November 11, 2017

Human Microbiome

Identification of universal gut microbial biomarkers of common human intestinal diseases by meta-analysis – Leonardo Mancabelli – FEMS Microbiology Ecology

Salivary proteins and microbiota as biomarkers for early childhood caries risk assessment – Abdullah S Hemadi – International Journal of Oral Science (Open Article)

Pancreatic cyst fluid harbors a unique microbiome – Shan Li – Microbiome (Open Article)

Minireview: Microbial Therapeutics Designed for Infant Health – Claire Watkins – Frontiers in Nutrition (Open Article)

Exclusive Enteral Nutrition Induces Remission in Pediatric Crohn’s Disease via Modulation of the Gut Microbiota – Dawei Gong – BioMed Research International

Review: Clostridium difficile infection in the elderly: an update on management – Tomefa E Asempa – Clinical Interventions in Aging

Healthy donor faecal transplant for corticosteroid non-responsive severe alcoholic hepatitis – Cyriac Abby Philips – BMJ Case Reports

The gut mycobiome composition is linked to carotid atherosclerosis – M.R. Chacón –  Beneficial Microbes  

Review: T Cell-Mediated Chronic Inflammatory Diseases Are Candidates for Therapeutic Tolerance Induction with Heat Shock Proteins – Ariana Barbera Betancourt – Frontiers in Immunology (Open Article)

Review: Recipe for IBD: can we use food to control inflammatory bowel disease? – Mario Witkowski – Seminars in Immunopathology (Open Article)

Measuring the impact of olive pomace enriched biscuits on the gut microbiota and its metabolic activity in mildly hypercholesterolaemic subjects – Lorenza Conterno  – European Journal of Nutrition (Open Article)

 

Animal Microbiome

New evidence showing that the destruction of gut bacteria by antibiotic treatment could increase the honey bee’s vulnerability to Nosema infection – Jiang Hong Li – PLoS ONE (Open Article)

Review: Mouse models for human intestinal microbiota research: a critical evaluation – Floor Hugenholtz – Cellular and Molecular Life Sciences (Open Article)

Characterization of the gut microbiota in early life stages of pikeperch Sander lucioperca – T. Dulski – Journal of Fish Biology

A High Grain Diet Dynamically Shifted the Composition of Mucosa-Associated Microbiota and Induced Mucosal Injuries in the Colon of Sheep – Yue Wang – Frontiers in Microbiology (Open Article)

Alteration of Gut Microbiota and Inflammatory Cytokine/Chemokine Profiles in 5-Fluorouracil Induced Intestinal Mucositis – Hong-Li Li – Frontiers in Cellular and Infection Microbiology (Open Article)

Captive bottlenose dolphins and killer whales harbor a species-specific skin microbiota that varies among individuals – M. Chiarello – Scientific Reports (Open Article)

Mitochondrial gene polymorphism is associated with gut microbial communities in mice – Misa Hirose – Scientific Reports (Open Article)

 

Environmental Microbiomes

Parallelized, aerobic, single carbon-source enrichments from different natural environments contain divergent microbial communities – Theodore M. Flynn – Frontiers in Microbiology (Provisionally accepted article, full text available soon)

Taxonomic and functional differences between microbial communities in Qinghai Lake and its input streams – ze ren – Frontiers in Microbiology (Provisionally accepted article, full text available soon)

 

Bioinformatics

HOMINID: A framework for identifying associations between host genetic variation and microbiome composition – Joshua Lynch – GigaScience (Open Article)

 

Air Microbiome

Microbiota of the ground air layers in natural and industrial zones of the Kola Arctic – Maria V. Korneykova – Journal of Environmental Science and Health, Part A

 

Beneficial Microbes

Whole-Genome Sequencing of Lactobacillus Species from Two Commercial Probiotic Products – Anna Colavecchio – Genome Announcements (Open Article)

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November 6, 2017

Today we have an interesting digest with several articles about human microbiome. Additionally, today we also remark part of the recently release book “Understanding the Gut-Bone Signaling Axis”, with interesting chapters treating the connections between microbiota and bone health.

(Each file with an asterisk in the start contains open access to fulltext)

 

Human Microbiome

Bone Mechanical Function and the Gut Microbiota – C. J. Hernandez – Understanding the Gut-Bone Signaling Axis (SpringerLink)

Prebiotics and Bone – Corrie M. Whisner – Understanding the Gut-Bone Signaling Axis (SpringerLink)

Inflammatory Bowel Disease: Effects on Bone and Mechanisms – Francisco A. Sylvester – Understanding the Gut-Bone Signaling Axis (SpringerLink)

Immunology of Gut-Bone Signaling – Fraser L. Collins –  Understanding the Gut-Bone Signaling Axis (SpringerLink)

Gut Microbiota and Bone Health – Darin Quach – Understanding the Gut-Bone Signaling Axis (SpringerLink)

Increased stool immunoglobulin A level in children with autism spectrum disorders – Jiaxiu Zhou – Research in Developmental Disabilities (ScienceDirect)

Gut Microbiota and Cancer Patients: A Broad-Ranging Relationship – Giovanni Cammarota – Mayo Clinic Proceedings

* Less Invasive Screening for Colorectal Cancer by Microbiota Analysis: Is it a Reality or an Illusion? – Hisashi Onodera – EBIoMedicine

Safety and Efficacy of Fecal Microbiota Transplant for Recurrent Clostridium difficile Infection in Patients With Cancer Treated With Cytotoxic Chemotherapy: A Single-Institution Retrospective Case Series – Mehrdad Hefazi – Mayo Clinic Proceedings

Gastric microbial community profiling reveals a dysbiotic cancer-associated microbiota – Rui M Ferreira – Gut (BMJ)

Gut microbiota and hypertension: From pathogenesis to new therapeutic strategies – Yongbo Kang – Clinics and Research in Hepatology and Gastroenterology (ScienceDirect)

Associations Between Microbiota, Mitochondrial Function, and Cognition in Chronic Marijuana Users – Jun Panee – Journal of Neuroimmune Pharmacology

Genetic mannose binding lectin deficiency is associated with airway microbiota diversity and reduced exacerbation frequency in COPD – Alison J Dicker – Thorax (BMJ)

Molecular characterization of Multidrug Resistant Bacteroides isolates from Hungarian clinical samples – Károly Péter Sárvária – Journal of Global Antimicrobial Resistance (ScienceDirect)

* Commentary: Human Intestinal Microbiota and Colorectal Cancer: Moving Beyond Associative Studies – Christian Jobin – Gastroenterology

Faecal microbiota transplantation versus placebo for moderate-to-severe irritable bowel syndrome: a double-blind, randomised, placebo-controlled, parallel-group, single-centre trial – Peter Holger Johnsen – The Lancet Gastroenterology & Hepatology

Estrogens and Female Liver Health – Karen L. Chena – Steroids (ScienceDirect)

 

Beneficial microbes

(Provisionally accepted, Full text available soon) Probiotic Bacteria Alter Pattern-Recognition Receptor Expression and Cytokine Profile in a Human Macrophage Model Challenged with Candida albicans and Lipopolysaccharide – Victor H. Matsubara – Frontiers in Microbiology

* Butyrate and propionate inhibit antigen-specific CD8+ T cell activation by suppressing IL-12 production by antigen-presenting cells – Claudia Nastasi – Scientific Reports (NPG)

 

Animal Microbiome

(Provisionally accepted, Full text available soon) The Gut Entomotype of Red Palm Weevil Rhynchophorus ferrugineus Olivier (Coleoptera: Dryophthoridae) and Their Effect on Host Nutrition Metabolism – Abrar Muhammad – Frontiers in Microbiology

Porcine small and large intestinal microbiota rapidly hydrolyze the masked mycotoxin deoxynivalenol-3-glucoside and release deoxynivalenol in spiked batch cultures in vitro – Silvia W. Gratz – Applied and Environmental Microbiology (ASM)

A stable core gut microbiota across fresh- to saltwater transition for farmed Atlantic salmon – Knut Rudi – Applied and Environmental Microbiology (ASM)

Fecal microbiota transplant from highly feed efficient donors shows little effects on age-related changes in feed efficiency-associated fecal microbiota in chickens – Sina-Catherine Siegerstetter – Applied and Environmental Microbiology (ASM)

Short communication: The effect of heat treatment of bovine colostrum on the concentration of oligosaccharides in colostrum and in the intestine of neonatal male Holstein calves – Amanda J. Fischer – Journal of Dairy Science

* Progressive Colonization of Bacteria and Degradation of Rice Straw in the Rumen by Illumina Sequencing – Yanfen Cheng – Frontiers in Microbiology

* Neuroprotective effect of Ruminococcus albus on oxidatively stressed SH-SY5Y cells and animals – Jieun Park – Scientific Reports (NPG)

* Gut dysbiosis and impairment of immune system homeostasis in perinatally-exposed mice to Bisphenol A precede obese phenotype development – Yann Malaisé – Scientific Reports (NPG)

Impact of Enteric Health and Mucosal Permeability on Skeletal Health and Lameness in Poultry – L. R. Bielke – Understanding the Gut-Bone Signaling Axis (SpringerLink)

Gut Microbiota Are Disease-Modifying Factors After Traumatic Spinal Cord Injury – Kristina A. Kigerl – Neurotherapeutics (SpringerLink)

 

Food Microbes

(Provisionally accepted, Full text available soon) Extractive Fermentation of Lactic Acid in Lactic Acid Bacteria Cultivation: A Review – Majdiah Othman – Frontiers in Microbiology

* Diversity within Italian Cheesemaking Brine-Associated Bacterial Communities Evidenced by Massive Parallel 16S rRNA Gene Tag Sequencing – Marilena Marino – Frontiers in Microbiology

The main spoilage-related psychrotrophic bacteria in refrigerated raw milk – J.C. Ribeiro Júnior – Journal of Dairy Science

* Preprint: Kombucha as a model system for multispecies microbial cooperation: theoretical promise, methodological challenges and new solutions ‘in solution’ – Alexander Niall May – BioRxiv

* New microbial resource: microbial diversity, function and dynamics in Chinese liquor starter – Yuhong Huang – Scientific Reports (NPG)

 

Environmental Microbes

(Provisionally accepted, Full text available soon) Illumina-Based Analysis of Endophytic and Rhizosphere Bacterial Diversity of the Coastal Halophyte Messerschmidia sibirica – Xueying Tian – Frontiers in Microbiology

Perturbation of seafloor bacterial community structure by drilling waste discharge – Tan T. Nguyen – Marine Pollution Bulletin

September 13,2017

Our midweek digest is a treat for wine drinkers- two studies looking at vineyard microbiomes and news of how Nestlé is moving into microbiome research. Lastly, read about an exciting workflow that makes it easier to map the resistome.

General Microbiome

Microbial communities in placentas from term normal pregnancy exhibit spatially variable profiles.

Parnell LA .Scientific Reports

Human gut microbiome

Host-microbe interaction in the gastrointestinal tract.

Parker A.Environmental Microbiology Report

Gut microbiota composition is associated with polypharmacy in elderly hospitalized patients.

Ticinesi A.Scientific Reports

Microbes in Infant Gut Development: Placing Abundance Within Environmental, Clinical and Growth Parameters.

Obermajer T.Scientific Reports

Animal experiments and microbiome

Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models.

Cekanaviciute E, PNAS

The microbiota influences cell death and microglial colonization in the perinatal mouse brain.

Castillo-Ruiz A. Brain, Behaviour, and Immunity

Microbial colonization is required for normal neurobehavioral development in zebrafish.

Phelps D,.Scientific Reports

Biotechnology 

Ozone-cathode microbial desalination cell; An innovative option to bioelectricity generation and water desalination.

Gholizadeh A. Chemosphere.

Plant and soil microbiome

Grape microbiome as a reliable and persistent signature of field origin and environmental conditions in Cannonau wine production.

Mezzasalma V. PLoS One.

Is microbial terroir related to geographic distance between vineyards?

Miura T. Environmental Microbiology Reports

Bacteria utilising plant-derived carbon in the rhizosphere of Triticum aestivum change in different depths of an arable soil.

Uksa M. Environmental Microbiology Reports

Mining the Volatilomes of Plant-Associated Microbiota for New Biocontrol Solutions.

Bailly A. Frontiers in Microbiology

More than 2500 years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis.

Michas A. Microbiome

Lung Microbiome

Functional characterization of the Mycobacterium abscessus genome coupled with condition specific transcriptomics reveals conserved molecular strategies for host adaptation and persistence.

Miranda-CasoLuengo AA.BMC Genomics

Mechanistic insight into the function of the microbiome in lung diseases.

Ubags NDJ. European Respiratory Journal

Antibiotics

A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity.

Ruiz VE.Nature Communications

Resistome

The recent emergence in hospitals of multidrug-resistant community-associated sequence type 1 and spa type t127 methicillin-resistant Staphylococcus aureus investigated by whole-genome sequencing: Implications for screening.

Earls MR. PLoS One

Rapid resistome mapping using nanopore sequencing.

van der Helm E.Nucleic Acids Research  

Network of microbial and antibiotic interactions drive colonization and infection with multidrug-resistant organisms

Wang J. PNAS

News

Nestlé moves into gut microbiome tests.

News- Nature Biotechnology

Protocol

Shotgun metagenomics, from sampling to analysis.

Quince C,Nature Biotechnology

Erratum 

Erratum to: Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey Species.

Hale VL. Microbial Ecology

August 18, 2017

Human Microbiome: Gut

Worse inflammatory profile in omnivores than in vegetarians associates with the gut microbiota composition – Ana Carolina Franco-de-Moraes – Diabetology & Metabolic Syndrome (BMC)

News and views: Spondyloarthropathies: Ruminococcus on the horizon in arthritic disease – Lars Vereecke & Dirk Elewaut – Nature Reviews Rheumatology

Increased human intestinal barrier permeability plasma biomarkers zonulin and FABP2 correlated with plasma LPS and altered gut microbiome in anxiety or depression – Bruce R Stevens – Gut (BMJ)

 

Human Microbiome: Respiratory tract

Strain level Streptococcus colonization patterns during the first year of life – Meredith Wright – Frontiers in Microbiology

State of the art: The airway microbiota in early cystic fibrosis lung disease – Katherine B. Frayman – Pediatric Pulmonology (Wiley)

 

Human Microbiome: Mouth

The saliva microbiome profiles are minimally affected by collection method or DNA extraction protocols – Yenkai Lim – Scientific Reports

 

Built microbiome

Bacterial diversity among four healthcare-associated institutes in Taiwan – Chang-Hua Chen – Scientific Reports

 

Animal Microbiome

Host Ecology Rather Than Host Phylogeny Drives Amphibian Skin Microbial Community Structure in the Biodiversity Hotspot of Madagascar – Molly C. Bletz – Frontiers in Microbiology

Microbiota in the coelomic fluid of two common coastal starfish species and characterization of an abundant Helicobacter-related taxon – Satoshi Nakagawa – Scientific Reports

Stability in metabolic phenotypes and inferred metagenome profiles before the onset of colitis-induced inflammation – M. Glymenaki – Scientific Reports

Microbiome-mediated neutrophil recruitment via CXCR2 and protection from amebic colitis – Koji Watanabe – PLoS Pathogens

Gut microbiota of a long-distance migrant demonstrates resistance against environmental microbe incursions – Alice Risely – Molecular Ecology (Wiley)

Unraveling the Fecal Microbiota and Metagenomic Functional Capacity Associated with Feed Efficiency in Pigs – Hui Yang –  Frontiers in Microbiology

Research Highlight: Tell me who you are and I’ll tell you what you eat – Irene Vacca – Nature Reviews Microbiology

Mucus organisation is shaped by colonic content; a new view – J. B. J. Kamphuis – Scientific Reports

Effect of barley supplementation on the fecal microbiota, caecal biochemistry, and key biomarkers of obesity and inflammation in obese db/db mice – Jose F. Garcia-Mazcorro – European Journal of Nutrition

Associations Between Nutrition, Gut Microbiome, and Health in A Novel Nonhuman Primate Model – Jonathan B. Clayton – BioRxiv

Milk microbiome and bacterial load following dry cow therapy without antibiotics in dairy cows with healthy mammary gland – Erika C. R. Bonsaglia –  Scientific Reports

Space-type radiation induces multimodal responses in the mouse gut microbiome and metabolome – David Casero – Microbiome (BMC)

 

Probiotics, Prebiotics and Synbiotics

Secretome of intestinal bacilli: a natural guard against pathologies – Olga N. Ilinskaya – Frontiers in Microbiology

The Probiotic Combination of Bifidobacterium longum subsp. infantis CECT 7210 and Bifidobacterium animalis subsp. lactis BPL6 Reduces Pathogen Loads and Improves Gut Health of Weaned Piglets Orally Challenged with Salmonella Typhimurium – Emili Barba-Vidal –  Frontiers in Microbiology

Bifidobacterium pseudocatenulatum LI09 and Bifidobacterium catenulatum LI10 attenuate D-galactosamine-induced liver injury by modifying the gut microbiota – Daiqiong Fang – Scientific Reports

Administration of two probiotic strains during early childhood does not affect the endogenous gut microbiota composition despite probiotic proliferation – Martin Frederik Laursen – BMC Microbiology

A randomized synbiotic trial to prevent sepsis among infants in rural India – Pinaki Panigrahi – Nature

 

Pathogen Research

High-Resolution Microbiome Profiling for Detection and Tracking of Salmonella enterica – Christopher J. Grim – Frontiers in Microbiology

In situ architecture, function, and evolution of a contractile injection system – Désirée Böck – Science

 

Bioactive compounds

Onion Peel Ethylacetate Fraction and Its Derived Constituent Quercetin 4`-O-Β-D Glucopyranoside Attenuates Quorum Sensing Regulated Virulence and Biofilm Formation – Hanan AlYousef – Frontiers in Microbiology

Promysalin is a salicylate-containing antimicrobial with a cell-membrane-disrupting mechanism of action on Gram-positive bacteria – Rahul D. Kaduskar – Scientific Reports

 

Bacteriophages

Selection of Functional Quorum Sensing Systems by Lysogenic Bacteriophages in Pseudomonas aeruginosa  – Miguel-Angel Saucedo-Mora – Frontiers in Microbiology

Characterization and formulation into solid dosage forms of a novel bacteriophage lytic against Klebsiella oxytoca – Teagan L. Brown – PLoS ONE

 

Soil and Environmental Microbiology

Distinct Seasonal Patterns of Bacterioplankton Abundance and Dominance of Phyla α-Proteobacteria and Cyanobacteria in Qinhuangdao Coastal Waters Off the Bohai Sea – Yaodong He – Frontiers in Microbiology

The Rhizosphere Bacterial Microbiota of Vitis vinifera cv. Pinot Noir in an Integrated Pest Management Vineyard – Giorgia Novello – Frontiers in Microbiology

Perspective: How microbes survive in the open ocean – Jonathan P. Zehr – Science

Ecophysiology of freshwater Verrucomicrobia inferred from metagenome-assembled genomes – Shaomei He – BioRxiv

Impact of litter quantity on the soil bacteria community during the decomposition of Quercus wutaishanica litter – Quanchao Zeng – PeerJ preprints

Microbial phylogeny determines transcriptional response of resistome to dynamic composting processes – Cheng Wang – Microbiome (BMC)

 

Bioinformatics and Genomics

Abundance-based reconstitution of microbial pan-genomes from whole-metagenome shotgun sequencing data – Florian Plaza Oñate – BioRxiv

Evaluation of the impact of Illumina error correction tools on de novo genome assembly – Mahdi Heydari –  BMC Bioinformatics

 

Non-microbiology picks

A pathology atlas of the human cancer transcriptome – Mathias Uhlen – Science

Increasing Symptoms in Irritable Bowel Symptoms With Ingestion of Galacto-Oligosaccharides Are Mitigated by α-Galactosidase Treatment – C J Tuck – The American Journal of Gastroenterology

Lessons from between the white lines for isolated data scientists – Benjamin S Baumer ​- PeerJ preprints

 

August 9, 2017

Events and jobs

ASM Journals Fellowship – American Society for Microbiology

General microbiome

A mechanistic Individual-based Model of microbial communities – Pahala Gedara Jayathilake – PLoS ONE

Human vaginal microbiome

Group B Streptococcus and the vaginal microbiota – Geoffrey H Rosen – The Journal of Infectious Diseases

Animal experiments

The microbial metabolite desaminotyrosine protects from influenza through type I interferon – Ashley L. Steed – Science

Development of Inflammatory Bowel Disease is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice – Thomas Sharpton – bioRxiv

Plant, root, and soil microbiome

Microbial Communities as Ecological Indicators of Ecosystem Recovery Following Chemical Pollution – Stéphane Pesce – Microbial Ecotoxicology

Assessment of rhizosphere processes for removing water-borne macrolide antibiotics in constructed wetlands – Yiping Tai – Plant and Soil

Poor-Soil Rhizosphere Enriched with Different Microbial Activities Influence the Availability of Base Elements – Faten Dhaw – Open Journal of Ecology

Water and extremophile microbiome

Impacts of leachates from livestock carcass burial and manure heap sites on groundwater geochemistry and microbial community structure – Man Jae Kwon – PLoS ONE

Built environment

Lignocellulose-Degrading Microbial Communities in Landfill Sites Represent a Repository of Unexplored Biomass-Degrading Diversity – Emma Ransom-Jones – mSphere

Probiotics / prebiotics

Utilization of Pyrosequencing to Monitor the Microbiome Dynamics of Probiotic Treated Poultry (Gallus gallus domesticus) during Downstream Poultry Processing – Vamsy Priya Guttala – Agricultural Sciences

Lactobacillus casei CCFM419 attenuates type 2 diabetes via a gut microbiota dependent mechanism – Gang Wang – Food & Function

Bioinformatics

Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information – Albert Barberán – mSphere

Techniques

Isolation of bacteriophages from air using vacuum filtration technique: An improved and novel method – Bhagyashree Magare – Journal of Applied Microbiology

Microbes in the news

Exploring the Equine Microbiome – Stacey Oke – The Horse

Study: Kitchen sponges carry more bacteria than a toilet – Darren Sweeney – Fox8 Cleveland

August 2, 2017

Enjoy your new  Microbiome Digest with some hot news on this very hot day. Methane- eating microbes found in lake deep beneath Antarctic ice sheet, while some some unexpected life was also found at the bottom of high Arctic Lakes.

 

Human respiratory microbiome
Distal airway microbiome is associated with immunoregulatory myeloid cell responses in lung transplant recipients – Nirmal S. Sharma – The Journal of Heart and Lung Transplatation
Human oral microbiome

 
The oral microbiota in patients with pancreatic cancer, patients with IPMNs, and controls: a pilot study – Sara H. Olson – Cancer Causes & Control

 
Metabolic Fingerprints from the Human Oral Microbiome Reveal a Vast Knowledge Gap of Secreted Small Peptidic Molecules – Anna Edlund –  mSystems
Prevalence of periodontal pathogens among italian patients with chronic periodontitis: a retrospective study on 2992 patients – L. Tettamanti- Oral & Implantology

 

 

Human gut microbiome

 
Metabolites and microbial composition of stool of women with fecal incontinence: Study design and methods – Lily A. Arya – Neurology Urodynamics

 
Microscopic Colitis After Fecal Microbiota Transplant – Matthew J. Fasullo – ACG Case Reports Journal
Alteration in the gastric microbiota and its restoration by probiotics in patients with functional dyspepsia – Muneki Igarashi  – BMJ Open Gastroenterology

 
Aggravation of collagen-induced arthritis by orally administered Porphyromonas gingivalis through modulation of the gut microbiota and gut immune system – Keisuke Sato – Scientific Reports

 
The gut microbiota, a new cardiovascular risk factor? – Caroline Chong-Nguyen – La Presse Médicale

 
The Association between Cardiorespiratory Fitness and Gut Microbiota Composition in Premenopausal Women – Yifan Yang – Nutrients

 
Gut microbiota metabolites for sweetening type I diabetes – Thamer Aljtaily – Cellular & Molecular Immunology

 
Vasopressin deletion is associated with sex-specific shifts in the gut microbiome – Christopher T. Fields – Gut Microbes

 
Stable engraftment of human microbiota into mice with a single oral gavage following antibiotic conditioning –  Christopher Staley – Microbiome

 
Animal microbiome 

 
Temporal dynamics of in-situ fiber-adherent bacterial community under ruminal acidotic conditions determined by 16S rRNA gene profiling – Renee M. Petri – PLOS One

 
Plant, root, and soil microbiome

 
Activity, biomass and composition of microbial communities and their degradation pathways in exposed propazine soil – C. Jiang  – Ecotoxicology and Environmental Safety

 
Response of microbial community and catabolic genes to simulated petroleum hydrocarbon spills in soils/sediments from different geographic locations– Qinglong Liu – Journal of Applied Microbiology

 
Primary productivity as a control over soil microbial diversity along environmental gradients in a polar desert ecosystem – Kevin M. Geyer – PeerJ

 
Steering Soil Microbiomes to Suppress Aboveground Insect Pests – Ana Pineda –  Trends in Plant Science

 
Importance of exposure dynamics of metal-based nano-ZnO, -Cu and -Pb governing the metabolic potential of soil bacterial communities  – Yujia Zhai – Ecotoxicology and Environmental Safety

 
Water and extremophile microbiome 

 
Production and degradation of fluorescent dissolved organic matter derived from bacteria –  Ken Arai – Journal of Oceanography

 
Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition – Adriana Alberti – Scientific Data
Watershed Urbanization Linked to Differences in Stream Bacterial Community Composition – Jacob D. Hosen – Frontiers in Microbiology

 
Influence of Igneous Basement on Deep Sediment Microbial Diversity on the Eastern Juan de Fuca Ridge Flank – Jessica M. Labonté – Frontiers in Microbiology

 
Coordinated regulation of growth, activity and transcription in natural populations of the unicellular nitrogen-fixing cyanobacterium Crocosphaera – Samuel T. Wilson – Nature Microbiology

 
The global biogeography of amino acid variants within a single SAR11 population is governed by natural selection – Tom O. Delmont – bioRxiv

 

Food microbiology

 
Microorganisms in Fermented Apple Beverages: Current Knowledge and Future Directions – Fabien J. Cousin – Microorganisms

 
Probiotics / prebiotics

 
Next-generation probiotics targeting Clostridium difficile through precursor-directed antimicrobial biosynthesis – Jennifer K. Spinler – Infection and Immunity

 
Biotechnology
Forum: Genetically Engineered Bacteria for Treating Human Disease – Buyun Ma – Trends in Pharmacological Sciences

 

Microbes in news

 

Methane-eating microbes found beneath Antarctica’s melting ice sheets

Unexpected Life Found at the Bottom of High Arctic Lakes

Tracking microbial succession in petroleum wells

July 16, 2017

Events and jobs
Postdoctoral Fellow – Astrobiology – University of Florida

Microbiology Laboratory Manager – Cranleigh Scientific, Northamptonshire, England

Human respiratory microbiome
Review: Microbiome in chronic obstructive pulmonary disease – Eduard Monso – Annals of Translational Medicine

Monitoring clinical and microbiological evolution of a cystic fibrosis patient over 26 years: experience of a Brazilian CF Centre – Cassiana da Costa Ferreira Leite – BMC Pulmonary Medicine

Distal airway microbiome is associated with immunoregulatory myeloid cell responses in lung transplant recipients – Nirmal S. Sharma – The Journal of Heart and Lung Transplantation

Human oral microbiome
Diabetes Enhances IL-17 Expression and Alters the Oral Microbiome to Increase Its Pathogenicity – E. Xiao – Cell Host and Microbe

Microbiome of peri-implantitis affected and healthy dental sites in patients with a history of chronic periodontitis – Danae Apatzidou – Archives of Oral Biology

Human gut microbiome
Review: Gut–CNS-Axis as Possibility to Modulate Inflammatory Disease Activity—Implications for Multiple Sclerosis – Ann-Katrin Fleck – International Journal of Molecular Sciences

Determination of certain bacterial groups in gut microbiota and endotoxin levels in patients with nonalcoholic steatohepatitis – Ceren Özkul – The Turkish Journal of Gastroenterology

Animal experiments
Meat and bone meal as partial replacement of fishmeal in diets for gilthead sea bream (Sparus aurata) juveniles: Diets digestibility, digestive function, and microbiota modulation – Sara Moutinho – Aquaculture

Arachidonic acid sex-dependently affects obesity through linking gut microbiota-driven inflammation to hypothalamus-adipose-liver axis – Pan Zhuang – Biochimica et Biophysica Acta (BBA) – Molecular Basis of Disease

Disparity in the nasopharyngeal microbiota between healthy cattle on feed, at entry processing and with respiratory disease – Mohamed Zeineldin – Veterinary Microbiology

Animal microbiome
Effects of chromium(III) on enzyme activities and bacterial communities during swine manure composting – Yanan Yin – Bioresource Technology

Antimicrobial Activity of Actinobacteria Isolated From the Guts of Subterranean Termites – R. A. Arango – Environmental Entomology

Oral Disease and Microbiota in Free-roaming cats – Ana Whyte – Topics in Companion Animal Medicine

Plant, root, and soil microbiome
Investigating the durable effect of the hot water treatment used in nurseries on pathogenic fungi inhabiting grapevine wood and involved in Grapevine Trunk Diseases – Emilie Bruez – Crop Protection

Understanding the mycobiota of maize from the highlands of Guatemala, and implications for maize quality and safety – José Rodrigo Mendoza – Crop Protection

The uniqueness and biogeochemical cycling of plant root microbial communities in a floating treatment wetland – Hidetoshi Urakawa – Ecological Engineering

Water and extremophile microbiome
The Other Microeukaryotes of the Coral Reef Microbiome – T.D. Ainsworth – Trends in Microbiology

Taxonomic and functional diversity of a coastal planktonic bacterial community in a river-influenced marine area – Stefan Thiele – Marine Genomics

Built environment
Stimulation effect of electric current density (ECD) on microbial community of a three dimensional particle electrode coupled with biological aerated filter reactor (TDE-BAF) – Yan Feng – BioResource Technology

Food microbiology
Review: Bacteriocin-Antimicrobial Synergy: A Medical and Food Perspective – Harsh Mathur – Frontiers in Microbiology

Review: Low FODMAP Diet in the Treatment of Irritable Bowel Syndrome: A Systematic Review and Meta-Analysis – Dania Schumann – Nutrition

Macrophages treated with non-digestible polysaccharides reveal a transcriptionally unique phenotype – Yongfu Tang – Journal of Functional Foods

Microbial Ecology
Interplay between antibiotic efficacy and drug-induced lysis underlie enhanced biofilm formation at subinhibitory drug concentrations – Wen Yu – bioRxiv

A phylogenetic and evolutionary analysis of antimycin biosynthesis – Rebecca Joynt – bioRxiv

Probiotics / prebiotics
Review: Prenatal and postnatal administration of prebiotics and probiotics – Kristin Sohn – Seminars in Fetal and Neonatal Medicine

Techniques
Phototrophic microorganisms in the symbiotic communities of Baikal sponges: Diversity of psbA gene (encoding D1 protein of photosystem II) sequences – OV Kaluzhnaya – Mol Biol (Mosk)
Unfortunately, this article is in Russian and I cannot access the original. The abstract was interesting though, the goal of the study is to determine whether psbA sequences can be used as a marker for phototrophic organisms.

New sequences
Noncontiguous finished genome sequences and description of Bacillus massiliglaciei, Bacillus mediterraneensis, Bacillus massilinigeriensis, Bacillus phocaeensis and Bacillus tuaregi, five new species identified by culturomics – F. Cadoret – New Microbes and New Infections

Whole-Genome Sequences of Influenza A(H1N1)pdm09 Virus Isolates from Kerala, India – Sara Jones – Genome Announcements

Phoenicibacter massiliensis‘ gen. nov., sp. nov., a new bacterium isolated from the human gut of a pygmy woman – M. Bilen – New Microbes and New Infections

Phenotypic and genomic comparison of Mycobacterium aurum and surrogate model species to Mycobacterium tuberculosis: implications for drug discovery – Amine Namouchi – BMC Genomics

Microbes in the news 
** Mini-Metagenomics Leads to Microbial Discovery – Abby Olena – The Scientist
Refers to Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples – Feiqiao Brian Yu – ELife **

APC Microbiome Institute appoints Spinning Clock to Mind Your Microbes brief – Andy Black – The Drum
An app for kids to learn about the microbiome!

Microbial diversity: ‘key benchmark in the coming Third Wave cosmetic revolution’ – Lucy Whitehouse – Cosmetics Design

Novel bacterial physiology identified in the creation of biofilms – Science Daily

Physicists Just Found a Way to Spin Teeny Tiny Robot Motors With Bacteria – Gemma Conroy – Science Alert

New bacteria being developed for cheese may save industry $10m a year, researchers say – Melanie Vujkovic – ABC

Bacteria-infected mosquitoes are coming to Fresno – but it’s a good thing! – Bryant-Jon Anteola – Fresno Bee

BYU student overcomes flesh-eating bacteria to compete on ‘American Ninja Warrior’ – Braley Dodson – Daily Herald

Bacteria Actively Drive Development of Colorectal Cancer – Newswise
Looking at Streptococcus gallolyticus and its ability to promote colorectal cancer in cell culture, animal models, and human tissue.

Bacteria Hysteria
How surgeons can stop the spread of germs by operating NAKED instead of wearing surgical gowns – Colin Fernandez – Daily Mail