Category Archives: Food Microbiology

July 16, 2017

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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

July 7, 2017

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Human Microbiome

Review: Altered molecular signature of intestinal microbiota in irritable bowel syndrome patients compared with healthy controls: A systematic review and meta-analysis – Liu et al. – Digestive and Liver Disease

Non-antibiotic Isotretinoin treatment differentially controls Propionibacterium acnes on skin of acne patients. – Ryan-Kewley et al. – Frontiers in Microbiology

Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy – Namasivayam et al. – Microbiome (BMC)

Research Highlights: Obesity: Gut microbiome and serum metabolome changes – Claire Greenhill – Nature Reviews Endocrinology

Research Highlights:  Gut microbiota: Link between the gut and adipose tissues – Alan Morris – Nature Reviews Endocrinology

Review: The gut microbiome and liver cancer: mechanisms and clinical translation – Yu & Schwabe – Nature Reviews Gastroenterology and Hepatology

 

Pathogens

Reactive Oxygen Species-Dependent Essential Genes in Salmonella Typhimurium – Karash and Min Kwon – BioRxiv

Whole transcriptome sequencing of Pseudomonas syringae pv. actinidiae-infected kiwifruit plants reveals species-specific interaction between long non-coding RNA and coding genes – Wang et al – Scientific Reports (Nature)

Effects of different substrates/growth media on microbial community of saliva-derived biofilm – Li et al – FEMS Microbiology letters

 

Methods (including bioinformatics)

Selective imaging of Gram-negative and Gram-positive microbiotas in the mouse gut – Wang et al. – Biochemistry (ACS)

Methodology: VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data – Ren et al. – Microbiome (BMC)

Methodology: A novel ultra high-throughput 16S rRNA gene amplicon sequencing library preparation method for the Illumina HiSeq platform – de Muinck et al. – Microbiome (BMC)

Completing bacterial genome assemblies with multiplex MinION sequencing – Wick et al. – BioRxiv

Axe: rapid, competitive sequence read demultiplexing using a trie – Murray & Borevitz – BioRxiv

 

Water microbiome

Unraveling the microbial interactions and metabolic potentials in pre- and post-treated sludge from a wastewater treatment plant using metagenomic studies – Sidhu et al. – Frontiers in Microbiology

Nutrient dynamics and stream order influence microbial community patterns along a 2914 km transect of the Mississippi River – Henson et al. – BioRxiv

 

Extremophiles

Oxidative weathering and microbial diversity of an inactive seafloor hydrothermal sulfide chimney – Li et al. – Frontiers in Microbiology

Hidden biofilms in a far northern lake and implications for the changing Arctic – Mohit et al. – npj Biofilms and Microbiomes

 

Probiotics – Fermented Food

Amplicon sequencing of the slpH locus permits culture-independent strain typing of Lactobacillus helveticus in dairy products – Moser et al. – Frontiers in Microbiology

Probiotic Enterococcus mundtii Isolate Protects the Model Insect Tribolium castaneum against Bacillus thuringiensis – Grau et al. – Frontiers in Microbiology

 

Animal Microbiome

Regulation of gut luminal serotonin by commensal microbiota in mice –  Hata et al. – PLoS ONE

 

News

News: How Gut Bacteria Tell Their Hosts What to Eat – Knvul Sheikh via Scientific American Mind (Nature)

News: Mind over Meal: Does Weight-Loss Surgery Rewire Gut-Brain Connections? – Bret Stetka via Scientific American Mind (Nature)

 

Fellowships

Post-Doctoral Research Fellow, Microbiome and Vaccine Induced Immunity – Seattle, WA, United States

Postdoctoral Fellow (Listeria monocytogenes research) – Dunedin, New Zealand

 

Other

The earth is flat (p > 0.05): significance thresholds and the crisis of unreplicable research – Amrhein et al. – PeerJ

 

July 3, 2017

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Pregnancy and early life
Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission – Sabrina Duranti –  Microbiome

 
Mini Review: The microbiome and disorders of the central nervous system – Valeria D. Felice – Pharmacology Biochemistry and Behavior

 
Human respiratory microbiome

 
Short Report: The metabolic footprint of the airway bacterial community in cystic fibrosis – Vaishnavi Narayanamurthy – Microbiome

 
Human gut microbiome

 
Gut microbial transformation of the dietary imidazoquinoxaline mutagen MeIQx reduces its cytotoxic and mutagenic potency – Jianbo Zhang –  Toxicological Science

 
Review: Practical considerations for large-scale gut microbiome studies – Doris Vandeputte – FEMS Microbiology Reviews

 
Association of altered gut microbiota composition with chronic urticaria – Edris Nabizadeh – Annals of Allergy, Asthma & Immunology

 
Animal microbiome 

 
A genomic investigation of ecological differentiation between free-living and Drosophila-associated bacteria – Nathan J. Winans –  Molecular Ecology

 
The Gut Bacterial Community Composition of Wild Cervus albirostris (White-Lipped Deer) Detected by the 16S Ribosomal RNA Gene Sequencing – Jun-gang Li –  Current Microbiology

 
Microbial influence on Drosophila biology – ME Martino – Current Opinion in Microbiology

 
Plant, root, and soil microbiome

 
Organic carbon and nitrogen availability determine bacterial community composition in paddy fields of the Indo-Gangetic plain – Arvind Kumar –  Biotech

 

Water and extremophile microbiome

 
Spatiotemporal Dynamics of the Bacterial Microbiota on Lacustrine Cladophora glomerata (Chlorophyta) – Michael J. Braus –  bioRxiv

 
Quantity and quality of particulate organic matter controls bacterial production in the Columbia River estuary – Byron C. Crump – Limnology and Oceanography

 
Relating genomic characteristics to environmental preferences and ubiquity in different microbial taxa – Marta Cobo-Simón –  BMC Genomics

 
Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing – Natàlia Corcoll – FEMS Microbiology Letters

 
Food microbiology

 

Cleaning and disinfection of biofilms composed of Listeria monocytogenes and background microbiota from meat processing surfaces – Annette Fagerlund – Applied and Environmental Microbiology

 

Probiotics / prebiotics

 
A human gut commensal ferments cranberry carbohydrates to produce formate – Ezgi Özcan – Applied and Environmental Microbiology

 
Review: Lifestyles in transition: evolution and natural history of the genus Lactobacillus – Rebbeca M. Duar – FEMS Microbiology Reviews

 
Phages and viruses

 
Synergistic elimination of bacteria by phage and the innate immune system – Chung Yin (Joey) Leung – Journal of Theoretical Biology

 
Biotechnology

 
Effect of zinc oxide nanoparticles on nitrogen removal, microbial activity and microbial community of CANON process in a membrane bioreactor – Xiaojing Zhang – Bioresource Technology

 
Microbes in the news

 
A new approach to tackling drug-resistant bacteria

New technology to cool the body: make the clothes made of microorganisms

 
Microbes on the market (news about biotech companies)

 
New Belgian Biotech will use Microorganisms to Replace Pesticides and Fertilizers

June 15, 2017

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Today’s digest is full of plant, animal, and soil microbiome studies as well as a nice serving of human gut science, specifically about FMT.

Events and jobs

Visiting Assistant Professor of Microbiology – Methodist University, North Carolina

GENEWIZ Week – many small events, contests, giveaways, and webinars (including mine on using Metagenomics for Biomarker Discovery posted here on Sunday’s blog post. Since my webinar was yesterday, it will be archived and can be downloaded from genewiz.com, starting next week – don’t forget to check it out!)

General microbiome

* Comprehensive analysis of microorganisms accompanying human archaeological remains – Anna Philips – Gigascience

Pregnancy and early life

Relationships Among Microbial Communities, Maternal Cells, Oligosaccharides, and Macronutrients in Human Milk – Williams JE – Journal of Human Lactation

Human oral microbiome

Targeted Antimicrobial Therapy in the Microbiome Era – Victoria N. Stone – Molecular Oral Microbiology

Human gut microbiome

* Identification of donor microbe species that colonize and persist long term in the recipient after fecal transplant for recurrent Clostridium difficile – Ranjit Kumar – npj Biofilms and Microbiomes

* Fecal microbiota transplantation in metabolic syndrome: History, present and future – P. F. de Groot – Gut microbes

Intestinal microbiota, fecal microbiota transplantation, and inflammatory bowel disease – Weingarden AR – Gut Microbes

Faecal microbiota study reveals specific dysbiosis in spondyloarthritis – Maxime Breban – Annals of Rheumatic Diseases

Metaproteomic analysis of human gut microbiota: where are we heading? – Pey Yee Lee – Journal of Biomedical Science

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Variability, stability, and resilience of fecal microbiota in dairy cows fed whole crop corn silage – Minh Thuy Tang – Applied Microbiology and Biotechnology

Plantago ovata in broiler chicken nutrition: Performance, carcass criteria, intestinal morphology, immunity, and intestinal bacterial population – A. Divani – Animal Physiology and Animal Nutrition

Chronic treatment with prebiotics, probiotics and synbiotics attenuated cardiac dysfunction by improving cardiac mitochondrial dysfunction in male obese insulin-resistant rats – Tunapong W – European Journal of Nutrition

Amelioration of obesity-related characteristics by a probiotic formulation in a high-fat diet-induced obese rat model – Joo-Hyun Shin – European Journal of Nutrition

Early Gut Microbiota Intervention Suppresses DSS-Induced Inflammatory Responses by Deactivating TLR/NLR Signalling in Pigs – Yi Xiao – Scientific Reports

* Profound perturbation induced by triclosan exposure in mouse gut microbiome: a less resilient microbial community with elevated antibiotic and metal resistomes – Bei Gao – BMC Pharmacology and Toxicology

Animal microbiome (for animals in the wild)

[PrePrint] Ecophysiology of freshwater Verrucomicrobia inferred from genomes recovered through time-series metagenomics – Shaomei He – bioRxiv

Long-Term Survey Is Necessary to Reveal Various Shifts of Microbial Composition in Corals – Shan-Hua Yang – Aquatic Microbiology (Frontiers in Microbiology)

Preferential suppression of Anopheles gambiae host sequences allows detection of the mosquito eukaryotic microbiome – Eugeni Belda – Scientific Reports

Social odours covary with bacterial community in the anal secretions of wild meerkats – Sarah Leclaire – Scientific Reports

Plant, root, and soil microbiome

Imidacloprid application changes microbial dynamics and enzymes in rice soil – Bibhab Mahapatra – Ecotoxicology and Environmental Safety

Comparison of ammonia oxidation bacteria community structure in paddy soil with different utilized years – Zhao WeiYe – Southwest China Journal of Agricultural Sciences

[MS Thesis] Variation of Soil Microbial Communities within a Consociation Soil Map Unit and a Vegetative Transect through an Oak Motte – Sarah Elizabeth Shawver – Tarleton State University

Effects of different intercropping patterns on rhizosphere soil bacteria colony characteristics and flue-cured tobacco yield and quality – Wei Jun – Guangxi Academy of Agricultural Sciences

Rhizospheric bacteria diversity of Cypripedium macranthum estimated via high throughput sequencing – Zhang Jian -Southwest China Journal of Agricultural Sciences

Denitrifying bacterial communities display different temporal fluctuation patterns across Dutch agricultural soils – Lopez-Lozano NE – Antonie van Leeuwenhoek

Ecophylogeny of the endospheric root fungal microbiome of co-occurring Agrostis stolonifera – Amandine Le Van – PeerJ

Consistent effects of nitrogen fertilization on soil bacterial communities in black soils for two crop seasons in China – Jing Zhou – Scientific Reports

A next generation sequencing approach with a suitable bioinformatics workflow to study fungal diversity in bioaerosols released from two different types of composting plants – Hamza Mbareche – Science of The Total Environment

The Effects of Cropping Regimes on Fungal and Bacterial Communities of Wheat and Faba Bean in a Greenhouse Pot Experiment Differ between Plant Species and Compartment – Granzow S – Frontiers in Microbiology

Water and extremophile microbiome

Unraveling the environmental and anthropogenic drivers of bacterial community changes in the Estuary of Bilbao and its tributaries – Mikel Aguirre – PLOS ONE

Food microbiology

Metagenomics insights into food fermentations – Francesca De Filippis – Microbial Biotechnology

Probiotics / prebiotics

Effect of probiotic Lactobacillus on lipid profile: A systematic review and meta-analysis of randomized, controlled trials – Yuncheng Wu – PLOS ONE

Growing Literature but Limited Evidence: A Systematic Review regarding Prebiotic and Probiotic Interventions for those with Traumatic Brain Injury and/or Posttraumatic Stress Disorder – Lisa A. Brenner – Brain, Behavior, Immunity

Microbes on the market

$10 million gift boosts gut microbiome research at Wash U

Ed’s non-microbiology picks 

Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site – Eva-Maria Strauch – Nature Biotechnology

Aberrant telomere length and mitochondrial DNA copy number in suicide completers –  Ikuo Otsuka – Scientific Reports

Impact of nutrition on social decision making – Sabrina Strang – PNAS

Oral vitamin D rapidly attenuates inflammation from sunburn: an interventional study – Jeffrey F. Scott – JID

Adaptive self-organization of Bali’s ancient rice terraces – J. Stephen Lansing – PNAS

Ravens remember the nature of a single reciprocal interaction sequence over 2 days and even after a month – J. J. A. Muller – Animal Behaviour

June 13, 2017

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Excellent reviews across all sections, with many from the Nature Journals. Also, multiple articles on the tree of life and animal experiments.

General microbiome
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life – Supratim Mukherjee – Nature Biotechnology

Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes – Violette Da Cunha – PLoS Genetics

Review: Natural Products and the Gene Cluster Revolution – Paul R. Jensen – Trends in Microbiology

Pregnancy and early life
Review: How nutrition and the maternal microbiota shape the neonatal immune system – Andrew J. MacPherson – Nature Reviews Immunology

Multi-site human microbiome
Review: Role of oral and gut microbiome in nitric oxide mediated colon motility – Miriam Y. Walker – Nitric Oxide

Human skin microbiome
Review: Chemical signaling in mosquito–host interactions: the role of human skin microbiota – William Takken – Current Opinion in Insect Science

Human oral microbiome
Reduced Susceptibility to Antiseptics Is Conferred by Heterologous Housekeeping Genes – Supathep Tansirichaiya – Microbial Drug Resistance

Human gut microbiome
*Alcohol-associated intestinal dysbiosis impairs pulmonary host defense against Klebsiella pneumoniae – Derrick R. Samuelson – PLoS Pathogens

Review: Fungal dysbiosis: immunity and interactions at mucosal barriers – Ilian D. Iliev – Nature Reviews Immunology

Review: Transmission of the gut microbiota: spreading of health – Hilary P. Browne – Nature Reviews Microbiology

Editorial: Post-dieting weight gain: the role of persistent microbiome changes – Christoph A Thaiss – Future Microbiology

Animal experiments
*Thermoneutral housing exacerbates nonalcoholic fatty liver disease in mice and allows for sex-independent disease modeling – Daniel A. Giles – Nature Medicine

*Cold-induced conversion of cholesterol to bile acids in mice shapes the gut microbiome and promotes adaptive thermogenesis – A. Worthmann – Nature Medicine

Integrated Metagenomic Analyses of the Rumen Microbiome of Cattles Reveals Key Biological Mechanisms Associated with Methane Traits – Haiying Wang – Methods

Long-term multi-species Lactobacillus and Bifidobacterium dietary supplement enhances memory and changes regional brain metabolites in middle-aged rats – Caroline O’Hagan – Neurobiology of Learning and Memory

Soy compared with milk protein in a Western diet changes fecal microbiota and decreases hepatic steatosis in obese OLETF rats – Matthew R. Panasevich – Journal of Nutritional Biochemistry

Targeted metabolomics analysis of aromatic amino acids and their gut microbiota-host co-metabolites in rat serum and urine by liquid chromatography with tandem mass spectrometry – Yifeng Zeng – Journal of Separation Science

Effect of cocoa’s theobromine on intestinal microbiota of rats – Sandra Martin-Pelaez – Molecular Nutrition and Food Research

Water and extremophile microbiome
Review: Microbial Extracellular Polymeric Substances (EPSs) in Ocean Systems – Alan W. Decho – Frontiers in Microbiology

Review: Linking genes to microbial biogeochemical cycling: lessons from arsenic – Yong-Guan Zhu – Environmental Science and Technology

Food microbiology
Review: Extremozymes from metagenome: Potential applications in food processing – Mahejibin Khan – Critical Reviews in Food Science and Nutrition

Phages and viruses
Review: Interplay between viruses and bacterial microbiota in cancer development – Dariia Vyshenska – Seminars in Immunology

Bioinformatics
A novel method to determine the minimum number of sequences required for reliable microbial community analysis – Jiajia Ni – Journal of Microbiological Methods

Power and sample size calculations for high-throughput sequencing-based experiments – Chung-I Li – Briefings in Bioinformatics
Only a short section on microbiome.

Techniques
*A stabilized microbial ecosystem of self-limiting bacteria using synthetic quorum-regulated lysis – Spencer R. Scott – Nature Microbiology

Body fluid prediction from microbial patterns for forensic application – Eirik Nataas Hanssen – Forensic Science International: Genetics

Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinIONTM portable nanopore sequencer – Alfonso Benítez-Páez – GigaScience

Review: Phenotyping of gut microbiota: Focus on capillary electrophoresis – Manuel Ferrer – Electrophoresis

Review: Panacea in progress: CRISPR and the future of its biological research introduction – Michael Carroll – Microbiological Research

June 8, 2017

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Modeling colon physiology to predict microbiota growth, a review of plant-bacteria genome-wide association studies, sporeforming bacteria isolated from beer.

General microbiome

Review: Systematic Review: The Impact of Cancer Treatment on the Gut and Vaginal Microbiome in Women With a Gynecological Malignancy – Ann Muls – International Journal of Gynecological Cancer

Pregnancy and early life

Contributions of the maternal oral and gut microbiome to placental microbial colonization in overweight and obese pregnant women – Luisa F Gomez-Arango – Scientific Reports

Human gut microbiome

Bread Affects Clinical Parameters and Induces Gut Microbiome-Associated Personal Glycemic Responses – Tal Korem – Cell Metabolism

* Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis – Jaeyun Sung – Nature Communications

The gut metagenome changes in parallel to waist circumference, brain iron deposition and cognitive function – Gerard Blasco – Journal of Clinical Endocrinology and Metabolism

Gut microbiota composition in relation to the metabolic response to 12-week combined polyphenol supplementation in overweight men and women – J Most – European Journal of Clinical Nutrition

Complete genome sequence of Clostridium perfringens CBA7123 isolated from a faecal sample from Korea – Yeon Bee Kim – Gut Pathogens

Review: The Research Progress on Intestinal Stem Cells and Its Relationship with Intestinal Microbiota – Qihang Hou – Frontiers in Immunology

Review: Gut microbiota: Intestinal fungi fuel the inflammatory fire in alcoholic liver disease – Hugh Thomas – Nature Reviews Gastroenterology and Hepatology

* Effect of water flow and chemical environment on microbiota growth and composition in the human colon – Jonas Cremer – PNAS

Animal experiments

Gut-Associated Lymphoid Tissue: A Key Tissue Inside the Mucosal Immune System of Hens Immunized with Escherichia coli F4 – Maria F Peralta – Frontiers in Immunology

Gut Dysbiosis and Neurobehavioral Alterations in Rats Exposed to Silver Nanoparticles – Angela B Javurek – Scientific Reports

Improved detection of gene-microbe interactions in the mouse skin microbiota using high-resolution QTL mapping of 16S rRNA transcripts – Meriem Belheouane – Microbiome

In Vitro Study of the Metabolic Characteristics of Eight Isoquinoline Alkaloids from Natural Plants in Rat Gut Microbiota – Chi-Yu He – Molecules

Animal microbiome

Symbionts in waiting: the dynamics of incipient endosymbiont complementation and replacement in minimal bacterial communities of psyllids – Jennifer L Morrow – Microbiome

Plant, root, and soil microbiome

Applying community ecological theory to maximize productivity of cultivated biocrusts – Matthew A Bowker – Ecological Applications

Is soil microbial diversity affected by soil and groundwater salinity? Evidences from a coastal system in central Italy – Loredana Canfora – Environmental Monitoring and Assessment

* Review: Genome-Wide Association Studies In Plant Pathosystems: Toward an Ecological Genomics Approach – Claudia Bartoli – Frontiers in Plant Science

Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits – Juan E Pérez-Jaramillo – The ISME Journal

Water and extremophile microbiome

Changes in Microbial (Bacteria and Archaea) Plankton Community Structure after Artificial Dispersal in Grazer-Free Microcosms – Hera Karayanni – Microorganisms

Identifying the core seed bank of a complex boreal bacterial metacommunity – Clara Ruiz-González – The ISME Journal

Genomic insights into temperature-dependent transcriptional responses of Kosmotoga olearia, a deep-biosphere bacterium that can grow from 20oC to 79oC – Stephen M J Pollo – bioRxiv

Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate-reducing benthic microbial populations – Zainab Abdulrahman Beiruti – bioRxiv

Food microbiology

Evolution of class 1 integrons: Mobilization and dispersal via food-borne bacteria – Timothy M Ghaly – PLOS ONE

* Sporeforming bacteria in beer: Occurrence, diversity, presence of hop resistance genes and fate in alcohol-free and lager beers – Allan R G Munford – Food Control

Probiotics/prebiotics

Probiotic Bifidobacterium bifidum G9-1 attenuates 5-fluorouracil-induced intestinal mucositis in mice via suppression of dysbiosis-related secondary inflammatory responses – Shinichi Kato – Clinical and Experimental Pharmacology and Physiology

Review: The Role of the Microbiome and the use Of Probiotics in Gastrointestinal Disorders in Adults in the Asia-Pacific Region – Uday C Goshal – Journal of Gastroenterology and Hematology

Phages and viruses

Evolution of selective-sequencing approaches for virus discovery and virome analysis – Arvind Kumar – Virus Research

Techniques

Review: Novel approaches in function-driven single-cell genomics – Devin F R Doud – FEMS Microbiology Reviews

Fast Method for the determination of Short-chain-length Polyhydroxyalkanoates (scl-PHAs) in Bacterial Samples by In Vial-Thermolysis (IVT) – Federica Abbondanzi – New Biotechnology

Microbes in the news

Are Pets the New Probiotic? – Richard Schiffman – The New York Times

Gut bacteria could protect cancer patients and pregnant women from Listeria, study suggests – EurekAlert

Impact of protective bacteria linked to infection route, study finds – EurekAlert

June 4, 2017

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Some exciting papers in the sections- General microbiome & Microbes in news, to get you through Sunday!

General microbiome

The 5D Framework: A Clinical Primer for Fecal Microbiota Transplantation to Treat Clostridium difficile infection – JR Allegretti – Gastrointestinal Endoscopy

Abatement of AO7 in a divided microbial fuel cells by sequential cathodic and anodic treatment powered by different microorganisms – G Riccobono – Journal of Electroanalytical Chemistry

THE MICROBIOME AND TRANSFUSION IN CANCER PATIENTS – H Goubran – Transfusion and Apheresis Science

« Olsenella congonensis» sp.nov., identified in human stool sample – M Bilen – New Microbes and New Infections

Description of “Blautia phocaeensis” sp.nov., and “Lachnoclostridium edouardi” sp. nov., isolated from healthy fresh stools of Saudii Arabia bedouins by culturomics – SI Traore  – New Microbes and New Infections

Sulfur-driven iron reduction coupled to anaerobic ammonium oxidation – P Bao – Environmental Science and Technology

 

Animal microbiome

Diversity and composition of cultivable gut bacteria in an endemic island bird and its mainland sister species – E Lobato – Symbiosis

Modulation of ruminal fermentation profile and microbial abundance in cows fed diets treated with lactic acid, without or with inorganic phosphorus supplementation – E Mickdam – Animal Feed Science and Technology

A pea (Pisum sativum L.) seed albumin extract prevents colonic DSS induced dysbiosis in mice – I Aranda-Olmedo – Journal of Functional Foods

 

Human respiratory microbiome

The Respiratory Microbiome: Beyond the Culture – E Monsó – Archivos de Bronconeumología

WS03.7 Coexistence of prey and predator bacteria in cystic fibrosis lung microbiota – J. de Dios-Caballero – Journal of Cystic Fibrosis

 

Human gut microbiome

The gut bacterium and pathobiont Bacteroides vulgatus activates NF-κB in a human gut epithelial cell line in a strain and growth phase dependent manner – P Ó Cuív – Anaerobe

Chlorogenic acid versus amaranth’s caffeoylisocitric acid – Gut microbial degradation of caffeic acid derivatives – M Vollmer – Food Research International

Consumption effect of a synbiotic beverage made from soy and yacon extracts containing Bifidobacterium animalis ssp. lactis BB-12 on the intestinal polyamine concentrations in elderly individuals – MSJ Manzoni – Food Research International

Review: Effect of diet and gut environment on the gastrointestinal formation of N-nitroso compounds: A review – J Kobayashi – Nitric Oxide

Atopic dermatitis and food sensitization in South African toddlers : Role of fiber and gut microbiota – M Mahdavinia – Annals of Allergy, Asthma & Immunology

 

Plant, root and soil microbiome

Significant Impacts of Increasing Aridity on the Arid Soil Microbiome – JW Neilson – mSystems

Consequences of tropical forest conversion to oil palm on soil bacterial community and network structure – SA Wood – Soil Biology and Biochemistry

The response of archaeal species to seasonal variables in a subtropical aerated soil: insight into the low abundant methanogens – W Xie – Applied Microbiology and Biotechnology

Relative roles of competition, environmental selection and spatial processes in structuring soil bacterial communities in the Qinghai-Tibetan Plateau – J Zhou – Applied Soil Ecology

Isolation and identification of endophytic bacteria with plant growth promoting and biocontrol potential from oak trees – F Tashi-Oshnoei – Forest Pathology

Illumina-Based Sequencing Analysis Directed Selection for Actinobacterial Probiotic Candidates for Banana Plants – X Du – Probiotics and Antimicrobial Proteins

The influence of land use intensity on the plant-associated microbiome of Dactylis glomerata L. – J Estendorfer – Frontiers in Plant Science

 

Water microbiome and extremophiles

An overlooked nitrogen loss linked to anaerobic ammonium oxidation in estuarine sediments in China – XR Yang – Journal of Soils and Sediments

 

Food microbiology

Evolution of microbiota during spontaneous and inoculated Tonda di Cagliari table olives fermentation and impact on sensory characteristics – R Comunian – LWT-Food Science and Technology

PCR-DGGE markers for qualitative profiling of microbiota in raw milk and ripened cheeses – B Nalepa – LWT-Food Science and Technology

Identification of enzymatic activities involved in agave fructan consumption by Bifidobacterium longum subsp. infantis ATCC 15697 – E Cuevas-Juárez – Journal of Functional Foods

 

Techniques

Photodynamic Therapy With Methylene Blue for Skin Ulcers Infected With Pseudomonas aeruginosa and Fusarium spp – C Aspiroz – Actas Dermo-Sifiliográficas

 

Phages

Antibacterial efficacy of nisin, bacteriophage P100 and sodium lactate against Listeria monocytogenes in ready-to-eat sliced pork ham – ACL Figueiredo – Brazilian Journal of Microbiology

 

More microbes

Spore forming bacteria in beer: occurrence, diversity, presence of hop resistance genes and fate in alcohol-free and lager beers – ARG Munford – Food Control

Survey of pathogens in threatened wild red-tailed Amazon parrot (Amazona brasiliensis) nestlings in Rasa Island, Brazil – FF Vaz – Brazilian Journal of Microbiology

Species specific substrates and products choices of 4-O-acetyltransferase from Trichoderma brevicompactum – S Sharma – Enzyme and Microbial Technology

Review: The Goldilocks model of immune symbiosis with Mycobacteria and Candida colonizers – RT Robinson – Cytokine

Immunological and epidemiological factors affecting candidiasis in HIV patients beginning antiretroviral therapy in an Asian clinic – EAT Wulandari – Archives of Oral Biology

Diversity and Ecology of and Biomineralization by Magnetotactic Bacteria – W Lin – Environmental Microbiology Reports

 

Microbes in news

Man Dies After His Tattoo Gets Infected with Ocean Bacteria – R Rettner – Live Science

Accelerated breeding of mutant bacteria may choke space race – J Seidel – News Corp Australia Network

Microgravity Can Permanently Mutate Bacteria to Make Them Faster Breeders –  D Nield – Science Alert

Vaginal bacteria can inhibit sexual transmission of Zika virus – Healio

Bacteria levels subside, Spring Lake beach reopens – R Zimmer – App.com

Meet C. diff, the gross bacteria on the soles of your shoes – E Roberts – Today

The Microscopic World of Bacteria Comes to Life with Sculpture – CR  Fernández – Labiotech

New Microbiology Data Reinforce Activity of Paratek’s Omadacycline Against Pathogens of Importance in Respiratory, Skin and Urinary Tract Infections – Paratek – Nasdaq Globe News Wire

A Traumatic Experience Can Reshape Your Microbiome – S Neilson – Huffington Post

Zymo Research to Launch Three New Kits for Microbiome Research at ASM Microbe 2017 – Zymo Research Corp. – PR Newswire

The gut microbiota plays key role in diabetes treatment – N Marriott –  Drug Target Review

In a first, Human Microbiome Project Launched in Northeast India! – TNT News

Metformin joins forces with gut microbes to improve blood sugars, new study finds – C Bienvenu – Diabetes.co.uk

 

 

May 27, 2017

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Today’s digest has some great papers in the section-Plant, root and soil microbiome

General microbiome

Concentration and Viability of Bacterial Aerosols Associated with Weather in Asian Continental Outflow: Current Understanding – D Zhang – Aerosol Science and Engineering

Specific Virus-Host Genome Interactions Revealed By Tethered Chromosome Conformation Capture – H Li – bioRxiv

Metabolic Integration of Bacterial Endosymbionts through Antimicrobial Peptides – P Mergaert – Trends in Microbiology

Isolation and Characterization of Phenol-Degrading Psychrotolerant Yeasts – N Filipowicz – Water, Air, & Soil Pollution

 

Animal microbiome

Impact of dietary Moringa oleifera leaves on intestinal pathogenic load and histological structure of growing rabbits raised under heat-stress conditions – AY El-Badawi – Animal Production Science

CD44 deletion leading to attenuation of experimental autoimmune encephalomyelitis results from alterations in gut microbiome in mice – KN Chitrala – European Journal of Immunology

Meta-analysis To Define a Core Microbiota in the Swine Gut – DB Holman – mSystems

 

Plant, root and soil microbiome

Let the Core Microbiota Be Functional – P Lemanceau – Trends in Plant Science

Phytobiomes – Editor-in-Chief: CA Young

Bio-mining the forest ecosystem of North East India for identification of antimicrobial metabolites from fungi through submerged fermentation – SI Devi – Bioresource Technology

Kisameet Glacial Clay: an Unexpected Source of Bacterial Diversity – SL Svensson – mBio

Microbiome-on-a-Chip: New Frontiers in Plant–Microbiota Research – CE Stanley – Trends in Microbiology

Soil microbial properties as affected by short-term contrasting tillages and cropping systems in a rainfed agro-ecosystem of Northern Odisha – KN Mishra – Evolutionary Ecology

Comparison of rhizosphere properties as affected by different Bt- and non-Bt-cotton (Gossypium hirsutum L.) genotypes and fertilization – M Ahamd – Environmental Monitoring and Assessment

Soil fungal diversity in natural grasslands of the Tibetan Plateau: associations with plant diversity and productivity – T Yang – New Phytologist

Bacterial Microbiome and Nematode Occurrence in Different Potato Agricultural Soils – JD Castillo – Microbial Ecology

Lipopeptides produced by B. amyloliquefaciens NJN-6 altered the soil fungal community and non-ribosomal peptides genes harboring microbial community – J Yuan – Applied Soil Ecology

The differential impact of a native and a non-native ragwort species (Senecioneae) on the first and second trophic level of the rhizosphere food web – P Harkes – Oikos

 

Food microbiology

Impact of thistle rennet from Carlina acanthifolia All. subsp. acanthifolia on bacterial diversity and dynamics of a specialty Italian raw ewes’ milk cheese – F Cardinali – International Journal of Food Microbiology

High-throughput metataxonomic characterization of the raw milk microbiota identifies changes reflecting lactation stage and storage conditions – CJ Doyle – International Journal of Food Microbiology

 

Built environment microbiology

Direct treatment of high-strength soft drink wastewater using a down-flow hanging sponge reactor: performance and microbial community dynamics – J Liao – Applied Microbiology and Biotechnology

 

Techniques

Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium – R Kumar – mSystems

Fermentation quality, in vitro digestibility and aerobic stability of total mixed ration silages prepared with whole-plant corn (Zea mays L.) and hulless barley (Hordeum vulgare L.) straw – X Yuan – Animal Production Science

Investigation of compatible solutes synthesis and transport of Virgibacillus halodenitrificans PDB-F2 with complete genome analysis – Y Zhou – International Biodeterioration & Biodegradation

An 18S rRNA Workflow for Characterizing Protists in Sewage, with a Focus on Zoonotic Trichomonads – JM Maritz – Microbial Ecology

 

More microbes

HIV Persistence Alters CXCR4 Expression Patterns In OP9-DL1-Mediated Differentiation Of In Vitro Infected Human Cord Blood CD34+ Cells – T Tsukamoto – bioRxiv

Bacterial Virus Ontology; Coordinating across Databases – C Hulo – MDPI

 

Microbes in news

New insights into the ancestors of all complex life – University of Bristol – News

How a Usually Harmless Bacteria Ended Up Killing 18 People in Wisconsin – S Zhang – The Atlantic

Where you can check beaches for bacteria – Daily Herald

Beware: How to avoid rare flesh-eating bacteria in Chesapeake Bay – M Basch – WTOP

Gut Microbiome Affects Two Nervous System Diseases – AL Komarrof – Journal Watch

Solution to many global challenges may be right under our feet – G Dufficy – AgriLand

Bugging cancer: gut bacteria and the big C – V Martinez – The Irish Times

 

Non-microbiology picks

Marginal Returns And Levels Of Research Grant Support Among Scientists Supported By The National Institutes Of Health – MS Lauer – bioRxiv

Conservation and restoration practices in humid climates – D Tejeda Sartorius – CAB Direct

May 24, 2017

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Human Microbiome

Non-pylori Helicobacters (NHPHs) induce shifts in gastric microbiota in Helicobacter pylori-infected patients – Peng et al. – Frontiers in Microbiology

Association between body mass index and Firmicutes/Bacteroidetes ratio in an adult Ukrainian population – Koliada et al. – BMC Microbiology

The effect of heritability and host genetics on the gut microbiota and metabolic syndrome – Young Lim et al. – Gut (BMJ)

Fungal microbiota dysbiosis in IBD – Sokol et al. – Gut (BMJ)

A tale of two risks: smoking, diabetes and the subgingival microbiome – Ganesan et al. – The ISME Journal

Animal Microbiome

The Structural and Functional Capacity of Ruminal and Cecal Microbiota in Growing Cattle Was Unaffected by Dietary Supplementation of Linseed Oil and Nitrate  – Popova et al. – Frontiers in Microbiology

Probiotics – Prebiotics

Gut Bacteria Missing in Severe Acute Malnutrition, Can We Identify Potential Probiotics by Culturomics? – Tidjani Alou et al – Frontiers in Microbiology

Detection and Physicochemical Characterization of Membrane Vesicles (MVs) of Lactobacillus reuteri DSM 17938 –  Grande et al. – Frontiers in Microbiology

Review: Resistant Starch Regulates Gut Microbiota: Structure, Biochemistry and Cell Signalling – Yang et al. – Cellular Physiology and Biochemistry

Food Microbiology

A Functional Metagenomic Analysis of Tetracycline Resistance in Cheese Bacteria – Flórez et al. – Frontiers in Microbiology

Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria – Bonham et al. – BioRxiv

Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access – Taboada et al. – Frontiers in Microbiology

In vitro assessment of Pediococcus acidilactici Kp10 for its potential use in the food industry – Abbasiliasi et al. – BMC Microbiology

Pathogen Research

In-depth Profiling of MvfR-Regulated Small Molecules in Pseudomonas aeruginosa after Quorum Sensing Inhibitor Treatment – Allegretta et al. – Frontiers in Microbiology

Metabolic anticipation in Mycobacterium tuberculosis – Eoh et al. – Nature Microbiology

Predicting Drug Resistance Evolution: Antimicrobial Peptides Vs. Antibiotics – Yi et al. – BioRxiv

Environmental Microbiology

Undocumented Potential For Primary Productivity In A Globally-Distributed Bacterial Photoautotroph – Graham et al. – BioRxiv

Epibionts dominate metabolic functional potential of Trichodesmium colonies from the oligotrophic ocean – Frischkorn et al. – The ISME Journal

Bioinformatics

BSocial: Deciphering Social Behaviors within Mixed Microbial Populations – Purswani et al. – Frontiers in Microbiology

A Phylogenetic Method To Perform Genome-Wide Association Studies In Microbes That Accounts For Population Structure And Recombination – Collins and Didelot – BioRxiv

Association Mapping From Sequencing Reads Using K-mers – Rahman et al. – BioRxiv

MATAM: Reconstruction Of Phylogenetic Marker Genes From Short Sequencing Reads In Metagenomes – Pericard et al. – BioRxiv

Other

Perspective: Our path to better science in less time using open data science tools – Stewart Lowndes et al. – Nature Ecology & Evolution

Teaching genetics prior to teaching evolution improves evolution understanding but not acceptance –  Mead et al. – PLoS Biology

Review: Adaptations of archaeal and bacterial membranes to variations in temperature, pH and pressure – Siliakus et al. – Extremophiles

May 21, 2017

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Events and jobs

FULLY FUNDED POSTDOCTORAL FELLOW POSITION TO STUDY MICROBIOME-BEHAVIOR INTERACTIONS: PORTUGAL

General microbiome

Bioinorganic antimicrobial strategies in the resistance era – Regiel-Futyra et al, Coordination Chemistry Reviews

Biofilm microenvironment induces a widespread adaptive amino-acid fermentation pathway conferring strong fitness advantage in Escherichia coli – Letoffe et al, PLoS Genetics

A bloodstream infection by Ruminococcus gnavus in a patient with a gall bladder perforation – Kim et al, Anerobe

Microbial community compositional analysis for membrane bioreactor treating antibiotics containing wastewater – Zhu et al, Chemical Engineering Journal

Thermophilic Moorella thermoautotrophica-immobilized cathode enhanced microbial electrosynthesis of acetate and formate from CO2 – Yu et al, Bioelectrochemistry

Arumberiamorph structure in modern microbial mats: implications for Ediacaran palaeobiology – Kolesnikov et al, Bulletin de la Société Géologique de France

Succession in the petroleum reservoir microbiome through an oil field production lifecycle – Vigneron et al, ISME

Human respiratory microbiome

Population Genomic Analysis of 1,777 Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolates, Houston, Texas: Unexpected Abundance of Clonal Group 307 – Long et al, Mbio

Human oral microbiome

Pro-resolving mediators in the regulation of periodontal disease – Van Dyke, Molecular Aspects of Medicine

A structure-derived snap-trap mechanism of a multispecific serpin from the dysbiotic human oral microbiome – Goulas et al, Journal of Biological Chemistry

Human gut microbiome

Is frozen fecal microbiota transplantation as effective as fresh fecal microbiota transplantation in patients with recurrent or refractory clostridium difficile infection: a meta-analysis? – Tang et al, Diagnostic Microbiology and Infectious Disease

Weight-loss interventions and gut microbiota changes in overweight and obese patients: a systematic review – Seganfredo et al, Obesity Reviews

 

Dysbiosis of Gut Microbiome and Its Impact on Epigenetic Regulation – Lee et al, Journal of Clinical Epigenetics

Hypoxia and Inactivity Related Physiological Changes (Constipation, Inflammation) Are Not Reflected at the Level of Gut Metabolites and Butyrate Producing Microbial Community: The PlanHab Study – Sket et al, Frontiers in Physiology

Is there a potential role of fecal microbiota transplantation in the treatment of inflammatory bowel disease? – Eun, Intestinal Research

Diet and contaminants: driving the rise to obesity epidemics? – Di Ciaula and Portincasa, Current Medical Chemistry

How to: Establish and run a stool bank – Terveer et al, Clinical Microbiology and Infection

Animal experiments

Transforming growth factor β: a master regulator of the gut microbiota and immune cell interactions – Bauche and Marie, Clinical and Translational Immunology

Aloin, a Component of the Aloe Vera Plant Leaf, Induces Pathological Changes and Modulates the Composition of Microbiota in the Large Intestine of F344/N Male Rats – Boudraeu et al, Toxicology Science

Diabetes-associated microbiota in fa/fa rats is modified by Roux-en-Y gastric bypass – Arora et al, ISME

Absorption and degradation of sulfated polysaccharide from pacific abalone in in vitro and in vivo models – Ai et al, Journal of Functional Foods

Dietary ZnO nanoparticles alters intestinal microbiota and inflammation response in weaned piglets – Xia et al, Oncotarget

Dietary delta-tocotrienol favors abundance and diversity of beneficial microbiomes in obese male mice – Shen et al, FASEB

Bile acid binding resin prevents fat accumulation through intestinal microbiota in high-fat diet-induced obesity in mice – Kusumoto et al, Metabolism

In vitro ability of mastitis causing pathogens to form biofilms – Schonborn et al, Journal of Dairy Research

Dysbiosis of Intestinal Microbiota and Decreased Antimicrobial Peptide Level in Paneth Cells during Hypertriglyceridemia-Related Acute Necrotizing Pancreatitis in Rats – Huang et al, Frontiers in Microbiology

Effects of replacing Leymus chinensis with whole-crop wheat hay on Holstein bull apparent digestibility, plasma parameters, rumen fermentation, and microbiota – Niu et al, Scientific Reports

Physiological responses of insects to microbial fermentation products: insights from the interactions between Drosophila and acetic acid – Kim et al, Journal of Insect Physiology

Animal microbiome

Molecular detection by analysis of the 16S rRNA gene of fecal coliform bacteria from the two Korean Apodemus species (Apodemus agrarius and A. peninsulae) – Rahman et al, Genetics and Molecular Research

Detection and genetic characterization of Pasteurella multocida from alpaca (Vicugna pacos) pneumonia cases – Rimac et al, Tropical Animal Health and Production

Plant, root, and soil microbiome

Soil depth and crop determinants of bacterial communities under ten biofuel cropping systems – Zhang et al, Soil Biology and Biochemistry

Ground cover and slope exposure effects on micro- and mesobiota in forest soils – Gomez-Brandon et al, Ecological Indicators

Root chemical traits and their roles in belowground biotic interactions – Tsunoda and van Dam, Pedobiologia

Proteomics analysis of Fusarium proliferatum under various initial pH during fumonisin production – Li et al, Journal of Proteomics

Culturable bacterial diversity from the chestnut (Castanea sativa Mill.) phyllosphere and antagonism against the fungi causing the chestnut blight and ink diseases – Valverde et al, AIMS Microbiology

Water and extremophile microbiome

The removal of nitrogen compounds from farming wastewater – The effect of different carbon substrates and different microbial activators – Mankiewicz-Boczek et al, Ecological Engineering

How do physicochemical properties influence the toxicity of silver nanoparticles on freshwater decomposers of plant litter in streams? – Batista et al, Ecotoxicology and Environmental Safety

The heterogeneity of composition and assembly processes of the microbial community between different nutrient loading lake zones in Taihu Lake – Zhao et al, Applied Microbiology and Biotechnology

Towards a sustainable biobased industry – Highlighting the impact of extremophiles – Kruger et al, New Biotechnology

Distribution and genetic diversity of microbial populations in the pilot-scale biofilter for simultaneous removal of ammonia, iron and manganese from real groundwater – Cheng et al, Chemosphere

Pilot plant demonstration of stable and efficient high rate biological nutrient removal with low dissolved oxygen conditions – Keene et al, Water Research

Study on The Removal of Hexavalent Chromium from Contaminated Groundwater using Emulsified Vegetable Oil – Wen et al, Process Safety and Environmental Protection

A Novel Roseosiphophage Isolated from the Oligotrophic South China Sea – Yang et al, Viruses

Oxidative Stickland reactions in an obligate aerobic organism — amino acid catabolism in the Crenarchaeon Sulfolobus solfataricus – Stark et al, FEBS

Microbial Diversity in Extreme Marine Habitats and Their Biomolecules – Poli et al, Microorganisms

Methanogenic community was stable in two contrasting freshwater marshes exposed to elevated atmospheric CO2 – Lin et al, Frontiers in Microbiology

Plant-microbial interactions in agriculture and the use of farming systems to improve diversity and productivity – Ishaq, AIMS Microbiology

Effect of arbuscular mycorrhizal fungi on survival and growth of micropropagated Comanthera mucugensis spp. mucugensis (Eriocaulaceae) – Pereira et al, African Journal of Agricultural Research

Native communities of arbuscular mycorrhizal fungi associated with Capsicum annuum L. respond to soil properties and agronomic management under field conditions – Carballar-Hernandez et al, Agriculture, Ecosystems & Environment

Food microbiology

Microbial cell-free extracts affect the biochemical characteristics and sensorial quality of sourdough bread – Cavallo et al, Food Chemistry

Analysis of the microbiota of refrigerated chopped parsley after treatments with a coating containing enterocin AS-48 or by high-hydrostatic pressure – Burgos et al, Food Research International

Microorganisms Found in MPR and Packaged Produce and Their Detection Methods – Acar and Soyer, Minimally Processed Refridgerated Fruits and Vegetables, Food Engineering Series

Applications of Kluyveromyces marxianus in Biotechnology – Varela et al, Yeast Diversity in Human Welfare

Mucin- and carbohydrate-stimulated adhesion and subproteome changes of the probiotic bacterium Lactobacillus acidophilus NCFM – Celebioglu et al, Journal of Proteomics

Techniques

Metaproteomics-guided selection of targeted enzymes for bioprospecting of mixed microbial communities – Speda et al, Biotechnology Biofuels

Microbes in the news

Probiotics are popular, but some questions remain – Reading Eagle