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 23, 2018

Optogenetic regulation of transcription to promote biosynthesis of desired chemicals from fungi, the effect of yeast and bacteria on floral nectar, guidelines and best practices for human microbiome sampling/sequencing/processing.

Plant, root, and soil microbiome

Evaluation of conventional and response surface level optimisation of n-dodecane (n-C12) mineralisation by psychrotolerant strains isolated from pristine soil at Southern Victoria Island, Antarctica – Syahir Habib – Microbial Cell Factories

Analysis of microbiota in bellflower root, Platycodon grandiflorum, obtained from South Korea – Daeho Kim – Journal of Microbiology and Biotechnology

Contrasting effects of yeasts and bacteria on floral nectar traits – Rachel L Vannette – Annals of Botany

Water and extremophile microbiome

Mechanisms of Methyl Mercury Net Degradation in Alder Swamps: The Role of Methanogens and Abiotic Processes – Rose-Marie Kronberg – Environmental Science & Technology Letters

Microbial mat of the thermal springs Kuchiger Republic of Buryatia: species composition, biochemical properties and electrogenic activity in biofuel cell – Denis Aleksandrovich Yuriev – IOP Conference Series: Earth and Environmental Sciences

Bioinformatics

Pre-print: A comprehensive automated pipeline for human microbiome sampling, 16S rRNA gene sequencing and bioinformatics processing – Luisa W Hugerth – bioRxiv

Pre-print/Review: Real-time analysis and visualization of pathogen sequence data – Richard A Neher – bioRxiv

Techniques

Yeast Biofilm as a Bridge Between Medical and Environmental Microbiology Across Different Detection Techniques – Luca Roscini – Infectious Diseases and Therapy

More microbes

Optogenetic regulation of engineered cellular metabolism for microbial chemical production – Evan M Zhao – Nature

Pre-print: Titan cells formation in Cryptococcus neoformans is finely tuned by environmental conditions and modulated by positive and negative genetic regulators – Benjamin Hommel – bioRxiv

Pre-print: High-resolution analysis of the pneumococcal transcriptome under a wide range of infection-relevant conditions – Rieza Aprianto – bioRxiv

Pre-print: Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae D39 – Jelle Slager – bioRxiv

Microbes in the news

Oral microbiome and anthropometry changes following caries arrest using silver-nitrate/fluoride-varnish – EurekAlert

Metagenomics of early childhood oral health and early childhood caries – EurekAlert

Synergistic effects of smoking and obesity on the subgingival microbiome – EurekAlert

Gut bacteria can mean life or death for birds – EurekAlert

Its name is LUCA. Now it’s needing second thoughts – Stephen Fleischfresser – Cosmos

Plants really do feed their friends – ScienceDaily

Bacteria eats greenhouse gas with a side of protein – Phys.org

Survival of the Slimiest: The Persistent Nature of Biofilms – Sonali D Advani – Medscape

Amy’s non-microbiology picks

Editorial: Asymmetry symposium unites economists, physicists and artists – Nature

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

February 21, 2018

Events and jobs

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

General microbiome

[editorial] Systems biology of the human microbiome – BP Bernabé, L Cralle, JA Gilbert – Current Opinion in Biotechnology, 2018

[pre-print] Growth tradeoffs produce complex microbial communities without direct interactions – Michael Manhart – bioRxiv

Exploring the Multifaceted Role of Microbes in Pharmacology – Mitali Mishra – Microbial Biotechnology

Human reproductive or urinary microbiome

Seminal bacterial composition in patients with obstructive and non-obstructive azoospermia – Houyang Chen – Experimental and Therapeutic Medicine

Human respiratory microbiome

Virome and bacteriome characterization of children with pneumonia and asthma in Mexico City during winter seasons 2014 and 2015 – Jose A. Romero-Espinoza – PLOS One

Human gut microbiome

[pdf[ Phytochemicals that influence gut microbiota as prophylactics and for the treatment of obesity and inflammatory diseases – Lucrecia Carrera-Quintanar – Hindawi

Dietary Fiber Treatment Corrects the Composition of Gut Microbiota, Promotes SCFA Production, and Suppresses Colon Carcinogenesis – F Bishehsari – Genes

A Cross-Talk Between Microbiota-Derived Short-Chain Fatty Acids and the Host Mucosal Immune System Regulates Intestinal Homeostasis and Inflammatory Bowel Disease – Pedro Gonçalves – Inflammatory Bowel Diseases

Animal microbiome

Differential microbial communities of omnivorous and herbivorous cattle in Southern China – Susanna K.P. Lau – Computational and Structural Biotechnology Journal

The gills of reef fish support a distinct microbiome influenced by host-specific factors – Zoe A. Pratte – Applied and Environmental Microbiology

Metagenomic analysis of orange colored protrusions from the muscle of Queen Conch Lobatus gigas (Linnaeus, 1758) – Jaison H. Cuartas – PeerJ

Plant, root, and soil microbiome

Bulk soil and maize rhizosphere resistance genes, mobile genetic elements and microbial communities are differently impacted by organic and inorganic fertilization – Birgit Wolters – FEMS Microbiology Ecology

Structural and metabolic diversity of rhizosphere microbial communities of Phragmites karka in a tropical coastal lagoon – Pratiksha Behera – Applied Soil Ecology

Responses of soil microbial communities to a short-term application of seaweed fertilizer revealed by deep amplicon sequencing – Mingpeng Wang – Applied Soil Ecology

[pdf] The Green Roof Microbiome: Improving Plant Survival for Ecosystem Service Delivery – Roberta Fulthorpe – Frontiers in Ecology and Evolution

Microbes and Their Role in Drought Tolerance of Agricultural Food Crops – Rout George Kerry – Microbial Biotechnology

Microscopic and Metagenomic Analyses of Peltigera ponojensis (Peltigerales, Ascomycota) – Linda E. Graham – International Journal of Plant Sciences

Frankia Diversity in Host Plant Root Nodules Is Independent of Abundance or Relative Diversity of Frankia Populations in Corresponding Rhizosphere Soils – Seifeddine Ben Tekaya – Applied and Environmental Microbiology

High frequency cropping of pulses modifies soil nitrogen level and the rhizosphere bacterial microbiome in 4-year rotation systems of the semiarid prairie – Chantal Hamel – Applied Soil Ecology

Bulk soil and maize rhizosphere resistance genes, mobile genetic elements and microbial communities are differently impacted by organic and inorganic fertilization – Birgit Wolters – FEMS Microbiology Ecology

Water and extremophile microbiome

Variability in metagenomic samples from the Puget Sound: Relationship to temporal and anthropogenic impacts – James C. Wallace – PLOS One

Linking the effect of antibiotics on partial-nitritation biofilters: performance, microbial communities and microbial activities – Alejandro Gonzalez-Martinez – Frontiers in Microbiology

The effect of epiphytic macroinvertebrates on microbial communities in different types of macrophyte-dominated shallow lakes – Tomasz Mieczan –  Knowl. Manag. Aquat. Ecosyst

Watershed-induced limnological and microbial status in two oligotrophic Andean lakes exposed to the same climatic scenario – Alex Echeverría-Vega – Frontiers in Microbiology

** A novel β-glucosidase isolated from the microbial metagenome of Lake Poraquê (Amazon, Brazil) – Danyelle Toyama – Biochimica et Biophysica Acta (BBA) – Proteins and Proteomics

Variations in culturable bacterial communities and biochemical properties in the foreland of the retreating Tianshan No. 1 glacier – Xiukun Wu – Brazilian Journal of Microbiology

Food microbiology

Microbial diversity and component variation in Xiaguan Tuo Tea during pile fermentation – Haizhou Li – PLOS One

Metagenomic Insights into Environmental Microbiome and Their Application in Food/Pharmaceutical Industry – Ramya Sree Boddu – Microbial Biotechnology

Phages and viruses

[pre-print] THEA: A novel approach to gene identification in phage genomes – Katelyn McNair – bioRxiv

Bioinformatics

* [pdf] Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models – Aeriel Belk – Genes

COREMIC: a web-tool to search for a niche associated CORE MICrobiome – Richard R. Rodrigues – PeerJ

Techniques

Isotope fractionation in biogas allows direct microbial community stability monitoring in anaerobic digestion – Jo De Vrieze – Environmental Science & Technology

Statistical assessment of DNA extraction methodology for culture-independent analysis of microbial community associated with diverse environmental samples – Rishi Mahajan – Molecular Biology Reports

Microbes in the news

These Bacteria Eat Toxic Metal, ‘Poop’ Gold Nuggets – Live Science

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

Earthquakes follow wastewater disposal patterns in southern Kansas

Ultra-processed foods ‘linked to cancer’

Promising cancer vaccine would use patient’s own cells to train the immune system

Does GMO corn increase crop yields? 21 years of data confirm it does—and provides substantial health benefits

Poor fitness linked to weaker brain fiber, higher dementia risk

Low cigarette consumption and risk of coronary heart disease and stroke: meta-analysis of 141 cohort studies in 55 study reports

Fewer Infants Died In States That Allowed Affordable Care Act

February 6, 2018

 

General microbiome

Preprint: Selection of appropriate metagenome taxonomic classifiers for ancient microbiome research – IM Velsko – bioRxiv

Advances in metabolic engineering in the microbial production of fuels and chemicals from C1 gas – CM Humphreys – Current Opinion in Biotechnology

 

Human skin microbiome

Individual and household attributes influence the dynamics of the personal skin microbiota and its association network – MHY Leung – Microbiome

 

Human gut microbiome

The intestinal protist Blastocystis is not a common member of the healthy infant gut microbiota in a Westernized country (Ireland) – PD Scanlan – Parasitology

Preprint: When metabolism meets physiology: Harvey and Harvetta – I Thiele – bioRxiv

Connection between BMI related plasma metabolite profile and gut microbiota – F Ottosson – The Journal of Clinical Endocrinology & Metabolism

Animal experiments 

Review: Gut microbiome and depression: what we know and what we need to know – G Winter – Reviews in the Neurosciences

Potential of Lactobacillus plantarum ZDY2013 and Bifidobacterium bifidum WBIN03 in relieving colitis by gut microbiota, immune and anti-oxidative stress – Y Wang – Canadian Journal of Microbiology

Air-Dried Brown Seaweed, Ascophyllum nodosum, Alters the Rumen Microbiome in a Manner That Changes Rumen Fermentation Profiles and Lowers the Prevalence of Foodborne Pathogens – M Zhou – mSphere

Animal microbiome 

Antimicrobial resistance in companion animals – DI Rendle – Equine Veterinary Journal

Plant, root and soil microbiome

Drought neutralises plant–soil feedback of two mesic grassland forbs – EL Fry – Oecologica

Effects of different fertilizers on methane emissions and methanogenic community structures in paddy rhizosphere soil – J Yuan – Science of The Total Environment

Halotolerant microbial consortia able to degrade highly recalcitrant plant biomass substrate. – L Cortes-Tolalpa – Applied Microbiology and Biotechnology

Microbial Diversity and Community Structure in Agricultural Soils Suffering from 4-year Pb Contamination – A Fengqiu – Canadian Journal of Microbiology

Evidence for species-specific plant responses to soil microbial communities from remnant and degraded land provides promise for restoration – ME Smith – Austral Ecology

Long term effects of Lespedeza bicolor revegetation on soil bacterial communities in Dexing copper mine tailings in Jiangxi Province, China – Z Wu – Applied Soil Ecology

Water microbiome and extremophile

Preprint: Spatiotemporal dynamics of river viruses, bacteria and microeukaryotes – TV Rossum – bioRxiv

Life on Phosphite: A Metagenomics Tale – Y Tapia-Torres – Trends in Microbiology

Biodegradation of n-alkanes on oil-seawater interfaces at different temperatures and microbial communities associated with the degradation. – S Lofthus – Biodegradation

Contrasting the genetic patterns of microbial communities in soda lakes with and without cyanobacterial bloom – AP Andreote – Frontiers in Microbiology

Microbial communities associated with the co-metabolism of free cyanide and thiocyanate under alkaline conditions – L Mekuto – 3 Biotech

Untapped bacterial diversity and metabolic potential within Unkeshwar hot springs, India – G Mehetre – Archives of Microbiology

Built environment 

Effects of wastewater constituents and operational conditions on the composition and dynamics of anodic microbial communities in bioelectrochemical systems – M Kokko – Bioresource Technology

Free-living bacteria and potential bacterial pathogens in sewage treatment plants – K Huang – Applied Microbiology and Biotechnology

Crawling-induced floor dust resuspension affects the microbiota of the infant breathing zone – H Hyytiäinen – Microbiome

 

Techniques

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

Preprint: Kaptive Web: user-friendly capsule and lipopolysaccharide serotype prediction for Klebsiella genomes – RR Wick – bioRxiv

The madness of microbiome: Attempting to find consensus “best practice” for 16S microbiome studies – J Pollock – Applied and Environmental Microbiology

Microbes in the news

The possibilities of microorganisms – The Varsity

New insight into the molecular weapons of the plant microbiome – EurekAlert

Ohio State scientists to send ancient bacteria into space to unlock secrets about life on other planets – The Columbus Dispatch

Workbench for virus design – Phys.org

What does your poo microbiome do? – Phys.org

The Importance of Infants’ Exposure to Microorganisms – The New York Times

Treatment of nitrogen-polluted sediment using marine anammox bacteria – Science Daily

Microbes and the market

Thermo Fisher Scientific Launches Axiom Microbiome Array for Research – Cision PR Newswire

Worldwide Microbiome Sequencing Services Market Driven by Business Overview, Company Profile, Products, Services and Solutions Prediction To 2022 – Facts Week

Non-Microbiology Picks

Chilly Climates, Balancing Acts, and Shifting Pathways: What Happens to Women in STEM Doctoral Programs – M Cabay – Social Sciences

 

January 24, 2018

General microbiome

Meta-analysis generates and prioritizes hypotheses for translational microbiome research – Claire Duvallet – microbial biotechnology

Resistance to Antibiotics: Are we prepared to Handle This Growing Ghost? – Ashima Kushwaha Bhardwaj – Omics Ebook Group

Pregnancy and early life

Neonate gut and respiratory microbiota: coordinated development through time and space – Alex Grier – bioRxiv

Human oral microbiome

Oral Microbiome Studies: Potential Diagnostic and Therapeutic Implications – A. Mira – Advances in Dental Research (SAGE Journals)

Rebalancing the Caries Microbiome Dysbiosis: Targeted Treatment and Sugar Alcohols – L. Zhan – Advances in Dental Research (SAGE Journals)

The Caries Microbiome: Implications for Reversing Dysbiosis – A.C.R. Tanner – Advances in Dental Research (SAGE Journals)

In Sickness and in Health—What Does the Oral Microbiome Mean to Us? An Ecological Perspective – P. D. Marsh – Advances in Dental Research (SAGE Journals)

Getting to Know “The Known Unknowns”: Heterogeneity in the Oral Microbiome – R. A. Burne – Advances in Dental Research (SAGE Journals)

Human gut microbiome

Adaptive Immune Education by Gut Microbiota Antigens – Qing Zhao – Immunology

Microbiota-Regulated Outcomes of Human Cancer Immunotherapy via the PD-1/PD-L1 Axis – Jaymin Patel – Biochemistry

Characterization of the fecal microbiota differs between age groups in Koreans – Sun-Young Kook – Intestinal Research

Diet, microbiota and inflammatory bowel disease: review – Bruna Luísa Radavelli – Nutrition & Food Science

The Human Gastric Microbiome Is Predicated upon Infection with Helicobacter pylori – Ingeborg Klymiuk – Frontiers in Microbiology

Gut Microbial Diversity in Women with Polycystic Ovary Syndrome Correlates with Hyperandrogenism – Pedro J Torres – JCEM

Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives with Adult Celiac Disease Patients and Controls – Sudarshan A Shetty – bioRxiv

Animal experiments 

Modeling Host-Microbiome Interactions in Caenorhabditis elegans – Teklu K. Gerbaba – Journal of Nematology

The anti-inflammatory IFITM genes ameliorate colitis and partially protect from tumorigenesis by changing immunity and microbiota – Zoya Alteber – Immunology & Cell Biology

A metagenomics approach to the intestinal microbiome structure and function in high fat diet-induced obesity mice fed with oolong tea polyphenols – Mei Cheng – Food & Function

Animal microbiome

Characterization of the Skin Microbiota of the Cane Toad Rhinella cf. marina in Puerto Rico and Costa Rica – Juan G. Abarca – Frontiers in Microbiology

Functional Characteristics of the Flying Squirrel’s Cecal Microbiota under a Leaf-Based Diet, Based on Multiple Meta-Omic Profiling – Hsiao-Pei Lu – Frontiers in Microbiology

Plant, root, and soil microbiome

Microbial Communities and Diversities in Mudflat Sediments Analyzed Using a Modified Metatranscriptomic Method – Yong-Wei Yan – Frontiers in Microbiology

Out of sight, but no longer out of mind – towards an increased recognition of the role of soil microbes in plant speciation – József Geml – New Phytologist

Clearcutting alters decomposition processes and initiates complex restructuring of fungal communities in soil and tree roots – Petr Kohout – The ISME Journal

Assembly and ecological function of the root microbiome across angiosperm plant species – Connor R. Fitzpatrick – PNAS

A Community-Based Culture Collection for Targeting Novel Plant Growth-Promoting Bacteria from the Sugarcane Microbiome – Jaderson Silveira Leite Armanhi – Frontiers in Plant Science

Temporal and Spatial Impact of Human Cadaver Decomposition on Soil Bacterial and Arthropod Community Structure and Function – Baneshwar Singh – Frontiers in Microbiology

Water and extremophile microbiome

Coastal urbanisation affects microbial communities on a dominant marine holobiont – Ezequiel M. Marzinelli – npj Biofilms and Microbiomes

Succession of microbial communities and changes of incremental oil in a post-polymer flooded reservoir with nutrient stimulation – Peike Gao – Applied Microbiology and Biotechnology

Evidence for Coupling of the Carbon and Phosphorus Biogeochemical Cycles in Freshwater Microbial Communities – O Roger Anderson – Frontier in Marine Science

Metagenomic Signatures of Microbial Communities in Deep-Sea Hydrothermal Sediments of Azores Vent Fields – Teresa Cerqueira – Environmental Microbiology

Bioinformatics

Predictive functional profiles using metagenomic 16S rRNA data: a novel approach to understanding the microbial ecology of aquaculture systems – Ángel Martín Ortiz-Estrada – Reviews in Agriculture

[MSc Thesis] Optimizing the Reconstruction of Microbial Population Genomes from Metagenomes – Bhavya Nalagampalli Papudeshi – San Diego State University, ProQuest Dissertations Publishing

Advantages of meta-total RNA sequencing (MeTRS) over shotgun metagenomics and amplicon-based sequencing in the profiling of complex microbial communities – Fabien Cottier – npj Biofilms and Microbiomes

Extension of the viral ecology in humans using viral profile hidden Markov models – Zurab Bzhalava – PLOS One

Metataxonomic approach to decipher the polymicrobial burden in diabetic foot ulcer and its biofilm mode of infection – Karthika Suryaletha – International Wound Journal

A strategy for association study on intestinal microbiome and brain metabolome across lifespan of rats – Tianlu Chen – Analytical Chemistry

Techniques

The effect of DNA extraction methods on observed microbial communities from fibrous and liquid rumen fractions of dairy cows – Jueeli D. Vaidya – Frontiers in Microbiology

Microbes in the news

Hyperandrogenism may alter gut microbiome in PCOS

Ed’s non-microbiology picks 

Using Fungi to Fix Bridges

Cooperating with machines – Jacob W. Crandall – Nature Communications

An investigation into the nutritional composition and cost of gluten-free versus regular food products in the UK – L. Fry – Journal of Human Nutrition and Dietetics

Prevalence and Trends in Prepregnancy Normal Weight — 48 States, New York City, and District of Columbia, 2011–2015 – CDC / Morbidity and Mortality Weekly Report

Exposed subsurface ice sheets in the Martian mid-latitudes – Colin M. Dundas – Science

Shorter sleep duration and longer sleep onset latency are related to difficulty disengaging attention from negative emotional images in individuals with elevated transdiagnostic repetitive negative thinking – Jacob A. Nota – Journal of Behavior Therapy and Experimental Psychiatry

January 19, 2018

Today’s digest features a review on gut microbial glycerol metabolism as a source of Acrolein, and an interesting article on the impact of climate cooling on ecosystem community structure and function in alpine soils. Happy reading!

 

Careers and Events

Research Fellow – National University of Singapore

Postdoctoral Fellow – Boston Children’s Hospital, Harvard Medical School

Scientific Officer/Senior Scientific Officer – The Cancer Research UK Beatson Institute

Staff Clinician – National Institutes of Health (NIH) National Heart, Blood and Lung Institute (NHLBI)

Human respiratory microbiome

Initial acquisition and succession of the cystic fibrosis lung microbiome is associated with disease progression in infants and preschool children – Marianne S. Muhlebach – Plos Pathogens

Human skin microbiome

Association of Disease Severity With Skin Microbiome and Filaggrin Gene Mutations in Adult Atopic Dermatitis – Maja-Lisa Clausen – JAMA Dermatology

Human gut microbiome

Review : Genetic and microbiome influence on lipid metabolism and dyslipidemia – Maria Matey Hernandez – Physiological Genomics

Review : Bile acids in glucose metabolism in health and disease – Hagit Shapiro – Journal of Experimental Microbiology

*Review: Gut Microbial Glycerol Metabolism as an Endogenous Acrolein Source – Jianbo Zhang – mBio

Review: How does ‘metabolic surgery’ work its magic? New evidence for gut microbiota – Peck Bailey C.E – Current Opinion in Endocrinology, Diabetes and Obesity

Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn’s disease – Gavin M. Douglas – Microbiome

Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease – Ahmed Moustafa – Clinical and translational gastroenterology

Animal experiments

Flaxseed-enriched diets change milk concentration of the antimicrobial danofloxacin in sheep – Jon Andoni Otero – BMC Veterinary Research

Colonization of the cervicovaginal space with Gardnerella vaginalis leads to local inflammation and cervical remodeling in pregnant mice – Luz-Jeannette Sierra – Plos One

Kudingcha and Fuzhuan Brick Tea Prevent Obesity and Modulate Gut Microbiota in High-Fat Diet Fed Mice – Guijie Chen – Molecular Nutrition and Food Research

Plant, root, and soil microbiome

*Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling – Linwei Wu – ISME Journal

Cultivable fungi present in Antarctic soils: taxonomy, phylogeny, diversity, and bioprospecting of antiparasitic and herbicidal metabolites – Eldon C. Q. Gomes – Extremophiles

Clearcutting alters decomposition processes and initiates complex restructuring of fungal communities in soil and tree roots – Petr Kohout – The ISME Journal

A large-scale field study of bacterial communities in cereal aphid populations across Morocco – Samir Fakhour – FEMS Microbiology Ecology

Microbial Mitigation-Exacerbation Continuum: A novel framework for microbiome effects on hosts in the face of stress – Aaron S. David – Ecology

Water and extremophile microbiome

Brief Report: Effects of grazing, phosphorus and light on the growth rates of major bacterioplankton taxa in the coastal NW Mediterranean – Olga Sánchez – Environmental Microbiology Reports

Development of a mediated whole cell-based electrochemical biosensor for joint toxicity assessment of multi-pollutants using a mixed microbial consortium – Guanyue Gao – Analytica Chimica Acta

The acute effects of erythromycin and oxytetracycline on enhanced biological phosphorus removal system: shift in bacterial community structure – Zhetai Hu – Environmental Science and Pollution Research

Probiotics / prebiotics

Valorization of Brewer’s spent grain to prebiotic oligosaccharide: production, xylanase catalyzed hydrolysis, in-vitro evaluation with probiotic strains and in a batch human fecal fermentation model – Mursalin Sajib – Journal of Biotechnology

In vitro fermentation of gum acacia – impact on the faecal microbiota – Sehad Alarifi -International Journal of Food Sciences and Nutrition

A bioluminescent test system reveals valuable antioxidant properties of lactobacillus strains from human microbiota – Maria Marsova – World Journal of Microbiology and Biotechnology

Yeasts / Fungi

Review: Sequence-based classification and identification of Fungi – David Hibbett – Mycologia

Phages and viruses

Detection of bovine Deltapapillomavirus DNA in peripheral blood of healthy sheep (Ovis aries) – S. Roperto – Transboundary and Emerging Diseases

Metagenomics

In-depth resistome analysis by targeted metagenomics – Val F. Lanza – Microbiome

Metabolomics

Qualitative metabolomics profiling of serum and bile from dogs with gallbladder mucocele formation – Jody L. Gookin – Plos One

Bioinformatics

A distance-based approach for testing the mediation effect of the human microbiome -Jie Zhang – Bioinformatics

Anitha’s non-microbiology picks

NASA test proves pulsars can function as a celestial GPS

The dark side of light: how artificial lighting is harming the natural world

Ultrathin 2-D metals get their own periodic table