sequestration and utilization of carbon dioxide by chemical and biological methods for biofuels and biomaterials by chemoautotrophs: Opportunities and challenges – Indu Shekhar Thakur et al. – Bioresource Technology

Small eukaryotic phytoplankton communities in tropical waters off Brazil are dominated by symbioses between Haptophyta and nitrogen-fixing cyanobacteria – Catherine Gérikas Ribeiro et al. – ISME

Neobodonids are dominant kinetoplastids in the global ocean – Olga Flegontova et al. – Environmental Microbiology

Food microbiology

Review: Whole genome sequencing as a typing tool for foodborne pathogens like Listeria monocytogenes – The way towards global harmonisation and data exchange – StefanieLüth et al. – Trends in Food Science & Technology

Phages and viruses

Book chapter: Tick-Borne Viruses and Host Skin Interface – Mária Kazimírová et al. – Skin and Arthropod Vectors

Preprint: The virome of Drosophila suzukii, an invasive pest of soft fruit – Nathan C Medd et al. – bioRxiv

Technology

Microfluidics-based liquid chromatography/mass spectrometry multiple reaction monitoring approach for the relative quantification of Burkholderia cenocepacia secreted virulence factors – Sofie Depluverez et al. – Rapid Communications in Mass Spectrometry

Microbes in the news

Surgeon sets new frontiers in battle against bacteria! – WBWire

The effect of antibacterials on the skin – Zoe Diana Draelo – Dermatology Times

Donor, Recipient Strain Analyses Offer Fecal Transplant Engraftment Clues – Genome Web

Australian Scientist Gets $1 Million to See if Probiotics Can Help Children with CF – Carolina Henriques – Cystic Fibrosis News Today

Do probiotics work? Answers to this and other gut-wrenching questions – Joanna Clay – USC News

Monitoring bacteria on whale skin – EurekAlert

Bacteria Hidden Under Our Feet May Be a New Weapon Against Superbugs – Kristin Houser – Futurism

Which probiotic is right for you? These are the exact bacteria strains to look for – Emily Laurence – Well and Good

How can we harness the power of bacteria-killing viruses? – Claire O’Connell – Sillcon Republic

Manipulating gut bacteria may cut obesity, diabetes risk – The Peninsula

Microbes on the market

Carbiotix launches world’s lowest cost microbiome test – Nathan Gray – Nutra Ingredients

Scientific Communication and Education

* Preprint: Building a local community of practice in scientific programming for Life Scientists – Sarah L.R. Stevens et al. – bioRxiv