November 15, 2017

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

General microbiome

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

Pregnancy and early life

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

Human respiratory microbiome

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

Human vaginal microbiome

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

Human gut microbiome

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

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

Animal experiments

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

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

Animal microbiome

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

Plant, root, and soil microbiome

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

Water and extremophile microbiome

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

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

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

Food microbiology

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

Probiotics/prebiotics

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

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

Phages and viruses

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

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

Bioinformatics

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

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

Metabolomics

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

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

Techniques

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

More microbes

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

Microbes in the news

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

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

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

Microbes on the market

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

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

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October 28, 2017

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Conductive properties of methanogenic biofilms – Cheng Li – Bioelectrochemistry

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Gut bacteria bolster disease research in labs – UNC Health Care

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

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

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

October 24, 2018

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

General microbiome

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

Aguilar-Trigueros CA- Trends in Ecology and Evolution

Gut microbiome

The Leaky Gut and Altered Microbiome in Chronic Kidney Disease.

Lau WL- Journal of Renal Nutrition

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

Tasnim N- Frontiers in Microbiology

Skin microbiome

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

Zeng B- Frontiers in Microbiology

Lung microbiome

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

Garg N- Cell Host and Microbe

Animal microbiome

Wild Mouse Gut Microbiota Promotes Host Fitness and Improves Disease Resistance

Rosshart SP- Cell

Plant and soil microbiome

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

Yuan Q- Soil Biology and Biochemistry

Bacterial communities in soil become sensitive to drought under intensive grazing

Jurburg SD- Science of the Total Environment

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

Xie K- Scientific reports

Marine and inland water microbiome

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

Lee MD-Applied and Environmental Microbiology

Dynamic microbial populations along the Cuyahoga River.

Cannon MV-  PloS one

Preprint

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

Bencardino D- BioRxiv

Microbiome News

I Wish I’d Known This Before I Gave Birth

-mindbodygreen.com

October 8, 2017

General microbiome

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

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

Events and jobs

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

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

Microbiology Faculty Position – University of Chicago

Human gut microbiome

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

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

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

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

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

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

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

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

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

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

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

Human oral microbiome

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

Animal experiments

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

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

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

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

Animal microbiome

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

Plant, root, and soil microbiome

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

Water and extremophile microbiome

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

Food microbiology

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

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

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

Probiotics / prebiotics

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

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

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

Microbes in the news

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

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

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

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

August 1, 2017

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

Human gut microbiome

Maternal modifiers of the infant gut microbiota: metabolic consequences

Mulligan CM. Journal of Endocrinology

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

Chen YC. The Journal of Clinical Endocrinology & Metabolism

Plant, soil, and air microbiome

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

Chang CH. Soil Biology and Biochemistry

Effect of nanoparticles on crops and soil microbial communities

Rajput VD. Journal of Soils and Sediments

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

Benítez E. Scientific reports

Unwrapping the rhizosheath

Pang J. Plant and Soil

Marine and inland waters

Marine archaea and archaeal viruses under global change

Danovaro R-F1000 Research

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

Guo X .Marine Pollution Bulletin

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

Baltar F. Frontiers in Marine Science

Microbiome Approaches/Techniques

A deep metaproteomics approach for the study of human microbiomes

Zhang X Analytical Chemistry, 2017

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

Shankar V. Scientific reports

Oral/Nasal Microbiome 

The periodontal war: microbes and immunity

Ebersole JL. PERIODONTOLOGY 2000

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

Parolin C. Scientific Reports

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

Mika M. Microbiome

Food Microbiology 

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

Liu Z.Food Microbiology

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

Hsu CK.International Journal of Food Microbiology, 2017

July 23, 2017

General microbiome

Systems biology of lactic acid bacteria: For food and thought – Bas Teusink, Current Opinion in Systems Biology

Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta) – Susan H. Brawley, PNAS

Parasite Microbiome Project: Systematic Investigation of Microbiome Dynamics within and across Parasite-Host Interactions – Nolwenn M. Dheilly, mSystems

Human respiratory microbiome

Airway microbiota signals anabolic and catabolic remodeling in the transplanted lung – Stéphane Mouraux, Journal of Allergy and Clinical Immunology

Human skin microbiome

The Skin Microbiome of Cohabiting Couples – Ashley A. Ross, mSystems

Human oral microbiome

Metabolic Fingerprints from the Human Oral Microbiome Reveal a Vast Knowledge Gap of Secreted Small Peptidic Molecules – Anna Edlund, mSystems

Human gut microbiome

Sequencing the gut metagenome as a non-invasive diagnosis for advanced nonalcoholic steatohepatitis – Lixin Zhu, Hepatology

Molecular Characterization of the Human Stomach Microbiota in Gastric Cancer Patients – Guoqin Yu, Frontiers in Microbiology

Inulin-type fructans and whey protein both modulate appetite but only fructans alter gut microbiota in adults with overweight/obesity: a randomized controlled trial – Raylene A. Reimer, Molecular Research and Food Research

Incomplete metabolism of phytoestrogens by gut microbiota from children under the age of three – Pilar Gaya, International Journal of Food Sciences and Nutrition

Animal experiments

An In Vitro Chicken Gut Model Demonstrates Transfer of a Multidrug Resistance Plasmid from Salmonella to Commensal Escherichia coli – Roderick M. Card, mBio

Maternally-transmitted microbiota affects odor emission and preference in Drosophila larva – Jean-Pierre Farine, Scientific Reports

Burn Injury Leads to Increase in Relative Abundance of Opportunistic Pathogens in the Rat Gastrointestinal Microbiome – Guangtao Huang, Scientific Reports

Linking Sex Differences in Non-Alcoholic Fatty Liver Disease to Bile Acid Signaling, Gut Microbiota, and High Fat Diet  – John Y.L. Chiang, The American Journal of Pathology

Early-life disruption of amphibian microbiota decreases later-life resistance to parasites – Sarah A. Knutie, Nature Communication

In vitro characteristics of an Atlantic salmon (Salmo salar L.) hind gut microbial community in relation to different dietary treatments – Kamarul Zaman Zarkasia,  Research in Microbiology

Effects of coconut oil on glycemia, inflammation, and urogenital microbial parameters in female Ossabaw mini-pigs – Annie E. Newell-Fugate, PLoS ONE

Effect of acute ozone exposure on the lung metabolomes of obese and lean mice – Joel Andrew Mathews, PLoS ONE

Animal microbiome

Skin Bacterial Community Reorganization Following Metamorphosis of the Fire-Bellied Toad (Bombina orientalis) – Arnaud Bataille, Microbial Ecology

Inferring microbial interactions in thermophilic and mesophilic anaerobic digestion of hog waste – Grace Tzun-Wen Shaw, PLoS ONE

Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation – Olov Svartström, ISME

Genome Sequences of Two Shewanella spp. Isolated from the Gut of the Sea Cucumber Apostichopus japonicus (Selenka, 1867) – Hyun-Hee Hong, Genome Anouncements

Feather-Degrading Bacteria: Their Biochemical and Genetic Characteristics – Paweł Kowalczyk, Arabian Journal for Science and Engineering

Plant, root, and soil microbiome

The tree species matters: Belowground carbon input and utilization in the myco-rhizosphere – Janine Sommera, European Journal of Soil Biology

Soil bacterial community response to vegetation succession after fencing in the grassland of China – Quanchao Zeng, Science of The Total Environment

Drought Stress Results in a Compartment-Specific Restructuring of the Rice Root-Associated Microbiomes – Christian Santos-Medellín, mBio

Improved grain yield of cowpea (Vigna unguiculata) under water deficit after inoculation with Bradyrhizobium elkaniiand Rhizophagus irregularis – Rui S. Oliveira, Crop and Pasture Science

Understanding the holobiont: the interdependence of plants and their microbiome – Carmen Sánchez-Cañizares, Current Opinion in Microbiology

Pseudomonas fluorescens R68 assisted enhancement in growth and fertilizer utilization of Amaranthus tricolor (L.) – C. Jimtha John, 3Biotech

Ecological guild and enzyme activities of rhizosphere soil microbial communities associated with Bt-maize cultivation under field conditions in North West Province of South Africa – Deidré A. B. van Wyk, Journal of Basic Microbiology

A genomic perspective on stoichiometric regulation of soil carbon cycling – Wyatt H Hartman, ISME

The rhizosphere microbiome of burned holm-oak: potential role of the genus Arthrobacter in the recovery of burned soils – Antonio J. Fernández-González, Scientific Reports

Biological control of potential antagonistic bacteria isolates to restrict Magnaporthe grisea infection on rice – David P. Tokpah, African Journal of Microbiology Research

Bacteria associated to plants naturally selected in a historical PCB polluted soil show potential to sustain natural attenuation – Lorenzo Vergani, Frontiers in Microbiology

Water and extremophile microbiome

Unraveling the Microbial Interactions and Metabolic Potentials in Pre- and Post-treated Sludge from a Wastewater Treatment Plant Using Metagenomic Studies – Chandni Sidhu, Frontiers in Microbiology

Metagenomics of urban sewage identifies an extensively shared antibiotic resistome in China – Jian-Qiang Su, Microbiome

Microbial Community Structure and Function Decoupling Across a Phosphorus Gradient in Streams – Erick S. LeBrun, Microbial Ecology

Microbial communities and their predicted metabolic functions in growth laminae of a unique large conical mat from Lake Untersee, East Antarctica – Hyunmin Koo, Frontiers in Microbiology

Draft genome sequence of Exiguobacterium aurantiacumstrain PN47 isolate from saline ponds, known as “Salar del Huasco”, located in the Altiplano in the North of Chile – Erwin Strahsburger, Brazilian Journal of Microbiology

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

Salinity Drives the Virioplankton Abundance but Not Production in Tropical Coastal Lagoons – Pedro C. Junger, Microbial Ecology

Characterization of a cold-adapted DNA photolyase from C. psychrerythraea 34H – Sudipto Munshi, Extremophiles

Marine archaeal dynamics and interactions with the microbial community over 5 years from surface to seafloor – Alma E Parada, ISME

Unusual metabolic diversity of hyperalkaliphilic microbial communities associated with subterranean serpentinization at The Cedars – Shino Suzuki, ISME

Comparative Omics and Trait Analyses of Marine Pseudoalteromonas Phages Advance the Phage OTU Concept – Melissa B. Duhaime, Frontier in Microbiology

Effects of Physiochemical Factors on Prokaryotic Biodiversity in Malaysian Circumneutral Hot Springs – Chia S. Chan, Frontiers in Microbiology

Climate oscillations reflected within the microbiome of Arabian Sea sediments – William D. Orsi, Scientific Reports

Microbiome of Trichodesmium Colonies from the North Pacific Subtropical Gyre – Mary R. Gradoville, Frontiers in Microbiology

Antarctic sea ice region as a source of biogenic organic nitrogen in aerosols – Manuel Dall’Osto, Scientific Reports

Built environment

A role for microbial selection in frescoes’ deterioration in Tomba degli Scudi in Tarquinia, Italy – Maria Cristina Tomassetti, Scientific Reports

Food microbiology

An Exploration into the Bacterial Community under Different Pasteurization Conditions during Substrate Preparation (Composting–Phase II) for Agaricus bisporus Cultivation – Fabricio Rocha Vieira, Microbial Ecology

Metagenome-based surveillance and diagnostic approaches to studying the microbial ecology of food production and processing environments – Conor J Doyle, Environmental Microbiology

Draft Genome Sequences of Three Lactobacillusparacasei Strains, Members of the Nonstarter Microbiota of Mature Cheddar Cheese – Ewelina Stefanovic, Genome Anouncements

Bioinformatics

Cohesion: a method for quantifying the connectivity of microbial communities – Cristina M Herren, ISME

Developing integrative systematics in the informatics and genomic era, and calling for a global Biodiversity Cyberbank – Jun Wen, Journal of Systematics and Evolution

Techniques

Rapid differentiation of bacterial communities using high resolution melting analysis – Steven Everman, Journal of Microbiological Methods

Proteomics in Inflammatory Bowel Disease: Approach Using Animal Models – Fadi H. Mourad, Digestive Diseases and Sciences

17, July 2017

In today’s digest, we learn more about how cloud-based computing is making it easier to analyses big datasets, and stochastic bottlenecks control bacterial colonization in animal host.

General Microbiome and Microbiology

New perspectives on dandruff and seborrheic dermatitis: lessons we learned from bacterial and fungal skin microbiota.

Paulino LC. European journal of dermatology

Harnessing microbiome‐based biotechnologies for sustainable mitigation of nitrous oxide emissions

Hu HW.Microbial Biotechnology

Human gut microbiome

Comparisons of Gut Microbiota Among Healthy Control, Patients With Conventional Adenoma, Sessile Serrated Adenoma, and Colorectal Cancer. Yoon H. Journal of Cancer Prevention

Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life. Xiong W. Microbiome

Assessing the impact of protein extraction methods for human gut metaproteomics

Zhang  X.Journal of Proteomics

Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls

Stewart CJ. Microbiome

Animal and insect microbiome

Host–Microbe Interactions: Winning the Colonization Lottery

Lazzaro BP and GM Fox. Current Biology

Strategies for managing rival bacterial communities: lessons from burying beetles.

Kilner RM. Journal of Animal Ecology

Changes in the Gut Microbial Communities Following Addition of Walnuts to the Diet. Byerley, LO. Journal of Nutritional Biochemistry

Microbiome modelling

The Microbiome and Big Data

Navas-Molina JA. Current Opinion in Systems Biology

Plant, soil, and air microbiome

Differences in soil biological activity by terrain types at the sub-field scale in central Iowa US.

Kaleita AL.PloS one

Intercropping affects genetic potential for inorganic nitrogen cycling by root-associated microorganisms in Medicago sativa and Dactylis glomerata

Zhao M. Applied Soil Ecology

Changes in microbial community composition following phytostabilization of an extremely acidic Cu mine tailings

Yang T. Soil Biology and Biochemistry

Effects of between‐site variation in soil microbial communities and plant‐soil feedbacks on the productivity and composition of plant communities.   Bauer JT.Journal of Applied Ecology

Response of soil microbial communities to elevated antimony and arsenic contamination indicates the relationship between the innate microbiota and contaminant fractions. Sun W. Environmental Science and Technology

Marine and inland waters

The contribution of microbial biotechnology to mitigating coral reef degradation Damjanovic. Microbial Biotechnology

Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization

Slaby BM. The ISME Journal

Deep-Sea Hydrothermal Vent Viruses Compensate for Microbial Metabolism in Virus-Host Interactions

He T.  mBio

Built Microbiome

Microbial communities on painted wet and dry external surfaces of a historic fortress in Niterói, Brazil. Ogawa A. Journal of International Biodeterioration & Biodegradation

Preprint

Short reads from honey bee (Apis sp.) sequencing projects reflect microbial associate diversity.Gerth M.PeerJ