April 19, 2018

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

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March 28, 2018

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

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 18, 2018

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

ReviewFrailty 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

ReviewCurrent 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

ReviewThe 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 6, 2018

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

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 13, 2018

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

Human gut microbiome

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

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

Animal experiments

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

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

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

Animal microbiome

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

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

Plant, root, and soil microbiome

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

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

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

Water and extremophile microbiome

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

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

Built environment

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

Food microbiology

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

Phages and viruses

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

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

Metabolomics

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

Microbes in the news

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

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

Microbes on the market

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

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

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