Category Archives: Human gut

January 6, 2018

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Today’s digest features a lot of great “gut microbiome papers”, with a focus on precision medicine.

Events and jobs
Scientist, Computational Biology – Flagship Pioneering, VL45  Company LocationCambridge, Massachusetts

Human gut microbiome
** Microbiota Accessible Carbohydrates Facilitate Clearance of Clostridium difficile – Andrew J Hryckowian – bioRxiv **

** Precision medicine using microbiota – Christian Jobin – Science
Highlights three articles, including:
* The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients – Vyara Matson – Science
* Gut microbiome influences efficacy of PD-1–based immunotherapy against epithelial tumors – Bertrand Routy – Science
* Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients – V. Gopalakrishnan – Science **

Exploring Gut Microbiota Composition as an Indicator of Clinical Response to Dietary FODMAP Restriction in Patients with Irritable Bowel Syndrome – Jørgen Valeur – Digestive Diseases And Sciences

Mucus Microbiome of Anastomotic Tissue During Surgery Has Predictive Value for Colorectal Anastomotic Leakage – Jasper B van Praagh – Annals Of Surgery

Review: Local Acetaldehyde-An Essential Role in Alcohol-Related Upper Gastrointestinal Tract Carcinogenesis – Mikko T Nieminen – Cancers

Review: The Gut-Brain Axis and the Microbiome: Clues to Pathophysiology and Opportunities for Novel Management Strategies in Irritable Bowel Syndrome (IBS). – Eamonn M M Quigley – Journal Of Clinical Medicine

Animal experiments
** Precision editing of the gut microbiota ameliorates colitis – Wenhan Zhu – Nature **

Polystyrene microplastics induce microbiota dysbiosis and inflammation in the gut of adult zebrafish – Yuanxiang Jin – Environmental Pollution

Profiling the lymphoid-resident T cell pool reveals modulation by age and microbiota – Aurélie Durand – Nature Communications

Cultivable anaerobic and aerobic bacterial communities in the fermentation chambers of Holotrichia parallela (coleoptera: scarabaeidae) larvae – Zhen-Yu Zhang – Plos One

The effect of DNA degradation bias in passive sampling devices on metabarcoding studies of arthropod communities and their associated microbiota – Henrik Krehenwinkel – Plos One

The evaluation of the quality of Feng Huang Oolong teas and their modulatory effect on intestinal microbiota of high-fat diet-induced obesity mice model – Yuhui Chen – International Journal Of Food Sciences And Nutrition

Animal microbiome
Host contributes to longitudinal diversity of fecal microbiota in swine selected for lean growth – Duc Lu – Microbiome

Review: Recent insights into the tick microbiome gained through next-generation sequencing – Telleasha L Greay – Parasites & Vectors

Plant, root, and soil microbiome
Responses of soil bacterial community after seventh yearly applications of composted tannery sludge – Ana Roberta Lima Miranda – Geoderma

Assessment of Cu applications in two contrasting soils—effects on soil microbial activity and the fungal community structure – Katharina M. Keiblinger – Ecotoxicology

Microorganisms reveal what plants do not: wheat growth and rhizosphere microbial communities after Azospirillum brasilense inoculation and nitrogen fertilization under field conditions – Luciana P. Di Salvo – Plant and Soil

16S rRNA analysis of diversity of manure microbial community in dairy farm environment – Pramod Pandey – Plos One

Agricultural constraints on microbial resource use and niche breadth in drainage ditches – Ellard R Hunting – Peerj

Water and extremophile microbiome
Accessing chemical diversity from the uncultivated symbionts of small marine animals – Thomas E Smith – Nature Chemical Biology

Macroalgal-bacterial interactions: Role of dimethylsulfoniopropionate in microbial gardening by Ulva (Chlorophyta) – Ralf W. Kessler – Molecular Ecology

Bacterial Recycling of Archaeal Biomass as a New Strategy for Extreme Life in the Dead Sea Deep Sediment – Camille Thomas – EarthArXiv

Unravelling the identity, metabolic potential, and global biogeography of the atmospheric methane-oxidising Upland Soil Cluster α – Jennifer Pratscher – Environmental Microbiology

Book: Optimization and Applicability of Bioprocesses – Hemant J. Purohit and other editors
Articles of interest include:
* Microbial CO2 Fixation Bioprocesses and Desert as Future Carbon Sink – Leena Agarwal
* Biofilm Microenvironments: Modeling Approach – Saheli Ghosh
* Visualization of Microorganisms in Bioprocesses – Tsuyoshi Yamaguchi

Built environment
The effect of temperature on airborne filamentous fungi in the indoor and outdoor space of a hospital – Fariba Abbasi – Environmental Science and Pollution Research

Probiotics / prebiotics / antibiotics
Cross-feeding modulates antibiotic tolerance in bacterial communities – Elizabeth M Adamowicz – bioRxiv

Review: Immune-Mediated Mechanisms of Action of Probiotics and Synbiotics in Treating Pediatric Intestinal Diseases – Julio Plaza-Díaz – Nutrients

Review: How Sweet Are Our Gut Beneficial Bacteria? A Focus on Protein Glycosylation in Lactobacillus. – Dimitrios Latousakis – International Journal Of Molecular Sciences

Phages and viruses
Review: Interactions between Enteric Bacteria and Eukaryotic Viruses Impact the Outcome of Infection – Angela K Berger – Viruses

Bioinformatics
Techniques
News Feature: Can microbes keep time for forensic investigators? – Carolyn Beans – PNAS

Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise – Taha Soliman – Peerj

Microbes in the news
Caltech breakthrough: Bacteria engineered with ‘sonar’ can track, fight disease – Eric Rosenbaum – CNBC

Microbes on the market
Can’t sleep? It could be your microbiome, says this Cambridge startup – Max Stendahl  – Boston Business Journal

Rebiotix and CoreBiome Collaborate on Evaluating Microbiomes of Patients Treated with Microbiota Restoration Therapy™ – Markets Insider

Seres Therapeutics Reports SER-287 Phase 1b Microbiome Analyses that Provide Mechanistic Support for Clinical Efficacy in Ulcerative Colitis – PipelineReview.com

January 5, 2018

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Today’s digest has an interesting commentary on the oral-gut connection and a brilliant piece on microbial diversity. Lastly, a look at how grapevines influence belowground diversity and networks

General Microbiome

A role for the endometrial microbiome in dysfunctional menstrual bleeding. Pelzer ES. Antonie Van Leeuwenhoek.

Performance and microbial community variations of anaerobic digesters under increasing tetracycline concentrations. Xiong Y. Applied Microbiology and Biotechnology

In Nature, There Is Only Diversity. McLaren MR. MBio.

Gut Microbiome

Commentary: Oral-gut connection: one step closer to an integrated view of the gastrointestinal tract? Lira-Junior R. Mucosal Immunology

Bile acids at the cross-roads of gut microbiome-host cardiometabolic interactions. Ryan PM. Diabeticology and Metabolic Syndrome

REVIEW: Diet, Microbiota, and Metabolic Health: Trade-Off Between Saccharolytic and Proteolytic Fermentation. Korpela K. Annual of Food Science and Technology

Nasal and Lung Microbiome

REVIEW: Fungi in Bronchiectasis: A Concise Review. Máiz L. Internatioanal Journal of Molecular Sciences

Alterations in the mucosa-associated fungal microbiota in patients with ulcerative colitis. Qiu X. Oncotarget

The association between anterior nares and nasopharyngeal microbiota in infants hospitalized for bronchiolitis. Luna PN. Microbiome

Fecal Microbiome

Editorial Comment: Fecal microbiota transplantation as a possible treatment of irritable bowel syndrome. Juncadella AC. Annals of Translational Medicine

Plant, Soil, and Water Microbiome

Co-variation between Distribution of Microbial Communities and Biological Metabolization of Organics in Urban Sewer Systems. Jin P. Environmental Science and Technology.

Do invasive plants structure microbial communities to accelerate decomposition in intermountain grasslands? McTee MR. Ecology and Evolution

Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality. Marasco R. Microbiome

Biodiversity of the microbial mat of the Garga hot spring. Rozanov AS. BMC Evolutionary Biology

Animal Experiments and Microbiome

Microbiota Reconstitution Does Not Cause Bone Loss in Germ-Free Mice. Quach D. mSphere

Physiological Translocation of Lactic Acid Bacteria during Pregnancy Contributes to the Composition of the Milk Microbiota in Mice. de Andrés J. Nutrients

Extreme sensitivity to ultraviolet light in the fungal pathogen causing white-nose syndrome of bats. Palmer JM. Nature Communication

OCCURRENCE OF PASTEURELLACEAE BACTERIA IN THE ORAL CAVITY OF SELECTED MARSUPIAL SPECIES. Hansen MJ. Journal of Zoo and Wildlife Medicine

Marine Microbiome

Agelas Wasting Syndrome Alters Prokaryotic Symbiont Communities of the Caribbean Brown Tube Sponge, Agelas tubulata.Deignan LK. Microbial Ecology

Environmental drivers of heterogeneity in the trophic-functional structure of protozoan communities during an annual cycle in a coastal ecosystem. Xu G. Marine Pollution Bulletin

Antibiotic Resitance

Editorial: Empiric antibiotic use in allogeneic hematopoietic cell transplantation: should we avoid anaerobe coverage? Shono Y. Blood Advances

Characterization of genetic determinants involved in antibiotic resistance in Aeromonas spp. and fecal coliforms isolated from different aquatic environments. Carnelli A. Research in Microbiology

 

 

January 4, 2017

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Implication of dysbiosis in arthritis in rats, studying soil crust biology and chemistry using metabolomics, a news article on exercise and the microbiome.

Human gut microbiome

Comprehensive analysis of polyamine transport and biosynthesis in the dominant human gut bacteria: Potential presence of novel polyamine metabolism and transport genes – Yuta Sugiyama – The International Journal of Biochemistry & Cell Biology

Animal experiments

Effects of HLA-B27 on Gut Microbiota in Experimental Spondyloarthritis Implicate an Ecological Model of Dysbiosis – Tejpal Gill – Arthritis & Rheumatology

Plant, root, and soil microbiome

Linking soil biology and chemistry in biological soil crust using isolate exometabolomics – Tami L Swenson – Nature Communications

Cooperative interactions between seed-borne bacterial and air-borne fungal pathogens on rice – Boknam Jung – Nature Communications

Synergistic action of rhizospheric fungi with Megathyrsus maximus root speeds up hydrocarbon degradation kinetics in oil polluted soil – Michael Dare Asemoloye – Chemosphere

Pre-print: Crop diversity increases disease suppressive capacity of soil microbiomes – Ariane L Peralta – bioRxiv

Microbes in the news

Exercise Alters Our Microbiome. Is That One Reason It’s So Good for Us? – Gretchen Reynolds – The New York Times

Bifidobacterium or fiber protect against deterioration of the inner colonic mucus layer – ScienceDaily

Scientists use sound to track tiny organisms in the body – Angela Chen – The Verge

Bacteria and Cancer: Another Connection – Derek Lowe – Science Translational Medicine

January 3, 2018

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Today we have a nice event /training in social science techniques organized by NERC in Manchester, Bristol and Edinburgh (UK), few microbiology jobs, an interesting review from Arun T. Nair in “Gut Microbiome”, quite a few papers about Synechococcus in “Water and extremophile microbiome”. Check as well “Microbes on market” where you can read about Google and Microsoft investing in medicine startup DNAnexus.

Events

Social science techniques for natural scientists training funded by NERC, UK

Jobs

Microbiologist – Kent, UK

Scientist/Sr.Scientist – Strain Development, CJM Talent Solutions, San Francisco, US

Associate/Assistant Professor : Miami, Florida, FL, US

General microbiome

Comparison of genomes and proteomes of four whole genome-sequenced Campylobacter jejuni from different phylogenetic backgrounds – Clifford G. Clark – PLOS

Phylogenetic inference of Coxiella burnetii by 16S rRNA gene sequencing – Heather P. McLaughlin -PLOS

The photosynthetic bacteria Rhodobacter capsulatus and Synechocystis sp. PCC 6803 as new hosts for cyclic plant triterpene biosynthesis – Anita Loeschcke -PLOS

Pregnancy and early life

Effect of innate antiviral glycoproteins in breast milk on seroconversion to rotavirus vaccine (Rotarix) in children in Lusaka, Zambia – Katayi Mwila-Kazimbaya – PLOS

Oral microbiome

Frequency and levels of candidate endodontic pathogens in acute apical abscesses as compared to asymptomatic apical periodontitis – Isabela N. Rôças – PLOS

Human vaginal microbiome

Combined oral and topical antimicrobial therapy for male partners of women with bacterial vaginosis: Acceptability, tolerability and impact on the genital microbiota of couples – A pilot study – Erica L. Plummer – PLOS

Candida albicans-derived mannoproteins activate NF-κB in reporter cells expressing TLR4, MD2 and CD14 – Traci Ness – PLOS

Replication-dependent size reduction precedes differentiation in Chlamydia trachomatis – Jennifer K. Lee – Nature Communications

Human gut microbiome

T6SS: The bacterial “fight club” in the host gut – Thibault G. Sana – PLOS Pathogens

Review: Gut Microbiota Dysfunction as Reliable Non-invasive Early Diagnostic Biomarkers in the Pathophysiology of Parkinson’s Disease: A Critical Review – Arun T Nair – Journal of Neurogastroenterology and Motility

Animal experiments

Effect of dietary xylooligosaccharides on intestinal characteristics, gut microbiota, cecal short-chain fatty acids, and plasma immune parameters of laying hens – X M Ding – Poultry Science

Influence of a diet enriched with virgin olive oil or butter on mouse gut microbiota and its correlation to physiological and biochemical parameters related to metabolic syndrome – Isabel Prieto – PLOS

Modulation of the diet and gastrointestinal microbiota normalizes systemic inflammation and β-cell chemokine expression associated with autoimmune diabetes susceptibility – Angela M. Henschel – PLOS

Dietary Lactobacillus acidophilus positively influences growth performance, gut morphology, and gut microbiology in rurally reared chickens  – C Forte – Poultry Science

Animal microbiome

Oral Disease and Microbiota in Free-Roaming Cats – Ana Whyte – Topics in Companion Animal Medicine

Review: Effect of Enterococcus Faecium Strain SF68 on Gastrointestinal Signs and Fecal Microbiome in Cats Administered Amoxicillin-Clavulanate – C. Torres-Henderson – Topics in Companion Animal Medicine

Water and extremophile microbiome

Clade and strain specific contributions of Synechococcus and Prochlorococcus to carbon export in the Sargasso Sea – Francesca De Martini – Limnology and Oceanography

Microbial proteins for organic material degradation in the deep ocean – David L. Kirchman – PNAS

Photosynthetic functions of Synechococcus in the ocean microbiomes of diverse salinity and seasons – Yihwan Kim – PLOS

Potential impact of global climate change on benthic deep-sea microbes – Roberto Danovaro – FEMS Microbiology Letters

Variability in the production of organic ligands, by Synechococcus PCC 7002, under different iron scenarios – Guillermo Samperio-Ramos – Journal of Oceanography

Effect of light on N2 fixation and net nitrogen release of Trichodesmium in a field study – Yangyang Lu – Biogeosciences

Microbial diversity of saline environments: searching for cytotoxic activities – Carolina Díaz-Cárdenas – AMB Express

Aerobic proteobacterial methylotrophs in Movile Cave: genomic and metagenomic analyses – Deepak Kumaresan – BMC Microbiome

Probiotics / prebiotics

Bifidobacteria or Fiber Protects against Diet-Induced Microbiota-Mediated Colonic Mucus Deterioration – Bjoern O. Schroeder – Cell Host and Microbe

Modifying progression of aging and reducing the risk of neurodegenerative diseases by probiotics and synbiotics – Huey Shi Lye – Frontiers In Bioscience

Phages and viruses

Isolation and characterization of a N4-like lytic bacteriophage infecting Vibrio splendidus, a pathogen of fish and bivalves – Pantelis Katharios – PLOS

High human papillomavirus (HPV) prevalence in South African adolescents and young women encourages expanded HPV vaccination campaigns – Zizipho Z. A. Mbulawa – PLOS

Zika virus infection modulates the bacterial diversity associated with Aedes aegypti as revealed by metagenomic analysis – Luis E. M. Villegas – PLOS

Localized Recombination Drives Diversification of Killing Spectra for Phage Derived Syringacins – David Baltrus – bioRxiv

Bioinformatics

Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing – Chao Fang – Giga Science

 

Techniques

Imaging bacteria inside their host by cryo-focused ion beam milling and electron cryotomography – João M Medeiros – Current Opinion in Microbiology

Microbes in the news

Tech company’s lights being used to kill germs in ambulances

Astronauts Identify Mystery Microbes in Space for the 1st Time

Microbes on the market

Seres Therapeutics Inc (MCRB) Holdings Increased by State Street Corp

Microsoft, Google invest in precision medicine startup DNAnexus

Tina’s non-microbiology picks

Synthetic Biology in the Driving Seat of the Bioeconomy – Yensi Flores Bueso – Trends in Biotechnology

Expect exoplanet atmospheres, organs with new functions and fewer traffic jams in 2018

January 2, 2018

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Happy New Year from the Microbiome Digest team!

General microbiome

Pre-print: Understanding How Microbiomes Influence The Systems They Inhabit: moving from a correlative to a causal research framework – E K Hall – bioRxiv

Human vaginal microbiome

A retrospective pilot study to determine whether the reproductive tract microbiota differs between women with a history of infertility and fertile women – Bryan A Wee – Australian and New Zealand Journal of Obstetrics and Gynaecology

Human gut microbiome

Rates of Gut Microbiome Divergence in Mammals – Alex H Nishida – Molecular Ecology

Animal microbiome

Processes shaping gut microbiota diversity in allopatric populations of the endemic lizard Podarcis lilfordi from Menorcan islets (Balearic Islands) – Laura Baldo – FEMS Microbiology Ecology

Individual- and Species-Specific Skin Microbiomes in Three Different Estrildid Finch Species Revealed by 16S Amplicon Sequencing – Kathrin Engel – Microbial Ecology

Plant, root, and soil microbiome

Vertical variation of a black soil’s properties in response to freeze-thaw cycles and its links to shift of microbial community structure – Ziming Han – Science of the Total Environment

Biomass, activity and structure of rhizosphere soil microbial community under different metallophytes in a mining site – Wenhao Yang – Plant and Soil

Symbiotic nitrogen fixation by rhizobia — the roots of a success story – Catherine Masson-Boivin – Current Opinion in Plant Biology

Water and extremophile microbiome

Microbial community structure and function in sediments from e-waste contaminated rivers at Guiyu area of China – Jun Liu – Environmental Pollution

Pre-print: Micro-scale ecology regulates particulate organic matter turnover in model marine microbial communities – Tim N Enke – bioRxiv

Food microbiology

Autochthonous facility-specific microbiota dominates washed-rind Austrian hard cheese surfaces and its production environment – Narciso M Quijada – International Journal of Food Microbiology

Bioinformatics

CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision – Damayanthi Herath – BMC Bioinformatics

Techniques

Serial Dilution-Based Growth Curves and Growth Curve Synchronization for High-Resolution Time Series of Bacterial Biofilm Growth – Fernando Govantes – Host-Pathogen Interactions

Microbes in the news

Fiber Is Good for You. Now Scientists May Know Why. – Carl Zimmer – The New York Times

Fast, Cheap Testing for Tuberculosis? Soon It May Be Possible – Donald G McNeil – The New York Times

How probiotics can help ward off health complications in premature babies – CTV News

Science, career, and publishing

Pre-print: Disequilibrium in Gender Ratios among Authors who Contributed Equally – Nichole A Broderick – bioRxiv

December 31, 2017

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A rich Digest to end 2017! There are several reviews on human gut microbiome and lots of papers on plant , root and soil microbiome. The airway microbiome is trending today and scientists are starting to examine rigorously the effect of herbal medicine on the gut microbiota. Happy Reading and Happy New Year!

General microbiology

Bacterial pathogens were detected from human exhaled breath using a novel protocol – Yunhao Zheng et al. – Journal of Aerosol Science

Bacteria Facilitate Enteric Virus Co-infection of Mammalian Cells and Promote Genetic Recombination – Andrea K. Erickson et al. – Cell Host & Microbe

Human airway microbiome

Review: Airway microbial metagenomics – Katarzyna Pienkowska et al. – Microbes and Infection

Respiratory syncytial virus and rhinovirus bronchiolitis are associated with distinct metabolic pathways – Christopher J Stewart et al. – Journal of Infectious Diseases

Tech Note: A breath of information: the volatilome – M. Mansurova et al. – Current Genetics

Short-term particulate matter exposure influences nasal microbiota in a population of healthy subjects – Jacopo Mariani et al. – Environmental Research

Exposure to traffic-related air pollution and the composition of the gut microbiota in overweight and obese adolescents – Tanya L. Alderete et al. – Environmental Research

Human gut microbiome

Gut microbiome contributes to impairment of immunity in pulmonary tuberculosis patients by alteration of butyrate and propionate producers – Abhijit Maji et al. – Environmental Microbiology

Review: Targeting the gut barrier for the treatment of alcoholic liver disease – Zhanxiang Zhou and Wei Zhong – Liver Research

Review: Microbial Regulation of Glucose Metabolism and Insulin Resistance – Crommen S and Simon MC – Genes

Review: Gut microbiota in the pathogenesis of inflammatory bowel disease – Nishida A et al. – Clinical Journal of Gastroenterology

Review: Human Intestinal Microbiota: Interaction Between Parasites and the Host Immune Response – Oswaldo Partida-Rodríguez et al. – Archives of Medical Research

Review: Gut dysbiosis and irritable bowel syndrome: the potential role of probiotics – Nicola Principi et al. – Journal of Infection

Review: Gut Microbiota in Obesity and Metabolic Abnormalities: A Matter of Composition or Functionality? – Sofia Moran-Ramo et al. – Archives of Medical Research

In vitro: An in vitro study to assess the impact of tetracycline on the human intestinal microbiome – Ji Young Jung et al. – Anaerobe

Human gut-microbiome-brain axis

Review: Targeting gut microbiome: A novel and potential therapy for autism – Yongshou Yang et al. – Life Sciences

Metabolomics

Dark matter in host-microbiome metabolomics: Tackling the unknowns–A review – B.Y. Loulou Peisl et al. – Analytica Chimica Acta

Animal experiments

Mouse: Intestinal Ralstonia pickettii augments glucose intolerance in obesity – Shanthadevi D. Udayappan et al. – PLoS One

Pig: Structural Modulation of Gut Microbiota during Alleviation of Suckling Piglets Diarrhoea with Herbal Formula – Cui Liu et al. – Evidence-Based Complementary and Alternative Medicine

Rat: Effects of HLA-B27 on Gut Microbiota in Experimental Spondyloarthritis Implicate an Ecological Model of Dysbiosis – Gill T et al. – Arthritis and Rheumatology

Changes in mouse gut bacterial community in response to different types of drinking water – Marcela F. Dias et al. – Water Research

Mouse: Particle size determines the anti-inflammatory effect of wheat bran in a model of fructose over-consumption: Implication of the gut microbiota – Francesco Suriano & Audrey M. Neyrinck et al. – Journal of Functional Foods

Mouse: Mushroom polysaccharides from Ganoderma lucidum and Poria cocos reveal prebiotic functions – Imran Khan et al. – Journal of Functional Foods

Animal microbiome

Bacterial diversity of wild-caught Lutzomyia longipalpis (a vector of zoonotic visceral leishmaniasis in Brazil) under distinct physiological conditions by metagenomics analysis – Ana Clara Araújo Machado Pires et al. – Parasites & Vectors

Drosophila Perpetuates Nutritional Mutualism by Promoting the Fitness of Its Intestinal Symbiont Lactobacillus plantarum – Gilles Storelli et al. – Cell Metabolism

Analysis of the influence of living environment and age on vaginal fungal microbiome in giant pandas (Ailuropoda melanoleuca) by high throughput sequencing – Danyu Chen et al. – Microbial Pathogenesis

Plant, root and soil microbiome

Phosphate levels influence the utilisation of rice rhizodeposition carbon and the phosphate-solubilising microbial community in a paddy soil – Xi-En Long et al. – Soil Biology and Biochemistry

Plant community and soil conditions individually affect soil microbial community assembly in experimental mesocosms – Aspen T. Reese et al. – Ecology and Evolution

Responses of bulk and rhizosphere soil microbial communities to thermoclimatic changes in a Mediterranean ecosystem – Javier Pascual et al. – Soil Biology and Biochemistry

Remediation of arsenic in mung bean (Vigna radiata) with growth enhancement by unique arsenic-resistant bacterium Acinetobacter lwoffii – Joyati Das and Priyabrata Sarkar – Science of the Total Environment
https://www.sciencedirect.com/science/article/pii/S0048969717335830

* Opinion: Why we need a National Living Soil Repository – Daniel K. Manter et al. – PNAS

Long-term effects of nitrogen fertilization on aggregation and localization of carbon, nitrogen and microbial activities in soil – Yidong Wang et al. – Science of the Total Environment

Vineyard microbiome variations during different fertilisation practices revealed by 16s rRNA gene sequencing – Loredana Canfora et al. – Applied Soil Ecology

* Co-occurrence patterns of soybean rhizosphere microbiome at a continental scale – Baogang Zhang et al. – Soil Biology and Biochemistry

Review: Symbiotic nitrogen fixation by rhizobia — the roots of a success story – Catherine Masson-Boivin and Joel L Sachs – Current Opinion in Plant Biology

Water and extremophile microbiome

PDF: From extreme environments to human pathogens: an evolutionary journey – Donato Giovannelli and Costantino Vetriani – Biochemical Society

Comparison of Iris pseudacorus wetland systems with unplanted systems on pollutant removal and microbial community under nanosilver exposure – Juan Huang et al. – Science of the Total Environment

Impacts of design configuration and plants on the functionality of the microbial community of mesocosm-scale constructed wetlands treating ibuprofen – Liang Zhang et al. – Water Research

Microbial community evolution in partial nitritation/anammox process: From sidestream to mainstream – Yandong Yang et al. – Bioresource Technology

Spatiotemporal changes in bacterial community and microbial activity in a full-scale drinking water treatment plant – Luanfeng Hou et al. – Science of the Total Environment

Built environment microbiome

Microbiological air contamination in university premises and the evaluation of drug resistance of staphylococci occurring in the form of a bioaerosol – Katarzyna Wolny-Koładka et al. – Indoor and Built Environment

Phages and viruses

Virome analysis of lily plants reveals a new potyvirus – Yongqiang Li et al. – Archives of Virology

Comparative Analysis of 37 Acinetobacter Bacteriophages – Dann Turner et al. – Viruses

Antiviral systems in vector mosquitoes – Tong Liu et al. – Developmental & Comparative Immunology

Microbes in the news

Launceston associate professors studying gut microbiome in elderly Tasmanians – Carly Dolan – Examiner

Biofilm made of mulberry silk to destroy dengue virus – TNN – Times of India

Rhode Island Health Department finds E. coli bacteria, issues boil water notice – PATRICIA RESENDE & TONY GUGLIOTT – NBC 10

Op-Ed: Survival tips in the age of drug-resistant bacteria – Kevin Kavanagh – Lexington Herald Leader

* One Big Family: This Beautiful Interactive Diagram Shows How Every Organism Is Related – Fiona McMillan – Forbes

Researchers propose different approach to beat antibiotic-resistant superbugs – News Medical

 

December 30, 2017

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Enjoy your daily dose of (mostly human gut) microbiome literature!

General microbiome

Q&A: Friends (but sometimes foes) within: the complex evolutionary ecology of symbioses between host and microbes – Nicole Gerardo, BMC Biology

The Dark Side of IFN-γ: Its Role in Promoting Cancer Immunoevasion – Marija Mojic, International Journal of Molecular Sciences

Two-stage pretreatment of excess sludge for electricity generation in microbial fuel cell – Yi Zhang, Environmental Technology

Human respiratory microbiome

Azithromycin versus placebo for the treatment of HIV-associated chronic lung disease in children and adolescents (BREATHE trial): study protocol for a randomised controlled trial – Carmen Gonzalez-Martinez, BMC Biology

Human skin microbiome

Characterization of the facial microbiome in twins discordant for rosacea – Asifa K. Zaidi, Experimental Dermatology

Human oral microbiome

Oral health in geroscience: animal models and the aging oral cavity – Jonathan Y. An, GeroScience

Extracellular matrix Influence in Streptococcus mutans gene expression in a cariogenic biofilm – Elkin Jahir Florez Salamanca, Molecular Oral Microbiology

Human gut microbiome

The Microbiome–Gut–Behavior Axis: Crosstalk Between the Gut Microbiome and Oligodendrocytes Modulates Behavioral Responses – Achilles Ntranos, Neurotherapeutics

Antibiotics Associated Disorders and Postbiotics Induced Rescue in Gut Health – Debarati Paul, Current Pharmaceutical Design

We are not alone in our body: insights into the involvement of microbiota in the etiopathogenesis and pharmacology of mental illness –  Claudia Pisanu, Current Drug Metabolism

Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003 – Francesca Bottacini, BMC Genomics

Microbiota dysbiosis in inflammatory bowel diseases: in silico investigation of the oxygen hypothesis – Michael A. Henson, BMC Systems Biology

Gut microbiota: Fibre restores healthy gut microbiota – Alan Morris, Nature Reviews Endocrinology

The human microbiome in evolution – Emily R. Davenport, BMC Biology

Clinical characteristics and long-term prognosis of elderly onset ulcerative colitis – Eun Mi Song, Gastroenterology and Hepatology

Environmental contributions to gastrointestinal and liver cancer in the Asia–Pacific region – Kwang-Pil Ko, Gastroenterology and Hepatology

Effect of oral tobacco use and smoking on outcomes of Crohn’s disease in India – Umang Arora, Gastroenterology and Hepatology

Irritable bowel syndrome in Asia: Pathogenesis, natural history, epidemiology, and management – Kok-Ann Gwee, Gastroenterology and Hepatology

Rifaximin has minor effects on bacterial composition, inflammation, and bacterial translocation in cirrhosis: A randomized trial – Nina Kimer, Gastroenterology and Hepatology

The role of the microbiome and the use of probiotics in gastrointestinal disorders in adults in the Asia-Pacific region – background and recommendations of a regional consensus meeting – Uday C Ghoshal, Gastroenterology and Hepatology

Animal experiments

Inclusion of Bacillus amyloliquefaciensstrain TOA5001 in the diet of broilers suppresses the symptoms of coccidiosis by modulating intestinal microbiota – Takamitsu Tsukahara, Animal Science Journal

Characterization of the cervical bacterial community in dairy cows with metritis and during different physiological phases – Yu Wang, Theriogenology

Replacement of alfalfa hay (Medicago sativa L.) with subabul (Leucaena leucocephala) leaf meal in diets of Najdi goats: effect on digestion activity of rumen microorganisms – Tahereh Mohammadabadi, Tropical Animal Health and Production

Animal microbiome

Individual- and Species-Specific Skin Microbiomes in Three Different Estrildid Finch Species Revealed by 16S Amplicon Sequencing – Kathrin Engel, Microbial Ecology

Plant, root, and soil microbiome

Changes of microbial population and N-cycling function genes with depth in three Chinese paddy soils – Huanhuan Wang, PLOS One

Water and extremophile microbiome

Candidatus Nitrosocaldus cavascurensis, an ammonia oxidizing, extremely thermophilic archaeon with a highly mobile genome – Sophie S Abby, bioRxiv

Microbes in the news

Artificial intelligence identifies bacteria images quickly, accurately – Greg Slabodkin, Health Data Management

Microbes on the market

Assembly Biosciences, Inc. (ASMB) Reaches $45.08 After 7.00% Up Move; GEOX SPA (GXSBF) Shorts Raised By 18.36% – Stephen Andrade, Herald KS

December 26, 2017

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Quite a few articles today especially in the plant/soil and water/extremophile sections. Plus: a new zebrafish model of the human gut microbiome, fiber and bifidos protect against north american diet-induced increased gut permeability in mice, prebiotics from the Morinda plant not only alter the gut microbiome but improve Alzheimers-like symptoms in a rat model, micro-eukaryotes may be an important factor in a deadly skin fungus infection in the Cascades Frog, and a new Leaf-FISH technique to visualize bacterial communities on plants. Happy Holidays!

Human oral microbiome

The oral microbiome—the relevant reservoir for acute pediatric appendicitis? – Carlotta Blod – International Journal of Colorectal Disease

Differences in carbon source usage by dental plaque in children with and without early childhood caries – Yan Zhao – International Journal of Oral Science

Review: Task Force on Design and Analysis in Oral Health Research: Host-Microbiome Interactions in Dysbiosis – T.E. Van Dyke – JDR Clinical & Translational Research

Human gut microbiome

Review: Probiotics and necrotizing enterocolitis – Ravi Mangal Patel – Seminars in Pediatric Surgery

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Animal experiments

Fusimonas intestini gen. nov., sp. nov., a novel intestinal bacterium of the family Lachnospiraceae associated with diabetes in mice – Hiroyuki Kusada – Scientific Reports

*Zebrafish Axenic Larvae Colonization with Human Intestinal Microbiota – Arias-Jayo Nerea – Zebrafish

*Bifidobacteria or Fiber Protects against Diet-Induced Microbiota-Mediated Colonic Mucus Deterioration – Bjoern O. Schroeder – Cell Host & Microbe

In Silico Analysis of the Small Molecule Content of Outer Membrane Vesicles Produced by Bacteroides thetaiotaomicron Indicates an Extensive Metabolic Link between Microbe and Host – William A. Bryant – Frontiers in Microbiology

*Prebiotic Effect of Fructooligosaccharides from Morinda officinalis on Alzheimer’s Disease in Rodent Models by Targeting the Microbiota-Gut-Brain Axis – Diling Chen – Frontiers in Aging Neuroscience

Animal microbiome

Effect of Environmental Factors and an Emerging Parasitic Disease on Gut Microbiome of Wild Salmonid Fish – Anti Vasemägi – mSphere

*Composition of Micro-eukaryotes on the Skin of the Cascades Frog (Rana cascadae) and Patterns of Correlation between Skin Microbes and Batrachochytrium dendrobatidis – Jordan G. Kueneman – Frontiers in Microbiology

Plant, root, and soil microbiome

Chemical investigation of metabolites produced by an endophytic fungi Phialemonium curvatum from the leaves of Passiflora edulis –  G. R. Nalin Rathnayake – Natural Product Research

Novel hydrocarbonoclastic metal-tolerant Acinetobacter and Pseudomonas strains from Aconcagua river oil-polluted soil – Valentina Méndez – Journal of soil science and plant nutrition

Spatial patterns of enzyme activities in the rhizosphere: Effects of root hairs and root radius – Xiaomin Ma – Soil Biology and Biochemistry

The rhizosphere microbial community response to a bio-organic fertilizer: finding the mechanisms behind the suppression of watermelon Fusarium wilt disease – Jia Zhao – Acta Physiologiae Plantarum

Efficiency of two inoculation methods of Pseudomonas putida on growth and yield of tomato plants – Luis G. Hernández-Montiel – Journal of soil science and plant nutrition

Rhizospere yeasts improve P uptake of a maize arbuscular mycorrhizal association – Marcela Sarabia – Applied Soil Ecology

Ammonia-oxidizing microorganisms: key players in the promotion of plant growth – Adenike Eunice Amoo – Journal of soil science and plant nutrition

Review: Potassium solubilizing bacteria (KSB): Mechanisms, promotion of plant growth, and future prospects ­ A review – H. Etesami – Journal of soil science and plant nutrition

Long-term phosphorus fertilization effects on arbuscular mycorrhizal fungal diversity in Uruguayan grasses – Silvina García – Journal of soil science and plant nutrition

Alcaligenes faecalisassociated with Mimosa calodendron rizhosphere assist plant survival in arsenic rich soils – Érica Barbosa Felestrino – Journal of soil science and plant nutrition

Functional land-use change effects on soil fungal communities in Chilean temperate rainforests – César Marín – Journal of soil science and plant nutrition

Probiotic strain Stenotrophomonas acidaminiphila BJ1 degrades and reduces chlorothalonil toxicity to soil enzymes, microbial communities and plant roots – Qingming Zhang – AMB Express

Low light availability alters root exudation and reduces putative beneficial microorganisms in seagrass roots –  Belinda C. Martin – Frontiers in Microbiology

Effects of biochar on nutrients and the microbial community structure of tobacco-planting soils – Gao Lin – Journal of soil science and plant nutrition

Root-associated bacterial and fungal community profiles of Arabidopsis thaliana are robust across contrasting soil P levels – Chanz Robbins – Phytobiomes

Water and extremophile microbiome

Biogeographical patterns of bacterial and archaeal communities from distant hypersaline environments – M.R. Mora-Ruiz del – Systematic and Applied Microbiology

Cloning, Over-Expression, and Purification of Carbonic Anhydrase from an Extremophilic Bacterium: An Introduction to Advanced Molecular Biology – Vijayakumar Somalinga – The American Biology Teacher

Salinivibrio kushneri sp. nov., a moderately halophilic bacterium isolated from salterns – Clara López-Hermoso – Systematic and Applied Microbiology

Genome sequencing and heterologous expression of antiporters reveal alkaline response mechanisms of Halomonas alkalicola – Lei Zhai – Extremophiles

Benthic phototrophic community from Kiran soda lake, south-eastern Siberia – Ekaterina I. Burganskaya – Extremophiles

Enhancing the adaptability of the deep-sea bacterium Shewanella piezotolerans WP3 to high pressure and low temperature by experimental evolution under H2O2 stress – Zhe Xie – Applied and Environmental Microbiology

Fungal community structure at pelagic and littoral sites in Lake Biwa determined with high-throughput sequencing – Peixue Song – Limnology

Spatiotemporal dynamics of marine bacterial and archaeal communities in surface waters off the northern Antarctic Peninsula – Camila N. Signori – Deep Sea Research Part II: Topical Studies in Oceanography

Microbial Ecology

Dissertation: The Macroecology of Microorganisms: From Pattern to Process – David Clark – University of Essex

Review: Using metabolic networks to resolve ecological properties of microbiomes – Emilie E.L. Muller – Current Opinion in Systems Biology

Microbial stress mediated intercellular nanotubes in an anaerobic microbial consortium digesting cellulose – Martina John – Scientific Reports

Built environment

Distribution of Legionella and bacterial community composition among regionally diverse US cooling towers – Anna C. Llewellyn – PLOS one

Food microbiology

Identification of natural antimicrobial peptides from bacteria through metagenomic and metatranscriptomic analysis of high-throughput transcriptome data of Taiwanese oolong teas – Kai-Yao Huang – BMC Systems Biology

Strain-Level Metagenomic Analysis of the Fermented Dairy Beverage Nunu Highlights Potential Food Safety Risks – Aaron M. Walsh – Applied and Environmental Microbiology

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Probiotics / prebiotics

Review: Recent Development of Prebiotic Research—Statement from an Expert Workshop – Giorgio La Fata – Nutrients

Effects of fermented soymilk with Lactobacillus casei Shirota on skin condition and the gut microbiota: a randomised clinical pilot trial – T. Nagino – Beneficial Microbes

Phages and viruses

Novel ssDNA viruses detected in the virome of bleached, habitat-forming kelp Ecklonia radiata –  Douglas Beattie – Frontiers in Marine Science

Bioinformatics

Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples – Jake Lin – BMC Genomics

Techniques

*Leaf-FISH: Microscale imaging of bacterial taxa on phyllosphere –  Elena L. Peredo – Frontiers in Microbiology

A new suite of plasmid vectors for fluorescence-based imaging of root colonizing pseudomonads –  Rosemarie Wilton – Frontiers in Plant Science

Synthetic microbial consortia enable rapid assembly of pure translation machinery – Fernando Villarreal – Nature Chemical Biology

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Microbes in the news

Essential science: Link between gut microbes and despair – Tim Sandle – Digital Science

Enjoy the holidays, but don’t forget your fiber – Tim Sandle – Digital Science

 

December 25, 2017

Posted on by

 

A short digest today covering the human oral and gut microbiome, animal experiments, animal microbiome, plant, root and soil microbiome, techniques and news. At last we also have some “Lab stock fun picks”. Merry Christmas!!

 

Human oral microbiome

The oral microbiome-the relevant reservoir for acute pediatric appendicitis? – C Blod – International Journal of Colorectal Disease

 

 

Human gut microbiome

Intestinal microbiome analysis revealed dysbiosis in sickle cell disease – SH Lim – American Journal of Hematology

 

Animal experiments 

Fermented Soybean Meal Increases Lactic Acid Bacteria in Gut Microbiota of Atlantic Salmon (Salmo salar). – N Catalán – Probiotics and Antimicrobial Proteins

 

Animal microbiome 

The Combined Effect of Temperature and Host Clonal Line on the Microbiota of a Planktonic Crustacean. – KE Sullam – Microbial Ecology

 

Plant, root, and soil microbiome

Grey relational analysis for evaluating the effects of different rates of wine lees-derived biochar application on a plant-soil system with multi-metal contamination. – M Xu – Environmental Science and Pollution Research International

http://Transcriptomic responses of catalase, peroxidase and laccase encoding genes and enzymatic activities of oil spill inhabiting rhizospheric fungal strains. – MD Asemoloye – Environmental Pollution

Augmentation with potential endophytes enhances phytostabilization of Cr in contaminated soil. – MT Ahsan – Environmental Science and Pollution Research International

 

 

Techniques

Strain profiling and epidemiology of bacterial species from metagenomic sequencing – D Albanese – Nature Communications

Mechanistic and structural insight into promiscuity based metabolism of cardiac drug digoxin by gut microbial enzyme – K Kumar – Journal of Cellular Biochemistry

 

Microbes in the news

Cooking a turkey? Here’s how to make sure you avoid getting food poisoning – thejournal.ie

How the US military killed an Irishman in San Fran with germ warfare – Irish Central

How to avoid getting sick from flying – keep clean, stay hydrated and try to get a window seat – South China Morning Post

It’s getting real tough to ‘ESKAPE’ hospital-acquired infections – Indian Express

 

Lab stock funny picks (source: Shutterstock)

My magnifying glass is more powerful than the microscope

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Sometimes I try to incorporate the additive model of primary colours in my research: Red, Green , Blue!!

stock-photo-male-doctor-working-in-the-lab-on-virus-vaccine-740000146

 

Seems some one has finally been able to culture virus on a solid (agar) medium..

stock-photo-a-scientist-holding-a-petri-dish-with-virus-and-bacteria-cells-79142374

 

Do you see what I see?

stock-photo-portrait-of-woman-and-man-mask-medical-glove-research-scientist-or-doctor-looking-at-a-test-tube-718908685

stock-photo-scientist-working-at-the-laboratory-731448346

stock-photo-scientist-working-at-the-laboratory-732166891

December 24, 2017

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Events and jobs
Microbiology/bioinformatics/bioche Freshers Wanted For Medical Coding – AS Medical Coding Technologies – Chennai, Cuddalore, Vellore

General microbiome
Review: Protective Microbiota: From Localized to Long-Reaching Co-Immunity. – Lynn Chiu – Frontiers In Immunology

Pregnancy and early life
Microbiome Influences Prenatal and Adult Microglia in a Sex-Specific Manner – Morgane Sonia Thion – Cell

Human respiratory microbiome
Differentially Regulated Host Proteins Associated with Chronic Rhinosinusitis Are Correlated with the Sinonasal Microbiome. – Kristi Biswas – Frontiers In Cellular And Infection Microbiology

Sputum microbiome temporal variability and dysbiosis in chronic obstructive pulmonary disease exacerbations: an analysis of the COPDMAP study. – Zhang Wang – Thorax

Human vaginal microbiome
Evaluation of lactitol, lactulose, raffinose, and oligofructose for maintenance of a Lactobacillus-dominated vaginal microbiota establishes a promising prebiotic candidate. – Stephanie L Collins – Applied And Environmental Microbiology

Review: Human vaginal pH and microbiota: an update. – Keshav Godha – Gynecological Endocrinology

Review: Impact of microbiota on the use and effects of isoflavones in the relief of climacteric symptoms in menopausal women – A review – Naice E.S. Monteiro – Journal of Functional Foods

Human oral microbiome
Review: Tongue Coating: its characteristics and role in intra-oral halitosis and general health: A review. – Kavitha Seerangaiyan – Journal Of Breath Research

Human gut microbiome
Bifidobacteria or Fiber Protects against Diet-Induced Microbiota-Mediated Colonic Mucus Deterioration – Bjoern O. Schroeder – Cell Host and Microbe

Fiber-Mediated Nourishment of Gut Microbiota Protects against Diet-Induced Obesity by Restoring IL-22-Mediated Colonic Health – Jun Zou – Cell Host and Microbe

Dysbiosis-Associated Change in Host Metabolism Generates Lactate to Support Salmonella Growth – Caroline C. Gillis – Cell Host and Microbe

Durability and Long-Term Clinical Outcomes of Fecal Microbiota Transplant (FMT) Treatment in Patients with Recurrent Clostridium difficile Infection. – Yafet Mamo – Clinical Infectious Diseases

Evaluation of a faecal dysbiosis test for irritable bowel syndrome in subjects with and without obesity. – Martin Aasbrenn – Scandinavian Journal Of Clinical And Laboratory Investigation

Structural basis for the regulation of β-glucuronidase expression by human gut Enterobacteriaceae. – Michael S Little – PNAS

Low-to-moderate intensity aerobic exercise training modulates irritable bowel syndrome through antioxidative and inflammatory mechanisms in women: Results of a randomized controlled trial – Behzad Hajizadeh Maleki – Cytokine

Differences in fecal microbial metabolites and microbiota of children with autism spectrum disorders – Dae-Wook Kang – Anaerobe

Review: The Microbiome in Primary Sclerosing Cholangitis: Current Evidence and Potential Concepts. – Johannes R Hov – Seminars In Liver Disease

Microbial ecology
Autoinducer 2-dependent Escherichia coli biofilm formation is enhanced in a dual-species co-culture. – Leanid Laganenka – Applied And Environmental Microbiology

Animal experiments
Prebiotic Supplementation Following Ileocecal Resection in a Murine Model is Associated With a Loss of Microbial Diversity and Increased Inflammation. – Michael Laffin – Inflammatory Bowel Diseases

An attenuated Salmonella Typhimurium strain and galacto-oligosaccharides (GOS) accelerate clearance of Salmonella infection in poultry through modifications to the gut microbiome. – M Andrea Azcarate-Peril – Applied And Environmental Microbiology

Akkermansia muciniphila induces gut microbiota remodelling and controls islet autoimmunity in NOD mice. – Arno Hänninen – Gut

Analysis of the Specificity of IgA Antibodies Produced in the Mouse Small Intestine. – N E Sharanova – Molekuliarnaia Biologiia (Molecular Biology, original in Russian)

Bacteriostatic Effect of Quercetin as an Antibiotic Alternative In Vivo and Its Antibacterial Mechanism In Vitro. – Shengan Wang – Journal Of Food Protection (in Arbor Acre (AA) broiler chickens)

Dietary protein level affects nutrient digestibility and ileal microbiota structure in growing pigs. – Kai Qiu – Animal Science Journal

Arctic berry extracts target the gut-liver axis to alleviate metabolic endotoxaemia, insulin resistance and hepatic steatosis in diet-induced obese mice. – Fernando F Anhê – Diabetologia

Microbiota transplantation reveals beneficial impact of berberine on hepatotoxicity by improving gut homeostasis. – Chenjie Qin – Science China. Life Sciences (in rats and mice)

Dysbiosis of gut microbiota by chronic coexposure to titanium dioxide nanoparticles and bisphenol A: Implications for host health in zebrafish – Lianguo Chen – Environmental Pollution

Dysbiosis of the fecal microbiota in feedlot cattle with hemorrhagic diarrhea – Mohamed Zeineldin – Microbial Pathogenesis

Characterization of Brachyspira communities from clinical cases of swine mucohaemorrhagic diarrhea through deep sequencing of the NADH oxidase (nox) gene – Lisa A. Johnson – Veterinary Microbiology

Injectable antimicrobials in commercial feedlot cattle and their effect on the nasopharyngeal microbiota and antimicrobial resistance – Devin B. Holman – Veterinary Microbiology

Grain grinding size of cereals in complete pelleted diets for growing lambs: effects on ruminal microbiota and fermentation – Sonia Andrés – Small Ruminant Research

Animal microbiome
Food Storage by the Savanna Termite Cornitermes cumulans (Syntermitinae): a Strategy to Improve Hemicellulose Digestibility? – Letícia Menezes – Microbial Ecology

The metagenome of Caracolus marginella gut microbiome using culture independent approaches and shotgun sequencing. – Robert J Rabelo-Fernandez – Data In Brief (snails)

Transcriptomic characterization of Caecomyces churrovis: a novel, non-rhizoid-forming lignocellulolytic anaerobic fungus. – John K Henske – Biotechnology For Biofuels (Found in Navajo Churro sheep fecal pellets)

** Enhancing the Resolution of Rumen Microbial Classification from Metatranscriptomic Data Using Kraken and Mothur. – Andre L A Neves – Frontiers In Microbiology **

Temporal and regional variability in the skin microbiome of humpback whales along the Western Antarctic Peninsula. – K C Bierlich – Applied And Environmental Microbiology (DOI not available yet, so linked to PubMed)

Wild eel microbiome reveals that skin mucus of fish could be a natural niche for aquatic mucosal pathogen evolution. – Miguel Carda-Diéguez – Microbiome

Seasonal, spatial, and maternal effects on gut microbiome in wild red squirrels. – Tiantian Ren – Microbiome

Water and extremophile microbiome
Biodegradation of weathered polystyrene films in seawater microcosms. – Evdokia Syranidou – Scientific Reports

Microbial stress mediated intercellular nanotubes in an anaerobic microbial consortium digesting cellulose. – Martina John – Scientific Reports

Metagenomic analysis reveals the impact of wastewater treatment plants on the dispersal of microorganisms and genes in aquatic sediments. – Binh T T Chu – Applied And Environmental Microbiology

Nutrient dynamics and stream order influence microbial community patterns along a 2914 km transect of the Mississippi River – Michael W Henson – bioRxiv

Metagenomic exploration reveals a marked change in the river resistome and mobilome after treated wastewater discharges – Itziar Lekunberri – Environmental Pollution

Built environment
Metagenomic survey of bacterial diversity in the atmosphere of Mexico City using different sampling methods – N. Serrano-Silva – Environmental Pollution

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

Food microbiology
Modulation of gut microbiota and gut-generated metabolites by bitter melon results in improvement in the metabolic status in high fat diet-induced obese rats – Juan Bai – Journal of Functional Foods

In vitro digestion by saliva, simulated gastric and small intestinal juices and fermentation by human fecal microbiota of sulfated polysaccharides from Gracilaria rubra – Tong Di – Journal of Functional Foods

Seasonal variances in bacterial microbiota and volatile organic compounds in raw milk – Beata Nalepa – International Journal of Food Microbiology

Structure of association networks in food bacterial communities – Eugenio Parente – Food Microbiology

Review: Lactose intolerance and gastrointestinal cow’s milk allergy in infants and children – common misconceptions revisited. – Ralf G Heine – The World Allergy Organization Journal

Probiotics / prebiotics / antibiotics
Effect of the consumption of a synbiotic diet mousse containing Lactobacillus acidophilus La-5 by individuals with metabolic syndrome: A randomized controlled trial – Douglas Xavier-Santos – Journal of Functional Foods

Review: Is Metformin Poised for a Second Career as an Antimicrobial? – Faiza Malik – Diabetes/Metabolism Research And Reviews

Review: Role of probiotics in the management of lung cancer and related diseases: An update – Anshul Sharma – Journal of Functional Foods

Phages and viruses
Isolation in small populations of Wayampi Amerindians promotes endemicity and homogenization of their faecal virome, but its distribution is not entirely random. – Vicente Pérez-Brocal – Fems Microbiology Ecology

Bioinformatics
Identification of bacterial species that can utilize fructose-asparagine. – Anice Sabag-Daigle – Applied And Environmental Microbiology

Techniques
On the Identification of Culturable Microorganisms for the Assessment of Biodiversity in Bioaerosols. – Philippe Duquenne – Annals Of Work Exposures And Health

Review: Illuminating the covert mission of mononuclear phagocytes in their regional niches – Shu Zhen Chong – Current Opinion in Immunology

Genomes
Draft genomes of Enterococcus faecium strains isolated from human feces before and after eradication therapy against Helicobacter pylori. – Nikita A Prianichnikov – Data In Brief

Microbes in the news
Biota Beats: Music from the Microbiome –  Clara Rodríguez Fernández – LabBioTech
Microbes on the market (news about biotech companies)

Bacteria and Cancer Immunotherapy: What’s in Your Gut? – Medical News Bulletin

Can You Teach an Old Gene New Tricks? – Grishma Gupte – SciWorthy

Doctor warns patients to avoid unnecessary antibiotics this winter – Tammy Palmer – LocalSyr.com